ID:

mmu-mir-6341

 Coordinate:

chr1:12425986-12426106 +

 Confidence:

Known

 Type:

Unknown

 [View on miRBase]
[View on UCSC Genome Browser {Cornell Mirror}]
Legend: mature star mismatch in alignment mismatch in read

Predicted structure

No conservation details.

-30.9 -30.3 -30.2
mature
  1. chr14:90806776-90806790 +
  2. chr14:116783029-116783043 +
  3. chr1:12426017-12426031 +
star

Sense Strand Reads

CTGTCTGGGATAAGATATGACAGTAGAACTTATACCCCCATCACTGATAATTTTCAACATATCCAAAAATTGAAGGAGCCCAGTGCAATGATATTGTCACTATATGGCTGATAGGCTTCCTCAGGAGATAGTATAACACTGAGGGTCAACTGAATTTTGTGTGTCTGGAGCTAGCACATTAGAAGCTTTGTAGTTAGTTCAGTGCGAAGAGAGGAAGCCCA
***********************************........((..(((((((((((((((...((((((....((.(((((((.....((((((((.((....((((....)))).....))..))))))))..))))).)).)).....)))))))))))).))))).......))))..)).*********************************** 		Read size # Mismatch Hit Count Total Norm Total SRR345200
brain		 SRR391845
embryo		 SRR391846
embryo		 SRR014234
ovary		 SRR391853
embryo		 SRR345196
brain		 SRR037924
embryo		 SRR391847
embryo		 SRR038744
brain		 SRR037902
testes		 SRR345205
brain		 SRR391848
embryo		 SRR038741
brain		 SRR391852
embryo		 SRR039153
muscle		 SRR073954
blood		 SRR042472
lymph		 SRR345201
brain		 SRR014235
testes		 SRR1509749
zygote		 SRR345197
brain		 SRR345199
brain
................................................................................CAGTGCAATAATATTGTCA.......................................................................................................................... 19 1 2 1.50 3 2 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
................................................................................CAGTGCAATGGTATTGTCAC......................................................................................................................... 20 1 2 1.00 2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
................................................................................CAGTGCAATGGTATTGTCACTATATA................................................................................................................... 26 2 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
................................................................................CAGTGCAATAGTATTGTCACCAT...................................................................................................................... 23 3 8 0.38 3 0 0 0 0 2 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
................................................................................CAGTGCAATGGTATTGTCCCT........................................................................................................................ 21 2 3 0.33 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
................................................................................CAGTGCAATAGTATTGTCACTAC...................................................................................................................... 23 3 3 0.33 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
.................................................................................AGTGCAATGATATTG............................................................................................................................. 15 0 3 0.33 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
................................................................................CAGTGCAATGGTATTGTCATT........................................................................................................................ 21 2 4 0.25 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
..............................................................................CACAGTGCAATGGTATTGTCA.......................................................................................................................... 21 2 4 0.25 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
................................................................................CAGTGCAATGGTATTGTCACCGT...................................................................................................................... 23 3 4 0.25 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
..................................................................................................................................................................................................TAGTGCAGTGCGAAGAGGGCAA..... 22 3 5 0.20 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
.................................................................................AGTGCAATGGTATTGTCACC........................................................................................................................ 20 2 5 0.20 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
......................................................................................................................................................................................AAGCTTCGTTGTTAGTTCAG................... 20 2 5 0.20 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
......................................................................................................................................................................................AAGCTTTGTTGTTAGTTCAGG.................. 21 2 6 0.17 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
..............................................................................................................................................................................AACATTAGAAGCTTTGTCGT........................... 20 2 8 0.13 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
...............................................................................................................................................................................................AGTTAGTTCAGTCCGACGATA......... 21 3 9 0.11 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
................................................................................CAATGCAATGGTATTGTCAC......................................................................................................................... 20 2 9 0.11 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
......................................................................................................................................................................................AAGGTTAGTAGTTAGTTCAG................... 20 2 10 0.10 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
.........................................................................AGGAGCCTTGTGCAGTGATATT.............................................................................................................................. 22 3 13 0.08 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
........................................................................................................................TCGGGAGAGAGTATAACAC.................................................................................. 19 2 16 0.06 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
........................................................................................................TGGCGGCTAGGCTTCCTCA.................................................................................................. 19 2 18 0.06 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
.........................................................................AGGAGCACGGTGCAAGGATAT............................................................................................................................... 21 3 20 0.05 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
........................................................................................................................................................................AGCTAGCGCATTAGA...................................... 15 1 20 0.05 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
........................................................................................................TGGCTGATAGGCTTAC..................................................................................................... 16 1 20 0.05 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
................................................................................................................................................................................................TTTAGTACAGTGCGACGAGA......... 20 3 20 0.05 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
...........AAGATAGAACAGTGGAACTTATA........................................................................................................................................................................................... 23 3 20 0.05 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
.....................................................................................................................................................................................................TTCAGTGCGAAGAGCGGC...... 18 2 20 0.05 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
.................TAACAGTAGAACCTACACCCC....................................................................................................................................................................................... 21 3 20 0.05 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Anti-sense strand reads

