ID:

mmu-mir-6407

 Coordinate:

chr19:53010656-53010756 -

 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.

-28.8
mature
  1. chr10:23598283-23598297 +
  2. chr10:58812350-58812364 -
  3. chr10:122887710-122887724 +
  4. chr12:55799820-55799834 +
  5. chr14:48147703-48147717 +
  6. chr15:66279945-66279959 +
  7. chr15:76696081-76696095 +
  8. chr16:90704488-90704502 +
  9. chr17:10757595-10757609 +
  10. chr18:74268032-74268046 +
  11. chr19:53010705-53010719 -
  12. chr1:192365170-192365184 +
  13. chr4:151151646-151151660 +
  14. chr5:6611881-6611895 +
  15. chr5:18478619-18478633 +
  16. chr5:36844759-36844773 +
  17. chr6:24730693-24730707 -
  18. chr6:92765035-92765049 -
  19. chr7:45698592-45698606 -
  20. chr8:30627962-30627976 -
star
  1. chr11:13744932-13744941 -
  2. chr11:42448350-42448359 -
  3. chr11:49236667-49236676 -
  4. chr11:115127885-115127894 -
  5. chr12:82184047-82184056 -
  6. chr16:10921513-10921522 -
  7. chr17:30189574-30189583 -
  8. chr1:35185961-35185970 -
  9. chr1:63429768-63429777 -
  10. chr1:116164474-116164483 -
  11. chr1:140070556-140070565 -
  12. chr2:83526127-83526136 -
  13. chr2:169067189-169067198 -
  14. chr4:101454586-101454595 -
  15. chr5:29236465-29236474 -
  16. chr5:53176274-53176283 -
  17. chr5:87780010-87780019 -
  18. chr6:89682796-89682805 -
  19. chr7:139068753-139068762 -
  20. chrX:159725307-159725316 -
  21. chr10:19149567-19149576 -
  22. chr12:71950479-71950488 -
  23. chr12:106837310-106837319 -
  24. chr12:110397452-110397461 -
  25. chr13:100785959-100785968 -
  26. chr15:73183663-73183672 -
  27. chr15:77748744-77748753 -
  28. chr15:84387655-84387664 -
  29. chr16:31063041-31063050 -
  30. chr16:66598558-66598567 -
  31. chr16:94151876-94151885 -
  32. chr18:81151325-81151334 -
  33. chr19:53010739-53010748 -
  34. chr1:59381322-59381331 -
  35. chr4:84065974-84065983 -
  36. chr4:135542169-135542178 -
  37. chr5:140414438-140414447 -
  38. chr6:114892351-114892360 -
  39. chr7:123206952-123206961 -
  40. chr8:97581654-97581663 -

