ID:

mmu-mir-6343

Coordinate:

chr1:76509560-76509643 +

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.

Sense Strand Reads

CAAGTTGAATAAATAGCTTTCCTAGAATGTCTCAGAATTTTCCAGTTATATTCAGATAGCTATTTATTGCAGAAAAGTGGGGCAGCCTGGCATTATGTTCTCCACTTCTATGTAAAGTAGGAGCTGACTGACACTAAGACTTCATCCTAGCAGTTATTTTATGCTGTGGAAAATGATGTCAATG *********************************........((((.((.((((.(((((.(((((((((...((((((((.(((.((....)).)))))))))))...))))..)))))))))).))))...)).))))........*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR391847 embryo	SRR391846 embryo	SRR345197 brain	SRR345198 brain	SRR345199 brain	SRR345200 brain	SRR391845 embryo	SRR039152 muscle	SRR039153 muscle	SRR095855BC2 heart	SRR391849 embryo
.......................................................................................................................GGAGCTGACTGATACTAATA.............................................	20	2	11	2.27	25	15	9	0	0	0	0	1	0	0	0	0
................................................................................................................TAAGGTAGGAGCTGTCTGACAC..................................................	22	2	1	1.00	1	0	0	1	0	0	0	0	0	0	0	0
.......................................................................................................................GGAGCTGACTGATACTAA...............................................	18	1	5	0.80	4	2	2	0	0	0	0	0	0	0	0	0
.......................................................................................................................GGAGCTGACTGACACTAATA.............................................	20	1	2	0.50	1	1	0	0	0	0	0	0	0	0	0	0
.......................................................................................................................GGAGCTGACTGGCACTAATAC............................................	21	2	2	0.50	1	1	0	0	0	0	0	0	0	0	0	0
................................................................................................................TAAAGTACGCGCTGACTGCCA...................................................	21	3	8	0.25	2	0	0	0	0	1	1	0	0	0	0	0
......................................................................................................................AGGAGCTGACTGATACTAATA.............................................	21	2	5	0.20	1	1	0	0	0	0	0	0	0	0	0	0
................................................................TATTGAAGAAAAGTCGGGC.....................................................................................................	19	2	12	0.17	2	0	0	0	0	0	0	0	1	1	0	0
...........................................................................AGTGGGGCAGCCTGGCGT...........................................................................................	18	1	8	0.13	1	0	0	0	1	0	0	0	0	0	0	0
................................................................................................................TAACGCAGGCGCTGACTGAC....................................................	20	3	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0
................................................................................................................TAAGGCAGGAGCTGACTGAC....................................................	20	2	20	0.05	1	0	0	0	1	0	0	0	0	0	0	0
......................................................................................................................TGGAGCTGACTGACACT.................................................	17	1	20	0.05	1	0	0	0	0	0	0	0	0	0	0	1
.......................................................................................................................................AAGACTTCATCC.....................................	12	0	20	0.05	1	0	0	0	0	0	0	0	0	0	1	0

Anti-sense strand reads

GTTCAACTTATTTATCGAAAGGATCTTACAGAGTCTTAAAAGGTCAATATAAGTCTATCGATAAATAACGTCTTTTCACCCCGTCGGACCGTAATACAAGAGGTGAAGATACATTTCATCCTCGACTGACTGTGATTCTGAAGTAGGATCGTCAATAAAATACGACACCTTTTACTACAGTTAC *********************************........((((.((.((((.(((((.(((((((((...((((((((.(((.((....)).)))))))))))...))))..)))))))))).))))...)).))))........*********************************	Read size	# Mismatch	Hit Count	Total Norm	Total	SRR345200 brain	SRR039153 muscle	SRR345201 brain	SRR095853 heart	SRR116846 epididymis	SRR248525 Thy1-_somatic_testes_cells	SRR345203 brain	SRR042465 spleen
......................................................................................................................................ATTCTGAAGTAGGAT...................................	15	0	9	0.78	7	5	0	0	0	0	1	1	0
.........................................................................................................ATGATAAATTTCATCCTCGACT.........................................................	22	2	2	0.50	1	0	1	0	0	0	0	0	0
...................................................AGTCTATCGCGAAATAACGT.................................................................................................................	20	2	4	0.25	1	0	0	1	0	0	0	0	0
................................................................................................................................ACTGACATTCTGAAGTAGGATC..................................	22	2	5	0.20	1	0	0	0	1	0	0	0	0
...............................................................................CCGGGCGGACCGTAATAC.......................................................................................	18	2	20	0.15	3	0	0	0	0	3	0	0	0
........................................................................................................................................TTTGAAGTAGGAGCGTCA..............................	18	2	20	0.05	1	0	0	0	0	0	0	0	1

