RetrogeneDB ID: retro_ptro_2655

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:132130082..132130410(-)
• Located in intron of: ENSPTRG00000022792

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000005534
• Aliases: None
• Description: Glutamyl-tRNA(Gln) amidotransferase subunit C, mitochondrial [Source:UniProtKB/TrEMBL;Acc:H2Q711]

Sequence

>retro_ptro_2655
CAAGGCAGTGGCCAGATCATGATTGAGGTGATTGAGCCCCTGGAGCCTCTAGTGCCTGTGGACTTTGGCAGTCTCGAGGC
AGTGGTCCGGTTGGAGAAAGACATCATCTTCGCCCATGGGCTCCACCCCATGGACACCGACGGGTGGAGCCCATGGAGTC
GGTCCTGGAGGGCAGATGTCTATACCTGAGATCTAACAATGTAGTAGGAGGCAACTGTGCTGAAGAATTACTACAAAACT
CCCATTGCGTCGTGAAGGAGTATTTTGTGGCTCCCCAGGTAATATCTCTTTGCCAAAGCTGGATGAACAAGAGCCTTTCT
CACACAGC

Alignment

ORF - retro_ptro_2655 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.79 %
• Parental protein coverage: 81.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QGSGRITAAVIEHLERLALVDFGSREAVTRLEKAIAFADRLRAVDTDG-VEPMESVLEDRCLYLRSDNVV
          QGSG.I...VIE.LE.L..VDFGS.EAV.RLEK.I.FA..L...DTDG.VEPMESVLE.RCLYLRS.NVV
Retrocopy QGSGQIMIEVIEPLEPLVPVDFGSLEAVVRLEKDIIFAHGLHPMDTDG<VEPMESVLEGRCLYLRSNNVV

Parental  EGNCADELLQNSHRVVEEYFVAP-PGNISLPKLDEQEPFPHS
          .GNCA.ELLQNSH.VV.EYFVAP.PGNISLPKLDEQEPF.HS
Retrocopy GGNCAEELLQNSHCVVKEYFVAP<PGNISLPKLDEQEPFSHS

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	0.04 RPM	15.30 RPM
SRP007412_cerebellum	0.07 RPM	25.95 RPM
SRP007412_heart	0.00 RPM	6.85 RPM
SRP007412_kidney	0.08 RPM	21.60 RPM
SRP007412_liver	0.03 RPM	13.75 RPM
SRP007412_testis	0.00 RPM	8.01 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2655 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2655 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2655 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3902
Pongo abelii	retro_pabe_3181

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013298	1 retrocopy	retro_amel_1364,
Equus caballus	ENSECAG00000011118	1 retrocopy	retro_ecab_462,
Felis catus	ENSFCAG00000024015	1 retrocopy	retro_fcat_1279,
Homo sapiens	ENSG00000257218	1 retrocopy	retro_hsap_3902,
Nomascus leucogenys	ENSNLEG00000015651	1 retrocopy	retro_nleu_1140,
Oryctolagus cuniculus	ENSOCUG00000009867	2 retrocopies	retro_ocun_585, retro_ocun_858,
Ochotona princeps	ENSOPRG00000004226	1 retrocopy	retro_opri_1008,
Pongo abelii	ENSPPYG00000005030	1 retrocopy	retro_pabe_3181,
Pan troglodytes	ENSPTRG00000005534	1 retrocopy	retro_ptro_2655 ,
Sus scrofa	ENSSSCG00000009907	1 retrocopy	retro_sscr_746,
Tursiops truncatus	ENSTTRG00000000144	1 retrocopy	retro_ttru_1695,