Sense Strand Reads

CCTTGTTCATAGATAGCTAGTGAGATGCTAAGTTAACAGATGCTCCTGTGGTGAGGTGACTTCCTCGGGTGCCACATTGCATTCTGGGGAGCAGCAGGGAAGCCTTGGCTGTCCCTGACAGGGCAAGTGTCATTTGGAAGTAATATTCACAGTGAGTCAGGCTGCAGCAGGGACTCTTTGGTCTTAGCCCCAAGTCTTCTG
*******************************************.(((......)))((.((((((.((((((......)))))).)))))))).(((((((((....))).))))))************************************************************************************ 		Read size # Mismatch Hit Count Total Norm Total SRR345198
brain		 SRR116846
epididymis		 SRR391852
embryo		 SRR345200
brain		 SRR345205
brain		 SRR391853
embryo		 SRR345196
brain		 SRR206939
brain		 SRR059766
thymus		 SRR248525
testes		 SRR345197
brain		 SRR345201
brain		 SRR345202
brain		 SRR345207
brain
................................................................TCGGGTGCCACTTTGCATT...................................................................................................................... 19 1 1 1.00 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
................................................................................................................................................................GCTGCGGCAGGGACGCTT....................... 18 2 20 0.45 9 0 9 0 0 0 0 0 0 0 0 0 0 0 0
..............................................................................................................................................................AGGCTGCAGTAGGGAATCTT....................... 20 2 14 0.29 4 0 0 3 0 0 1 0 0 0 0 0 0 0 0
..............................................................................................................................................................AAGCTGCGGCAGGGACTCTT....................... 20 2 9 0.11 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
................................................................TCGGGTGCCAGATTGTATT...................................................................................................................... 19 2 10 0.10 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
...............................................................................................................................................................GGCTGCAGTAGGGAATCTT....................... 19 2 20 0.10 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0
................................................................TCGGGTACGAGATTGCATTCT.................................................................................................................... 21 3 11 0.09 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
....................TGAGATGCTAAGCTAACATA................................................................................................................................................................. 20 2 12 0.08 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0
...........................................TGCTGTGGTGAGGTGACT............................................................................................................................................ 18 1 15 0.07 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0
.....................................................................AGCCACATTGCATGCTGGGG................................................................................................................ 20 2 16 0.06 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0
..................................................................................................................................................................AGCAGCATGGACTCTTTGGT................... 20 2 16 0.06 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0
.......................................................................................................................................................GTGAGTCACGCGGCAGCAG............................... 19 2 16 0.06 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
....................................................................................................................................CTCGGAAGTAGTATTCACAGT................................................ 21 3 20 0.05 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0
.................................................................................TTCTGGGGAGCCGCATGG...................................................................................................... 18 2 20 0.05 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0
......................................................................................................................................................................GCAGGGACTCTT....................... 12 0 20 0.05 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0
................................................................TCGGGTGCCAGATTGTAT....................................................................................................................... 18 2 20 0.05 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0
................................................................TCGGGTGGCAGATTGCAT....................................................................................................................... 18 2 20 0.05 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0
...................................................................................CCGGGGAGCAGGAGGGAAGTCT................................................................................................ 22 3 20 0.05 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1
..................................................................................................................................................................TGCAGCAGGGACTCTGTTGT................... 20 2 20 0.05 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0
.......................................................................................GGAGCAGCAGGGAAG................................................................................................... 15 0 20 0.05 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0
..........................................................ACTTCCTCGG..................................................................................................................................... 10 0 20 0.05 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0
................................................................TCGGGTGCCAGATTGTATTTT.................................................................................................................... 21 3 20 0.05 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0

Anti-sense strand reads

GGAACAAGTATCTATCGATCACTCTACGATTCAATTGTCTACGAGGACACCACTCCACTGAAGGAGCCCACGGTGTAACGTAAGACCCCTCGTCGTCCCTTCGGAACCGACAGGGACTGTCCCGTTCACAGTAAACCTTCATTATAAGTGTCACTCAGTCCGACGTCGTCCCTGAGAAACCAGAATCGGGGTTCAGAAGAC
************************************************************************************.(((......)))((.((((((.((((((......)))))).)))))))).(((((((((....))).))))))******************************************* 		Read size # Mismatch Hit Count Total Norm Total SRR037905
brain		 SRR248524
testes		 SRR345201
brain		 SRR345199
brain		 SRR345204
brain		 SRR037902
testes		 SRR345197
brain		 SRR345196
brain
......................................................................................................................................ACCTTCATTATAAGTGTCACTCAGT.......................................... 25 0 1 1.00 1 0 1 0 0 0 0 0 0
.....................................................TCCACGGAAGGCGCCCACGGCG.............................................................................................................................. 22 3 1 1.00 1 1 0 0 0 0 0 0 0
.................................ATTGTCTACGAGGACACGA..................................................................................................................................................... 19 1 4 0.25 1 0 0 0 1 0 0 0 0
..................................................CACTCCAGCGAAGGTGCCCAC.................................................................................................................................. 21 3 4 0.25 1 0 0 1 0 0 0 0 0
.................................................ACGCTCCAGTGAAGGAGCCCAC.................................................................................................................................. 22 3 5 0.20 1 0 0 0 0 1 0 0 0
..................................................CGCTCCAGCGAAGGAGCCCAC.................................................................................................................................. 21 3 7 0.14 1 0 0 1 0 0 0 0 0
.......................................................................................CCTCGTCGTCGCTTCGGA................................................................................................ 18 1 8 0.13 1 0 0 0 0 0 0 1 0
..................................................CACTCCAGCGAAGAAGCCCAC.................................................................................................................................. 21 3 12 0.08 1 0 0 0 1 0 0 0 0
..............................................................................................................................................................TCCGACGTCGTCCCCGATAAAT..................... 22 3 13 0.08 1 0 0 0 0 0 1 0 0
............TATCGATCACTGCACGAT........................................................................................................................................................................... 18 2 20 0.05 1 0 0 0 0 0 1 0 0
.........................................................................................................................................................CTCAGTCGGACGTCGTCC.............................. 18 1 20 0.05 1 0 0 0 0 0 0 0 1