Re-alignment of all predicted orthologs

Species	Coordinate	ID	Alignment
mm10	chr1:76509510-76509693 +	mmu-mir-6343	CAAGTTGAATAAATAGCTTTCCTAGAATGTCTCAGAAT-TTTCCAGTTATATTCAGATAGCTATTTATTGCAGAAAAGTGGGGCAGCCTGGCATTATGTTCTCCACTTCTATGTAAAGTAGGAGCTGACTGACAC-TAAGACTTCATCCTAGCAGTTATTTTATGCTGTGGAAAATGATGTCAATG
cavPor3	scaffold_89:4709380-4709563 -		CAAATACAATAAATAGATTTCCAAGAATGTCTCAGAAGT-CTCCAGTTATATTCAGATTGCTATTTATTGCAGCAAAGTGGAGCAGCCGGGCATTATGCTCAGCTCTTCTATGTGGAGCAGAGACAGGCTGACAC-TGAAGCTTAATCACAGTGGTTATTTTATGGCATAGAAAATGATGTCAATA
dipOrd1	scaffold_977:119270-119450 +		CAAGCAGAA----TAGATTTCCAAGAATGTCTCCAACGTTTACCGGTTATATTCAGATTGCTATTTATTGCAGAAAAGTGGGGCAGCTCTGTATTATGTTTGGTGCTTCTACATAGAGTCAAGGCTGACTGACAC-TGAATCTTCATCACAGCAGTTATTTTATGCCAGAGAAAACAATGTCAATG
hetGal2	Unknown		------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ochPri2	scaffold_3453:148625-148804 +		GAAATAGGA-----AGAATTCTCAGAATGTCTCAGAAGTCTTCCAGTGATATTCAAGTTTCTATTTATTGCAGAAAAGTGGGCCAGTCTTGCATTATCTTGAGCATTTGTATGCAGCGTCAAGAATGACTGACGT-CAGAACTTAACCGCTGTAGTTATTGCATGTTATGGAAAAGGAAGCAGATA
oryCun2	chr7:161770232-161770406 +		AAAATAGAA----TAGATTTCTCAGAATGTCTAAGAAT---TCTAGTTTTATTCAGGTTTCTATTTATTGAAGAAAACTGGGGCAGGCTTACGTTATATTCAGCACTTCTATGCAGAGCAGAGAATGACTGA----TAAAACTTAACCATACTAGTTATTTCATGTCATGGAAAGTGATGCCAATA
rn5	chr9:89893677-89893860 +		CAAGTTGAATAAATAGCTTTCCTAGAATGTCTCAGAAAT-TTCCAGTTATATTCAGATTGCTCTTTATTGCAGAAAAGTGGGGCAGCCTGGCATTATGTTCTCCACTTCTATGTAAAGTAGGAGCTGACTGACAC-TAAGACTTCATCCTAGCAGTTATTTTATGCTGTGGAAAATGATGTCAATG
speTri2	JH393379:2761400-2761584 +		CAAACAGAATAAATAGATTTCCAAGAATGTCTTAGAAGTTTTCCATTTATATTCAGACTGCTATTTATTGCAGAAAAGTAGAGCAATCTTGAATTATATTCAGCACATCTAAGTAGAGTAGAGGTTGACTGACACTTAAAACTTAATTACAACAGT-ATTTTATGCTGTGGAGAATGATGTCAATA