GACAGACCCTATTCTATACTGTCATCTTGAATATGGGGGTAGTGACTATTAAAAGTTGTATAGGTTTTTAACTTCCTCGGGTCACGTTACTATAACAGTGATATACCGACTATCCGAAGGAGTCCTCTATCATATTGTGACTCCCAGTTGACTTAAAACACACAGACCTCGATCGTGTAATCTTCGAAACATCAATCAAGTCACGCTTCTCTCCTTCGGGT
***********************************........((..(((((((((((((((...((((((....((.(((((((.....((((((((.((....((((....)))).....))..))))))))..))))).)).)).....)))))))))))).))))).......))))..)).*********************************** 		Read size # Mismatch Hit Count Total Norm Total SRR037929
embryo		 SRR345200
brain		 SRR039154
muscle		 GSM361394
brain		 GSM361399
brain		 SRR037925
embryo		 SRR042455
blood		 SRR345198
brain		 SRR1509748
spermatozoa		 SRR037924
embryo		 SRR042484
salivary gland		 SRR059767
thymus		 SRR042483
muscle		 SRR345202
brain
................................................................................GTCACGTTACTATAACAGTT......................................................................................................................... 20 1 3 1.33 4 0 0 0 2 2 0 0 0 0 0 0 0 0 0
..........ATTGTATACTGTCATCTTGA............................................................................................................................................................................................... 20 1 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
...............................................................................................CAGTGATATTCAGACTATCCGAA....................................................................................................... 23 2 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
...............................................................................................CAGTGATAGCCCGACTATTCGA........................................................................................................ 22 3 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0
........................................................................TTTCTCGGCTCACGTTAATATAAC............................................................................................................................. 24 3 2 0.50 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0
...............................................................................................CAGTGATATTCAGACTATCCGAT....................................................................................................... 23 3 3 0.33 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
...............................................................................................CAGTGGTATTCCGACTATCCGAT....................................................................................................... 23 3 4 0.25 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0
...............................................................................................CAGTTGTAGACCGACTATCCGAA....................................................................................................... 23 3 4 0.25 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0
..........ATTCCATACTGTCATCTCGA............................................................................................................................................................................................... 20 2 9 0.11 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0
..........ATTCAATACTGACATCTTGA............................................................................................................................................................................................... 20 2 9 0.11 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
.............................................CTATTAAAAGATGTATAGATTGT......................................................................................................................................................... 23 3 20 0.10 2 0 0 0 0 0 0 0 0 2 0 0 0 0 0
...............................................................................................CAGTGCTATTCAGACTATCCG......................................................................................................... 21 3 11 0.09 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0
.......................................................................CTGCCTCGGTTCACGTTAC................................................................................................................................... 19 2 14 0.07 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0
