RetrogeneDB ID: retro_ptro_1986

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:52085063..52085837(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFRS13A
• Ensembl ID: ENSPTRG00000024234
• Aliases: None
• Description: None

Sequence

>retro_ptro_1986
TCCAGCTACCTGCGTCCTCCAAGGTGCCTCTGTTCATCAGGAATGGAGCCAGTAACAGCAGGTTCAAAGATTTATGGCAT
GAATTTGGTCATTATGATCCTATAGTTGATGTGTATGTTCCACTTGATTTCTACACTCACTGTCCAAGAGGAGTTGCTTA
TGTTCAATTGGAAGATGTTCGTGATGCTGAAGATGCTTTACATAATTTGGACAGAAAGTGGATTTGTGGATGTCAAATGG
AAACAGTTTGCACAGGGGGATTGGAAGACCCCAAATCAGATGAAAGCAAAGGAAGGTAGGAGTATGTACAGTTCTTCACG
CTATGATTATGACAGATATAGATGTTCTAGAAGCCAAAGTTATGAAAGAAGATCAAGAAGTCGGTCTTTTGCTTACATCT
ATAGAAGATCTTGTAGTCCTAGAAAGAGTGGATGGACTGGAAGACCATGGTGTAGCAGAAGCCATTCCAACAGTGATAGA
GTCAAACACTGAAATCAGTCTTTTTCAAGATCTAAATCCAATTCAAGATCAAGGTCCAAGTCCCAGCCCAAGAAAGAAAT
GAAGGCTAAATCGTGTTCTAGGTCTGCATCGCATGCCAAAACTAGAGGCACCTCTAAAACAGATTCCAAAACATATTACA
AGTCTTGCTCAAGACATAAAAAGGAATCAAGGAAAAAAGAACCGCCTTGTTCCAAATCCCAGTCAAGGTCACAGTCTAGG
CCTAGGTCAAAATCTAGATCAAGATCTTGGACTAGTCCTAAATCCAGTGGCCAC

Alignment

ORF - retro_ptro_1986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.67 %
• Parental protein coverage: 99.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRYLRPPN-TSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN
          S.YLRPP....LF.RN.A...R..DL..EFG.Y.PIVDVYVPLDFYT..PRG.AYVQ.EDVRDAEDALHN
Retrocopy SSYLRPPR<VPLFIRNGASNSRFKDLWHEFGHYDPIVDVYVPLDFYTHCPRGVAYVQLEDVRDAEDALHN

Parental  LDRKWICGRQIEIQFAQGDRKTPNQMKAK-EGRNVYSSSRYDDYDRYRRSRSRSYERRRSRSRSFDYNYR
          LDRKWICG.Q.E.....G....P.....K.EGR..YSSSRY.DYDRYR.SRS.SYE.RRSRSRSF.Y.YR
Retrocopy LDRKWICGCQME-TVCTGGLEDPKSDESK>EGRSMYSSSRY-DYDRYRCSRSQSYE-RRSRSRSFAYIYR

Parental  RSYSPRNSRPTGRPRRSRSHSDNDRFKHRNRSFSRSKSNSRSRSKSQPKKEMKAKSRSRSASHTKTRGTS
          RS.SPR.S..TGRP..SRSHS..DR.KH.N.SFSRSKSNSRSRSKSQPKKEMKAKS.SRSASH.KTRGTS
Retrocopy RSCSPRKSGWTGRPWCSRSHSNSDRVKH*NQSFSRSKSNSRSRSKSQPKKEMKAKSCSRSASHAKTRGTS

Parental  KTDSKTHYKSGSRYEKESRKKEPPRSKSQSRSQSRSRSKSRSRSWTSPKSSGH
          KTDSKT.YKS.SR..KESRKKEPP.SKSQSRSQSR.RSKSRSRSWTSPKSSGH
Retrocopy KTDSKTYYKSCSRHKKESRKKEPPCSKSQSRSQSRPRSKSRSRSWTSPKSSGH

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_prefrontal_cortex	0.02 RPM	24.08 RPM
SRP007412_cerebellum	0.18 RPM	60.08 RPM
SRP007412_heart	0.00 RPM	27.57 RPM
SRP007412_kidney	0.00 RPM	34.28 RPM
SRP007412_liver	0.00 RPM	24.06 RPM
SRP007412_testis	0.00 RPM	74.93 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1986 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1986 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1986 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,