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
mm10 chr19:53010606-53010806 - mmu-mir-6407 CCTTGTTCATAGATAGCTAGTGAGATGCTAAGTTAACAGATGCTCCTGTGGTGA--------------------GGT------------------------------GACTTCCTCGGGTGC-CACAT-TGCATTCTGGGGAGCAGCAGGGAAGCCTTGGCTGTCCCTGACAGGGCAAGTGTCATTTGGAAGTAATATTCACAGTGAGTCAGG-----CTGCAGCAGGGACTCTTTGGTCTTAGCCC-------CAAGTCTTCTG
cavPor3 scaffold_11:5561975-5562150 + CCTTGTTCCCA----------------CTGAGTC-CTGAATGCCACTGTGATGGGAT------------GATGGGGT------------------------------GAGTTCC------------------GT-TTGGGGAGCAGCAGCAAAGATTTGGCTGTG--TGACAGAACAAGTATGATTTGAAAGTGGCACCAACA-TGAGTCAGG-----CCACAGA--GAATTCCTTAGTCTTAGCCCTG-CAAACAAGTCTTGTA
dipOrd1 scaffold_17266:21935-22128 - GCCTATTCACAAGTGGCCAT----AAG-----------------------CTGTCCTGGT------------------------------GTCAGGTGCAGTAGAATGAGTTCTTCTGGGGC-TGAAGTGTCATCTCAGGGAGCAGCAGGTCAGCCTTGGCTGTGTCTGAGAGGGCAGGTGTGATTAGGAAGTAGTATTCACAGTGATTCAGG-----CTTCCAA--GAATTCCTAGGTCTTAGG-----AAAGCAAGTCT-GGG
hetGal2 Unknown -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ochPri2 scaffold_473:138855-139044 - CCCCATTCACAGGTGGCTGG----AAC-----TT-ACAAGTGGCACGGTGGTGGGGTGGTTGTGGTGGTGATGGGGTAAGCTCCCCTGGCGT--------------------------GGGC-CACCGTTTCTTCCTGGGGAGCAACAGGGAGGC------TGTGGCTGACAGCACACGTGTGACTTTGAAGTGGCAGTCATTGTGTGTCAGA-----CCATGGC--GGACTCCTAGGGC-------------------------
oryCun2 chr18:57475999-57476212 - gggTGTTgtgtGgTGtgTGT----gACCTGAGTT-ACAAGTGGCAGCATGATGGGGTGGTTGTGGTGGTGGTGGGGT------------------------------GAGCTCTCCTGGGGCCCCCAGTTTTCTCCTGGGGAGCACCAGGGAGGC------TGTGGGTGACAGCACA-GTGTGATTTGGAAGTGGCAGTCACAGCGAGTCAGA-----CTACAGT--GAACTCCTAGGGC--AGCATGGAAAGGCAAGTCTTGAG
rn5 chr1:281140905-281141070 - CCCTGTTCATAGGTAGCTAGTGAGAAGCTAAGTT-ACAGATGCTTCTGTAGTGA--------------------GGT------------------------------GACTTCCTCAGGTGC-CACAC-TGCATTCTGGG-------------------------------------AGTGTGACTTGGAAGCAGTATTCACAGTGAGTTAGGTCAGCCTGCAGCAGGGACTC--TGGTCTTAGCCC-------CAAGTCTTTGG
speTri2 JH393296:821596-821804 - TCCTAGATACAGGTGACTGT----AACTTTAGTT-ACCAATGCCCCTGTGGTGGGGTAGTTG-GGTGACTATGGGGT------------------------------GAATTCCTCTAG-GC-TGCACTTTCATCCTG-GGAGCAGCAGGGAGGCCTTCATTGTGTTGAGTGGAGTGAGTGTGAGTTGCAAGGGGTAGTCACAGG--------------CACAGG--GAATTCCTAGGTCTTAACATTG-AAAGCAATTCTCGAG