.....................................................................AACTTGCTCTGTTCACGTTAC................................................................................................................................... 21 3 15 0.07 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0
.......................................................................CTTGCTCGGTTCACGTTAC................................................................................................................................... 19 2 18 0.06 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0
..........ATTGTATACTGACATCTTGA............................................................................................................................................................................................... 20 2 20 0.05 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0
........................................................................TTTCTCGGCTCACGTTAATATA............................................................................................................................... 22 3 20 0.05 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0
...............................................................................................................ATCCGAAGGAGT.................................................................................................. 12 0 20 0.05 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
mm10 chr1:12425936-12426156 + mmu-mir-6341 CTGTCTG----GGATAAGATAT-GACAGTAGAACTTATACCCCCATCACT-------------------------------------------------------------GATAATTTTC-------------------AACATATCCAAAAATTGAAGGAGCCCAGTGCAATGATATTGTCACTATATGGCTGATAGGCTTCCTCAGGAGATAGTATAACACTGAGGGTCAACTGA-ATTTTGTGTGTCTGGAGCTAGCACATTAGAAGCTTTGTAGTTAGTTCAGT-GCGAAGAGAGGAAGCCCA
cavPor3 Unknown CTGGGAGAGCAGCATGAGACAGAGCCAGTAGGTCTCAGATTCATGTGATTATTACCTCATCATataatagtcctggctaacagccttgaagaaaagcaaacacatagctagaatatttgtctattataattaggagatattacagacccgggagttggaggggcccagtggaatgaccttataattatataactgactgatttcctcaagaggtgatgtggcaccagaggctcggtatttttctgtattcctagatttcaaacatcagcagtttt--agtttgatcagccttggtgagtgatatccca
dipOrd1 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
hetGal2 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ochPri2 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
oryCun2 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
rn5 chr5:11260427-11260651 - CTGTC---------TAAGATAT-GACAGTAGAACTTATACC-CCA--------------TCGCCTGATTCACT-----------------------------------AAGGATAATTTTC-------------------AACACGTCCA-AAGCTGAAGGGTCCCGATGCAATGATATTGTCACTCTGTGGCTGATTGGCTTCCTCCAGAGATCATATAACACTAAGGACTAATTA--TTTTTGTGTTTCTGGAGCAAGAACATTAGAAGATTTGTAGTTAGTTCAGTCATGAAGAGAGAAAGCTC-
speTri2 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
mm10
CTGTCTG----GGATAAGATAT-GACAGTAGAACTTATACCCCCATCACT-------------------------------------------------------------GATAATTTTC-------------------AACATATCCAAAAATTGAAGGAGCCCAGTGCAATGATATTGTCACTATATGGCTGATAGGCTTCCTCAGGAGATAGTATAACACTGAGGGTCAACTGA-ATTTTGTGTGTCTGGAGCTAGCACATTAGAAGCTTTGTAGTTAGTTCAGT-GCGAAGAGAGGAAGCCCASizeHit CountTotal NormTotalSRR042455
blood		SRR042459
blood		SRR042460
blood		SRR069834
blood		SRR073954
blood		SRR073955
blood		SRR525238
Blood		SRR525237
Blood		SRR042456
bone marrow		SRR042457
bone marrow		SRR042461
bone marrow		SRR042462
bone marrow		GSM317181
brain		GSM317182
brain		GSM361394
brain		GSM361395
brain		GSM361398
brain		GSM361399
brain		GSM361402
brain		GSM361407
brain		GSM361408
brain		GSM361415
brain		GSM361430
brain		GSM510444
brain		SRR037904
brain		SRR037905
brain		SRR037906
brain		SRR037907
brain		SRR038741
brain		SRR038744
brain		SRR039610
brain		SRR042477
brain		SRR060845
brain		SRR206939
brain		SRR206940
brain		SRR206941
brain		SRR206942
brain		SRR345196
brain		SRR345197
brain		SRR345198
brain		SRR345199
brain		SRR345200
brain		SRR345201
brain		SRR345202
brain		SRR345203
brain		SRR345204
brain		SRR345205
brain		SRR345206
brain		SRR345207
brain		SRR037919
embryo		SRR037920
embryo		SRR037921
embryo		SRR037922
embryo		SRR037923
embryo		SRR037924
embryo		SRR037925
embryo		SRR037926
embryo		SRR037927
embryo		SRR037928
embryo		SRR037929
embryo		SRR037930
embryo		SRR391845
embryo		SRR391846
embryo		SRR391847
embryo		SRR391848
embryo		SRR391849
embryo		SRR391850
embryo		SRR391851
embryo		SRR391852
embryo		SRR391853
embryo		SRR116846
