RetrogeneDB ID: retro_mmus_1311

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:112328699..112329175(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Srsf10
• Ensembl ID: ENSMUSG00000028676
• Aliases: Srsf10, FUSIP2, Fusip1, NSSR1, NSSR2, Nssr, SRrp40, Sfrs13a, Srsf13a, TASR, TASR1, TASR2
• Description: serine/arginine-rich splicing factor 10 [Source:MGI Symbol;Acc:MGI:1333805]

Sequence

>retro_mmus_1311
AATACATTTCTGTTCATCAGAAACCTGGCTGATGACCCCAGGTCTGAAGATTTAAGCCTGGAATTTGGTCATTATGGTCC
AAAAGTAAGTGTTTATGTTCTACTTGATTTCTACACTCGGTGTCCAGGAGGATTTTGTATATGTTCAGTTTCAGGATGTT
CGTGATGCTGAGGATGTTTTACCTAATTTGCACAGAAAATGGATTTGTGGGCATCAAATTGAAATACATTTAGAACAGGG
GAAGAAACCCAATCAAATGAAAGCCAAGGATGGGAGGAATGTATAGAGCTCTTCACGATATGATGATGACTGATAGATGT
TCAGGAAATACAAGTTATGAAGGGAGGAGATCAAGGAGTCGCTCCTTTGATTATAACCATAGGAGATCGCTCAGTCCTAG
AAACAGTAGACCAACTGGAAGACCACAGGGTAGCCGAAGCCATTTCAGCAATGATAGATTCAAACACCAAAAGCAG

Alignment

ORF - retro_mmus_1311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.51 %
• Parental protein coverage: 61.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRG-FAYVQFEDVRDAEDALHNLDRKWIC
          NT.LF.RN.ADD.RSEDL..EFG.YGP.V.VYV.LDFYTR.P.G.F.YVQF.DVRDAED.L.NL.RKWIC
Retrocopy NTFLFIRNLADDPRSEDLSLEFGHYGPKVSVYVLLDFYTRCPGG>FVYVQFQDVRDAEDVLPNLHRKWIC

Parental  GRQIEIQFAQGDRKTPNQMKAKEGRNVYSSSRYDD-YDRYRRSRSRSYERRRSRSRSFDYNYRRSYSPRN
          G.QIEI...QG..K.PNQMKAK.GRNV.SSSRYDD..DR.....S....R.R..SRSFDYN.RRS.SPRN
Retrocopy GHQIEIHLEQG--KKPNQMKAKDGRNV*SSSRYDD>TDRCSGNTSYEGRRSR--SRSFDYNHRRSLSPRN

Parental  SRPTGRPRRSRSHSDNDRFKHRNR
          SRPTGRP..SRSH..NDRFKH...
Retrocopy SRPTGRPQGSRSHFSNDRFKHQKQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	36.54 RPM
SRP007412_cerebellum	0.00 RPM	30.39 RPM
SRP007412_heart	0.00 RPM	17.37 RPM
SRP007412_kidney	0.00 RPM	28.95 RPM
SRP007412_liver	0.00 RPM	15.68 RPM
SRP007412_testis	0.00 RPM	37.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1311 was not detected

EST

No EST(s) were mapped for retro_mmus_1311 retrocopy.

TSS

No TSS is located nearby retro_mmus_1311 retrocopy 5' end.

Lab

retro_mmus_1311 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1311 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004836	1 retrocopy	retro_chof_7,
Callithrix jacchus	ENSCJAG00000020883	9 retrocopies	retro_cjac_1126, retro_cjac_1170, retro_cjac_2176, retro_cjac_2595, retro_cjac_2638, retro_cjac_3852, retro_cjac_628, retro_cjac_705, retro_cjac_864,
Cavia porcellus	ENSCPOG00000024533	1 retrocopy	retro_cpor_1098,
Dasypus novemcinctus	ENSDNOG00000008699	3 retrocopies	retro_dnov_1327, retro_dnov_1809, retro_dnov_2244,
Erinaceus europaeus	ENSEEUG00000014286	1 retrocopy	retro_eeur_522,
Homo sapiens	ENSG00000188529	5 retrocopies	retro_hsap_1343, retro_hsap_1940, retro_hsap_2445, retro_hsap_3054, retro_hsap_4295,
Loxodonta africana	ENSLAFG00000026905	1 retrocopy	retro_lafr_148,
Myotis lucifugus	ENSMLUG00000028520	1 retrocopy	retro_mluc_89,
Mus musculus	ENSMUSG00000028676	5 retrocopies	retro_mmus_1081, retro_mmus_1311 , retro_mmus_1814, retro_mmus_3480, retro_mmus_982,
Ochotona princeps	ENSOPRG00000018613	3 retrocopies	retro_opri_1067, retro_opri_295, retro_opri_916,
Pan troglodytes	ENSPTRG00000024234	4 retrocopies	retro_ptro_1295, retro_ptro_1413, retro_ptro_1986, retro_ptro_918,