RetrogeneDB ID: retro_mmus_3480

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:80362548..80363232(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083444
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_3480
ATGTCCCAATACCTGTGTCTAATCAACACATCTCTGTTCACCAGAAATGTGGAGGGCCGATATCAGGTCTGAAGATTTAT
GACAGGAGTTCGGTTGGTGTGGTCCAATTGTAGATGTTTATGTTACACTTGATTGGTATAAGGGTCTTCCAAGAGGATTT
GCATATGTTCAATTTGAGTGTGTTCATGATGCTGAAGATGCTTTACATACTTTGGACAGAAAATGGATTTGTGGGTGTCA
AATTGAAATACAGTTCACACAGGGATATTGGAAGACACTAAATCAAATGAAAGACAAGTTAGGGAAGAATGTATACAGCT
CTTGACAATATGAGGATTATGACAGATATAGACAGTCTCAAAGTGTAAGTTATGAAAGAAGGAGATCAAGGAGTTGCTCC
TTTGATCATAACTCTAGGAGATTTTACAGTTCTAGAAACAGTAGACCAACTGGAAGACCATGGCATTGCTGAAGCCATTC
ATACAATGATAGATTCAAACACCAAAATTGATCTTTTTCAAGATCTAAATCCAATTTAAGATCACTGTCCAAGTCCTATC
CCACAATGAAGGCTAAATCACGTTTTATGCCTGGATCTCAAACCAAAGCTAGAGGCACCCCTAAAATTGATTCCAAAACA
CATTATATGTCTTGTTCAAGATAGGAAAGGAATCAAGAAAAAAA

Alignment

ORF - retro_mmus_3480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.98 %
• Parental protein coverage: 87.79 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSRYLRPPNTSLFVRNVAD-DTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH
          MS.YL...NTSLF.RNV...D.RSEDL..EFG..GPIVDVYV.LD.Y...PRGFAYVQFE.V.DAEDALH
Retrocopy MSQYLCLINTSLFTRNVEG>DIRSEDL*QEFGWCGPIVDVYVTLDWYKGLPRGFAYVQFECVHDAEDALH

Parental  NLDRKWICGRQIEIQFAQGDRKTPNQMKAKEGRNVYSSSRYDDYDRYRRSRSRSYERRRSRSRSFDYNYR
          .LDRKWICG.QIEIQF.QG..KT.NQMK.K.G.NVYSS..Y.DYDRYR.S.S.SYERRRSRS.SFD.N.R
Retrocopy TLDRKWICGCQIEIQFTQGYWKTLNQMKDKLGKNVYSS*QYEDYDRYRQSQSVSYERRRSRSCSFDHNSR

Parental  RSYSPRNSRPTGRPRRSRSHSDNDRFKHRNRSFSRSKSNSRSRSKSQPKKEMKAKSRSRSASHTKTRGTS
          R.YS.RNSRPTGRP....SHS.NDRFKH.N.SFSRSKSN.RS.SKS.P...MKAKSR....S.TK.RGT.
Retrocopy RFYSSRNSRPTGRPWHC*SHSYNDRFKHQN*SFSRSKSNLRSLSKSYP--TMKAKSRFMPGSQTKARGTP

Parental  KTDSKTHYKSGSRYE-KESRKK
          K.DSKTHY.S.SR.E.KESRKK
Retrocopy KIDSKTHYMSCSR*E<KESRKK

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 actvity near the 5' end of retro_mmus_3480 was not detected

EST

No EST(s) were mapped for retro_mmus_3480 retrocopy.

TSS

No TSS is located nearby retro_mmus_3480 retrocopy 5' end.

Lab

retro_mmus_3480 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3480 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,