Re-alignment of all predicted orthologs with sRNA reads

Species

Read alignment

mm10

CAAGTTGAATAAATAGCTTTCCTAGAATGTCTCAGAAT-TTTCCAGTTATATTCAGATAGCTATTTATTGCAGAAAAGTGGGGCAGCCTGGCATTATGTTCTCCACTTCTATGTAAAGTAGGAGCTGACTGACAC-TAAGACTTCATCCTAGCAGTTATTTTATGCTGTGGAAAATGATGTCAATG	Size	Hit Count	Total Norm	Total	SRR042455 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
.........................................................................................................................................AAGACTTCATCC.....................................	12	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

cavPor3

CAAATACAATAAATAGATTTCCAAGAATGTCTCAGAAGT-CTCCAGTTATATTCAGATTGCTATTTATTGCAGCAAAGTGGAGCAGCCGGGCATTATGCTCAGCTCTTCTATGTGGAGCAGAGACAGGCTGACAC-TGAAGCTTAATCACAGTGGTTATTTTATGGCATAGAAAATGATGTCAATA	Size	Hit Count	Total Norm	Total
No Reads

dipOrd1

CAAGCAGAA----TAGATTTCCAAGAATGTCTCCAACGTTTACCGGTTATATTCAGATTGCTATTTATTGCAGAAAAGTGGGGCAGCTCTGTATTATGTTTGGTGCTTCTACATAGAGTCAAGGCTGACTGACAC-TGAATCTTCATCACAGCAGTTATTTTATGCCAGAGAAAACAATGTCAATG	Size	Hit Count	Total Norm	Total
No Reads

hetGal2

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	Total
No Reads

ochPri2

GAAATAGGA-----AGAATTCTCAGAATGTCTCAGAAGTCTTCCAGTGATATTCAAGTTTCTATTTATTGCAGAAAAGTGGGCCAGTCTTGCATTATCTTGAGCATTTGTATGCAGCGTCAAGAATGACTGACGT-CAGAACTTAACCGCTGTAGTTATTGCATGTTATGGAAAAGGAAGCAGATA	Size	Hit Count	Total Norm	Total
No Reads

oryCun2

AAAATAGAA----TAGATTTCTCAGAATGTCTAAGAAT---TCTAGTTTTATTCAGGTTTCTATTTATTGAAGAAAACTGGGGCAGGCTTACGTTATATTCAGCACTTCTATGCAGAGCAGAGAATGACTGA----TAAAACTTAACCATACTAGTTATTTCATGTCATGGAAAGTGATGCCAATA	Size	Hit Count	Total Norm	Total	GSM1528820 Adult_testes	GSM1528821 Adult_testes_Mili_IP
No Reads

rn5

CAAGTTGAATAAATAGCTTTCCTAGAATGTCTCAGAAAT-TTCCAGTTATATTCAGATTGCTCTTTATTGCAGAAAAGTGGGGCAGCCTGGCATTATGTTCTCCACTTCTATGTAAAGTAGGAGCTGACTGACAC-TAAGACTTCATCCTAGCAGTTATTTTATGCTGTGGAAAATGATGTCAATG	Size	Hit Count	Total Norm	Total	GSM1528817 Adult_testes	GSM1528818 Adult_testes_Mili_IP	GSM1528819 10dpp_testes
No Reads

speTri2

CAAACAGAATAAATAGATTTCCAAGAATGTCTTAGAAGTTTTCCATTTATATTCAGACTGCTATTTATTGCAGAAAAGTAGAGCAATCTTGAATTATATTCAGCACATCTAAGTAGAGTAGAGGTTGACTGACACTTAAAACTTAATTACAACAGT-ATTTTATGCTGTGGAGAATGATGTCAATA	Size	Hit Count	Total Norm	Total
No Reads

Generated: 06/17/2015 at 11:02 AM