RetrogeneDB ID: retro_pabe_3235

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7_random:12708987..12709400(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRPEL1
• Ensembl ID: ENSPPYG00000014573
• Aliases: None
• Description: grpE protein homolog 1, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_001127196]

Sequence

>retro_pabe_3235
GCGGCTCTATGCGTGAGGCTGGTGCCACGCGGTCTCCCGGTGTTGGCATTGTCTCCAGGCCTTCTCCTCAGTTCTGCACA
CAGCTACAAAACAAAAGAACAGTTGCCAGCACTTGGAAGAGGATGTGGATCCAAACCAAATGGGGGACAGATACTCCCTC
TATGGACGAGATACTCATGGAAGAAGTCAAGTTAGAAGAGCAGCTGAAGGAGGCTGTGGAAGAAGATAAGCAAGCACTGG
GAGATACTGAGGGCTCGCAGCAGATCAGCCAAAAATTGGTGGAGGAGGGAAATATGTATAGCATTCAGGGCTTCTGCAAG
GACTCGTTAGAGGTTGCAGATGTTTTGGAGAAGGCAACACAGTGTGTTCCAGAAGAAGAAATTAAAGACAATAACCCTCA
CCTGAAGAACCTC

Alignment

ORF - retro_pabe_3235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.9 %
• Parental protein coverage: 64.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AAQCVRLARRSLPTLALS-LRPSPR-LLCTATKQKNSGQNLEEDMG-QSEQKADPPATEKTLLEEKVKLE
          AA.CVRL..R.LP.LALS..RPSP...L.TATKQKNS.Q.LEED...Q.....D.P.....L.EE.VKLE
Retrocopy AALCVRLVPRGLPVLALS<SRPSPQ<VLHTATKQKNSCQHLEEDVD>QTKWGTDTPSMDEILMEE-VKLE

Parental  EQLKETVEKYKRALADTENLRQRSQKLVEEAKXXGIQAFCKDLLEVADVLEKATQCVPKEEIKDDNPHLK
          EQLKE.VE..K.AL.DTE...Q.SQKLVEE.....IQ.FCKD.LEVADVLEKATQCVP.EEIKD.NPHLK
Retrocopy EQLKEAVEEDKQALGDTEGSQQISQKLVEEGNMYSIQGFCKDSLEVADVLEKATQCVPEEEIKDNNPHLK

Parental  NL
          NL
Retrocopy NL

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	37.21 RPM
SRP007412_cerebellum	0.00 RPM	31.74 RPM
SRP007412_heart	0.00 RPM	22.76 RPM
SRP007412_kidney	0.00 RPM	42.63 RPM
SRP007412_liver	0.00 RPM	38.10 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3235 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3235 has 0 orthologous retrocopies within eutheria group .

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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 ,
Pongo abelii	ENSPPYG00000015933	2 retrocopies	retro_pabe_1063, retro_pabe_3764,
Pan troglodytes	ENSPTRG00000015894	3 retrocopies	retro_ptro_2544, retro_ptro_2633, retro_ptro_2636,
Sarcophilus harrisii	ENSSHAG00000007667	1 retrocopy	retro_shar_766,