epididymis		GSM566419
fibroblast		GSM566420
fibroblast		SRR039183
fibroblast		SRR039184
fibroblast		SRR039185
fibroblast		SRR039186
fibroblast		SRR042475
fibroblast		SRR390297
fibroblast		SRR390298
fibroblast		SRR042484
salivary gland		SRR042476
heart		SRR095853
heart		SRR095855BC1
heart		SRR095855BC10
heart		SRR095855BC2
heart		SRR095855BC3
heart		SRR095855BC4
heart		SRR095855BC5
heart		SRR095855BC6
heart		SRR095855BC7
heart		SRR095855BC8
heart		SRR095855BC9
heart		SRR065052
jejunum		SRR065053
jejunum		SRR065054
jejunum		SRR065055
jejunum		SRR065056
jejunum		SRR042480
kidney		SRR040488
liver		SRR042479
liver		SRR065045
liver		SRR065046
liver		SRR065047
liver		SRR065048
liver		SRR065049
liver		SRR065050
liver		SRR077864
liver		SRR077865
liver		SRR077866
liver		SRR042478
lung		SRR042468
lymph		SRR042469
lymph		SRR042470
lymph		SRR042472
lymph		SRR042473
lymph		SRR039152
muscle		SRR039153
muscle		SRR039154
muscle		SRR042483
muscle		SRR014234
ovary		SRR037896
ovary		SRR037897
ovary		SRR037898
ovary		SRR037899
ovary		SRR042486
ovary		SRR042481
pancreas		SRR065058
pancreas		SRR065059
pancreas		SRR042482
skin		SRR042463
spleen		SRR042465
spleen		SRR042466
spleen		SRR042467
spleen		SRR042471
spleen		SRR042487
spleen		SRR059768
spleen		SRR059769
spleen		SRR059770
spleen		SRR059771
spleen		SRR059772
spleen		SRR059773
spleen		GSM475281
testes		GSM509275
testes		GSM509279
testes		SRR014231
testes		SRR014235
testes		SRR014236
testes		SRR028731
testes		SRR037900
testes		SRR037901
testes		SRR037902
testes		SRR037903
testes		SRR042485
testes		SRR051939
testes		SRR051940
testes		SRR069809
Type_A_spermatogonia		SRR069810
pachytene_spermatocytes		SRR069811
round_spermatid		SRR248523
Thy1+_spermatogonia		SRR248524
Thy1+_spermatogonia		SRR248525
Thy1-_somatic_testes_cells		SRR248526
Thy1-_somatic_testes_cells		SRR248527
spermatogonia		SRR363956
testes		SRR363957
testes		SRR363958
testes		SRR363959
testes		SRR363960
testes		SRR363963
testes		SRR363964
testes		SRR553582
brain		SRR553583
cerebellum		SRR553584
heart		SRR553585
kidney		SRR553602
sertoli_cells		SRR553603
spermatids		SRR553604
spermatocytes		SRR553586
testes		SRR042464
thymus		SRR059765
thymus		SRR059766
thymus		SRR059767
thymus		SRR032476
uterus		SRR032477
uterus		SRR1509747
oocyte		SRR1509748
spermatozoa		SRR1509749
zygote		SRR1509750
spermatogonia		SRR1509751
foetal_primordial_germ_cells		SRR1647947
Dgcr8_WT_leptotene_zygotene_spermatocytes		SRR1647948
Dgcr8_cKO_leptotene_zygotene_spermatocytes		SRR1647949
Dicer_WT_leptotene_zygotene_spermatocytes		SRR1647950
Dicer_cKO_leptotene_zygotene_spermatocytes		SRR1647951
Dgcr8_WT_pachytene_spermatocytes		SRR1647952
Dgcr8_cKO_pachytene_spermatocytes		SRR1647953
Dicer_WT_pachytene_spermatocytes		SRR1647954
Dicer_cKO_pachytene_spermatocytes
......................................................................................................................................................................AGTGCAATGATATTG...............................................................................................................................1530.331000000000000000000000000000000000000000000000000000000000000000100000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
cavPor3
CTGGGAGAGCAGCATGAGACAGAGCCAGTAGGTCTCAGATTCATGTGATTATTACCTCATCATataatagtcctggctaacagccttgaagaaaagcaaacacatagctagaatatttgtctattataattaggagatattacagacccgggagttggaggggcccagtggaatgaccttataattatataactgactgatttcctcaagaggtgatgtggcaccagaggctcggtatttttctgtattcctagatttcaaacatcagcagtttt--agtttgatcagccttggtgagtgatatcccaSizeHit CountTotal NormTotal
No Reads
dipOrd1
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
hetGal2
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
ochPri2
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
oryCun2
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM1528820
Adult_testes		GSM1528821
Adult_testes_Mili_IP
No Reads
rn5
CTGTC---------TAAGATAT-GACAGTAGAACTTATACC-CCA--------------TCGCCTGATTCACT-----------------------------------AAGGATAATTTTC-------------------AACACGTCCA-AAGCTGAAGGGTCCCGATGCAATGATATTGTCACTCTGTGGCTGATTGGCTTCCTCCAGAGATCATATAACACTAAGGACTAATTA--TTTTTGTGTTTCTGGAGCAAGAACATTAGAAGATTTGTAGTTAGTTCAGTCATGAAGAGAGAAAGCTC-SizeHit CountTotal NormTotalGSM1528817
Adult_testes		GSM1528818
Adult_testes_Mili_IP		GSM1528819
10dpp_testes
No Reads
speTri2
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads

Generated: 06/17/2015 at 11:26 AM