RetrogeneDB ID: retro_pabe_1115

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:58194855..58195617(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF10
• Ensembl ID: ENSPPYG00000001726
• Aliases: SRSF10, FUSIP1, SFRS13A
• Description: splicing factor, arginine/serine-rich 13A [Source:RefSeq peptide;Acc:NP_001125358]

Sequence

>retro_pabe_1115
AACACATCTCTCTTCTTCAGGAACGTGGCCAATGACACCAGGTATGAAGATTTACAGTGTGAACTTGGTCATTATGGTCC
TACAGTTGATGTGTATGTTCCGCTTGATTTCTACATTCGCTGTCCAAGAGAATTTGCTTATATTCAATTTGAGGATGTTT
GTGATGCTGAAGATGCTTACATAATTTGGACAGAAAGTGGATTTGTGGATGGCAGATTAAAATATAGTTTGCCTATGGGG
ATCAGAAGACACGAAATCAGATGAAAGCCAAGGAAGGGAGGAATGTGTACAGTTCTTCATGCTATGATGATTATGACAGA
TACAGACATTCTAGAAGCCAAAGTTGTGAAAGTAGGAGATCAAGAAGGCGGTCTTCTGATTACAACCATAGAAGGTCATA
TAGTCCTAGAAACAGTAGACCGACTGGAAGACCACACATAGCAGAAGCCATTACAAATATGATAGATTCAAAACACTGAA
ATTAATCTTTTTCAAAATCTAAATCCAATTCAAGATCACGGTCCAAGTCCCAGCCCAAGAGAGAAATGAAGGCTGAATCA
CATTCTAGGTCTGCATCTCACACCAAAACTAGAGGCGCCTCAAAAATAGATTCCAAAACACATTATAAGTCTGGCTCAAG
ACATGAAAAGGAATTAGGGAAAAAAAGAACCACCTAGATCCAAATCTCAGTCAAAATCACAGTCTATGTCTAGGTCAAAA
TCTGTATCAAGGTCTTGGACTAGTCCTATGTTCAATGGCCAT

Alignment

ORF - retro_pabe_1115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.46 %
• Parental protein coverage: 96.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDA-LHNLDRKWIC
          NTSLF.RNVA.DTR.EDL..E.G.YGP.VDVYVPLDFY.R.PR.FAY.QFEDV.DAEDA.LHNLDRKWIC
Retrocopy NTSLFFRNVANDTRYEDLQCELGHYGPTVDVYVPLDFYIRCPREFAYIQFEDVCDAEDA<LHNLDRKWIC

Parental  GRQIEIQFAQGDRKTPNQMKAKEGRNVYSSSRYDDYDRYRRSRSRSYERRRSRSRSFDYNYRRSYSPRNS
          G.QI.I.FA.GD.KT.NQMKAKEGRNVYSSS.YDDYDRYR.SRS.S.E.RRSR.RS.DYN.RRSYSPRNS
Retrocopy GWQIKI*FAYGDQKTRNQMKAKEGRNVYSSSCYDDYDRYRHSRSQSCESRRSRRRSSDYNHRRSYSPRNS

Parental  RPTGRPR-RSRSHSDNDRF-KHRNRSFSRSKSNSRSRSKSQPKKEMKAKSRSRSASHTKTRGTSKTDSKT
          RPTGRP...SRSH...DRF.KH.N.SFS.SKSNSRSRSKSQPK.EMKA.S.SRSASHTKTRG.SK.DSKT
Retrocopy RPTGRPH<HSRSHYKYDRF>KH*N*SFSKSKSNSRSRSKSQPKREMKAESHSRSASHTKTRGASKIDSKT

Parental  HYKSGSRYEKES-RKKEPPRSKSQSRSQSRSRSKSRSRSWTSPKSSGH
          HYKSGSR.EKE...KKEPPRSKSQS.SQS.SRSKS.SRSWTSP...GH
Retrocopy HYKSGSRHEKEL>GKKEPPRSKSQSKSQSMSRSKSVSRSWTSPMFNGH

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	0.00 RPM	25.71 RPM
SRP007412_cerebellum	0.12 RPM	40.49 RPM
SRP007412_heart	0.00 RPM	18.94 RPM
SRP007412_kidney	0.00 RPM	26.19 RPM
SRP007412_liver	0.00 RPM	20.35 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1115 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1115 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1115 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1343
Pan troglodytes	retro_ptro_918
Gorilla gorilla	retro_ggor_1044

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009869	2 retrocopies	retro_amel_1810, retro_amel_355,
Bos taurus	ENSBTAG00000008072	1 retrocopy	retro_btau_759,
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,
Gorilla gorilla	ENSGGOG00000000392	4 retrocopies	retro_ggor_1044, retro_ggor_1411, retro_ggor_1522, retro_ggor_2870,
Myotis lucifugus	ENSMLUG00000028520	1 retrocopy	retro_mluc_89,
Mustela putorius furo	ENSMPUG00000015845	1 retrocopy	retro_mputfur_353,
Nomascus leucogenys	ENSNLEG00000013180	3 retrocopies	retro_nleu_1647, retro_nleu_1825, retro_nleu_202,
Oryctolagus cuniculus	ENSOCUG00000029326	1 retrocopy	retro_ocun_717,
Otolemur garnettii	ENSOGAG00000015374	2 retrocopies	retro_ogar_2650, retro_ogar_2987,
Pongo abelii	ENSPPYG00000001726	4 retrocopies	retro_pabe_1115 , retro_pabe_1601, retro_pabe_1796, retro_pabe_2529,
Rattus norvegicus	ENSRNOG00000007992	3 retrocopies	retro_rnor_1657, retro_rnor_2800, retro_rnor_2829,
Sus scrofa	ENSSSCG00000021615	2 retrocopies	retro_sscr_528, retro_sscr_554,
Ictidomys tridecemlineatus	ENSSTOG00000000956	1 retrocopy	retro_itri_1333,
Tursiops truncatus	ENSTTRG00000016150	2 retrocopies	retro_ttru_1098, retro_ttru_695,