RetrogeneDB ID: retro_ptro_2544

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:65292145..65292612(+)
• Located in intron of: ENSPTRG00000019251

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRPEL1
• Ensembl ID: ENSPTRG00000015894
• Aliases: None
• Description: GrpE protein homolog [Source:UniProtKB/TrEMBL;Acc:H2QP70]

Sequence

>retro_ptro_2544
GTGGTGGCTCAATGCGTGAGGCTGGTGCCATGCAGTCTCCTGGTGTTGGCATTGTCTCCCAGCCTTCTCAGTTCTGCACA
CAGCTACAAAACAAAAGAACAGTTGCCAGCACTTGGAAGAGGATGTGGATCCAAACCAAATGGAGGACAGATACTCCCTC
TACGGACAAGATACTCATGGAAGAAGTCAAGTTAGAAGAGCAGCTGAAGGAGGCTGTAGAAGAAGATAAGCAAGCATTGG
CAGATACTGAGGACTTGCAGCAGATCAGCCAAAAATTGGTGGAGGAGGCAAATATGTGTAGCATTCAGGGCTTCTGCAAG
GACTCGTTAGAGGTTGCAGATGTTTTGGAGAAGGCAACACAGTGTGTTCCAGAAGAAGAAATTAAAGACAATAACCCTCA
CCTGAAGAACCTCTGTGAAACTCTCACAATGAGTGAAGTCCAGATTCAGGAAGTGTTCAGCAAGCAC

Alignment

ORF - retro_ptro_2544 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.5 %
• Parental protein coverage: 72.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAQCVRLARRSLPALALSLRPSP-RLLCTATKQKNSGQNLEEDMG-QSEQKADPPATEKTLLEEKVKLE
          ..AQCVRL...SL..L.L.L.PS....L.TATKQKNS.Q.LEED...Q.....D.P.T.K.L.EE.VKLE
Retrocopy VVAQCVRLVPCSL--LVLALSPSL>SVLHTATKQKNSCQHLEEDVD>QTKWRTDTPSTDKILMEE-VKLE

Parental  EQLKETVEKYKRALADTENLRQRSQKLVEEAKLYGIQAFCKDLLEVADVLEKATQCVPKEEIKDDNPHLK
          EQLKE.VE..K.ALADTE.L.Q.SQKLVEEA....IQ.FCKD.LEVADVLEKATQCVP.EEIKD.NPHLK
Retrocopy EQLKEAVEEDKQALADTEDLQQISQKLVEEANMCSIQGFCKDSLEVADVLEKATQCVPEEEIKDNNPHLK

Parental  NLYEGLVMTEVQIQKVFTKH
          NL.E.L.M.EVQIQ.VF.KH
Retrocopy NLCETLTMSEVQIQEVFSKH

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	0.16 RPM	24.36 RPM
SRP007412_cerebellum	0.18 RPM	25.13 RPM
SRP007412_heart	0.06 RPM	26.55 RPM
SRP007412_kidney	0.24 RPM	42.71 RPM
SRP007412_liver	0.03 RPM	53.55 RPM
SRP007412_testis	0.21 RPM	38.46 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2544 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2544 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2544 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3746

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014364	1 retrocopy	retro_cfam_1776,
Homo sapiens	ENSG00000109519	3 retrocopies	retro_hsap_3746, retro_hsap_3864, retro_hsap_3870,
Loxodonta africana	ENSLAFG00000002590	1 retrocopy	retro_lafr_535,
Monodelphis domestica	ENSMODG00000002955	1 retrocopy	retro_mdom_28,
Mustela putorius furo	ENSMPUG00000010471	1 retrocopy	retro_mputfur_32,
Nomascus leucogenys	ENSNLEG00000011822	1 retrocopy	retro_nleu_2642,
Otolemur garnettii	ENSOGAG00000032291	1 retrocopy	retro_ogar_1765,
Procavia capensis	ENSPCAG00000011314	1 retrocopy	retro_pcap_388,
Pongo abelii	ENSPPYG00000014573	1 retrocopy	retro_pabe_3235,
Pan troglodytes	ENSPTRG00000015894	3 retrocopies	retro_ptro_2544 , retro_ptro_2633, retro_ptro_2636,
Pan troglodytes	ENSPTRG00000017396	2 retrocopies	retro_ptro_3226, retro_ptro_877,
Sarcophilus harrisii	ENSSHAG00000007667	1 retrocopy	retro_shar_766,