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
mm10
CCTTGTTCATAGATAGCTAGTGAGATGCTAAGTTAACAGATGCTCCTGTGGTGA--------------------GGT------------------------------GACTTCCTCGGGTGC-CACAT-TGCATTCTGGGGAGCAGCAGGGAAGCCTTGGCTGTCCCTGACAGGGCAAGTGTCATTTGGAAGTAATATTCACAGTGAGTCAGG-----CTGCAGCAGGGACTCTTTGGTCTTAGCCC-------CAAGTCTTCTGSizeHit 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
testes		SRR069810
testes		SRR069811
testes		SRR248523
testes		SRR248524
testes		SRR248525
testes		SRR248526
testes		SRR248527
testes		SRR363956
testes		SRR363957
testes		SRR363958
testes		SRR363959
testes		SRR363960
testes		SRR363963
testes		SRR363964
testes		SRR553582
brain		SRR553583
cerebellum		SRR553584
heart		SRR553585
kidney		SRR553602
testes		SRR553603
testes		SRR553604
testes		SRR553586
testes		SRR042464
thymus		SRR059765
thymus		SRR059766
thymus		SRR059767
thymus		SRR032476
uterus		SRR032477
uterus
...............................................................................................................................................................................................................................GCAGGGACTCTT..............................12200.05100000000000000000000000000000000000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
...........................................................................................................................................GGAGCAGCAGGGAAG...............................................................................................................15200.05100000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000100000000000000000000000
............................................................................................................ACTTCCTCGG...................................................................................................................................................10200.05100000000000000000000000000000000000000000100000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
cavPor3
CCTTGTTCCCA----------------CTGAGTC-CTGAATGCCACTGTGATGGGAT------------GATGGGGT------------------------------GAGTTCC------------------GT-TTGGGGAGCAGCAGCAAAGATTTGGCTGTG--TGACAGAACAAGTATGATTTGAAAGTGGCACCAACA-TGAGTCAGG-----CCACAGA--GAATTCCTTAGTCTTAGCCCTG-CAAACAAGTCTTGTASizeHit CountTotal NormTotal
No Reads
dipOrd1
GCCTATTCACAAGTGGCCAT----AAG-----------------------CTGTCCTGGT------------------------------GTCAGGTGCAGTAGAATGAGTTCTTCTGGGGC-TGAAGTGTCATCTCAGGGAGCAGCAGGTCAGCCTTGGCTGTGTCTGAGAGGGCAGGTGTGATTAGGAAGTAGTATTCACAGTGATTCAGG-----CTTCCAA--GAATTCCTAGGTCTTAGG-----AAAGCAAGTCT-GGGSizeHit CountTotal NormTotal
No Reads
hetGal2
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotal
No Reads
ochPri2
CCCCATTCACAGGTGGCTGG----AAC-----TT-ACAAGTGGCACGGTGGTGGGGTGGTTGTGGTGGTGATGGGGTAAGCTCCCCTGGCGT--------------------------GGGC-CACCGTTTCTTCCTGGGGAGCAACAGGGAGGC------TGTGGCTGACAGCACACGTGTGACTTTGAAGTGGCAGTCATTGTGTGTCAGA-----CCATGGC--GGACTCCTAGGGC-------------------------SizeHit CountTotal NormTotal
No Reads
oryCun2
gggTGTTgtgtGgTGtgTGT----gACCTGAGTT-ACAAGTGGCAGCATGATGGGGTGGTTGTGGTGGTGGTGGGGT------------------------------GAGCTCTCCTGGGGCCCCCAGTTTTCTCCTGGGGAGCACCAGGGAGGC------TGTGGGTGACAGCACA-GTGTGATTTGGAAGTGGCAGTCACAGCGAGTCAGA-----CTACAGT--GAACTCCTAGGGC--AGCATGGAAAGGCAAGTCTTGAGSizeHit CountTotal NormTotalGSM1528820
Adult_testes		GSM1528821
Adult_testes_Mili_IP
No Reads
rn5
CCCTGTTCATAGGTAGCTAGTGAGAAGCTAAGTT-ACAGATGCTTCTGTAGTGA--------------------GGT------------------------------GACTTCCTCAGGTGC-CACAC-TGCATTCTGGG-------------------------------------AGTGTGACTTGGAAGCAGTATTCACAGTGAGTTAGGTCAGCCTGCAGCAGGGACTC--TGGTCTTAGCCC-------CAAGTCTTTGGSizeHit CountTotal NormTotalGSM1528817
Adult_testes		GSM1528818
Adult_testes_Mili_IP		GSM1528819
10dpp_testes
No Reads
speTri2
TCCTAGATACAGGTGACTGT----AACTTTAGTT-ACCAATGCCCCTGTGGTGGGGTAGTTG-GGTGACTATGGGGT------------------------------GAATTCCTCTAG-GC-TGCACTTTCATCCTG-GGAGCAGCAGGGAGGCCTTCATTGTGTTGAGTGGAGTGAGTGTGAGTTGCAAGGGGTAGTCACAGG--------------CACAGG--GAATTCCTAGGTCTTAACATTG-AAAGCAATTCTCGAGSizeHit CountTotal NormTotal
No Reads

Generated: 04/30/2015 at 09:27 PM