RetrogeneDB ID: retro_ptro_1663

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:184313734..184314081(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXNL4A
• Ensembl ID: ENSPTRG00000010136
• Aliases: None
• Description: thioredoxin-like 4A [Source:HGNC Symbol;Acc:30551]

Sequence

>retro_ptro_1663
GTTGTCATTCGCTTCGGCCACGGCTGGGACCCCACATGCATGAAAATGGATAAGGTCTTGTACAGCATCATTGAGAAGGT
TAAAGATTTTGCAGTTATTTTTCTTGTGGATATTACCAAAGTACCTGACTTCAACAAAATGTATGAGTTATATGATCCAT
GCACTATCATGTTTTTCTTCAGGAACAAGCACATCATGGTTGTCTTGGGGACTGGCAACAACAAGATTAACTGGGCCATG
GAGGACAAGCAGGAGATGGTCGACATCATAGAGACCGTGGACTGTAGGGCCCTCAATGGTGGCGACCTGGTCTTGTCCCC
AAAAACTACTCCACCAAGTCCAGATAC

Alignment

ORF - retro_ptro_1663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.51 %
• Parental protein coverage: 85.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVIR-GHDWDPTCMKME-VLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLG
          VVIR.GH.WDPTCMKM..VLYSI.EKVK.FAVI.LVDIT.VPDFNKMYELYDPCT.MFFFRNKHIM..LG
Retrocopy VVIRFGHGWDPTCMKMDKVLYSIIEKVKDFAVIFLVDITKVPDFNKMYELYDPCTIMFFFRNKHIMVVLG

Parental  TGNNNKINWAMEDKQEMVDIIETVYRGARKGRGLVVS-PKDYSTKYRY
          TG.NNKINWAMEDKQEMVDIIETV...A..G..LV.S.PK.YSTK.RY
Retrocopy TG-NNKINWAMEDKQEMVDIIETVDCRALNGGDLVLS<PKNYSTKSRY

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	0.05 RPM	27.24 RPM
SRP007412_cerebellum	0.04 RPM	16.17 RPM
SRP007412_heart	0.00 RPM	14.57 RPM
SRP007412_kidney	0.00 RPM	21.92 RPM
SRP007412_liver	0.00 RPM	22.23 RPM
SRP007412_testis	0.53 RPM	16.55 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1663 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1663 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1663 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_2805

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010130	2 retrocopies	retro_cjac_2805, retro_cjac_3659,
Homo sapiens	ENSG00000141759	2 retrocopies	retro_hsap_2185, retro_hsap_4900,
Gorilla gorilla	ENSGGOG00000005285	2 retrocopies	retro_ggor_1731, retro_ggor_3060,
Loxodonta africana	ENSLAFG00000003190	1 retrocopy	retro_lafr_198,
Myotis lucifugus	ENSMLUG00000009188	1 retrocopy	retro_mluc_562,
Macaca mulatta	ENSMMUG00000001613	2 retrocopies	retro_mmul_2636, retro_mmul_913,
Nomascus leucogenys	ENSNLEG00000008378	2 retrocopies	retro_nleu_1268, retro_nleu_314,
Otolemur garnettii	ENSOGAG00000034753	1 retrocopy	retro_ogar_1751,
Pan troglodytes	ENSPTRG00000010136	1 retrocopy	retro_ptro_1663 ,
Rattus norvegicus	ENSRNOG00000017596	2 retrocopies	retro_rnor_1358, retro_rnor_2458,
Ictidomys tridecemlineatus	ENSSTOG00000022277	1 retrocopy	retro_itri_1063,
Tarsius syrichta	ENSTSYG00000009428	1 retrocopy	retro_tsyr_240,