RetrogeneDB ID: retro_pabe_3181

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:127584729..127585057(-)
• Located in intron of: ENSPPYG00000018008

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000005030
• Aliases: None
• Description: None

Sequence

>retro_pabe_3181
CAAGCCAGTGGCCGGATCATGACTGAGGTGATTGAGCCCCTGGAGCCTCTAGTGCCTGTGGACTTTGGCAGTCACGAGGC
AGTGGTGCGGCTGGAGAGAGCCATCGTCTTCGCCCATGGGCTCCACCCCATGGACACCGACGGGTGGAGCCGATGGAGTC
GGTCCTGGAGGGCAGATGTCTATACCTGAGATCTAACAATGTAGTAGAAGGCAACTGTGCTGAAGAATTACTACAAAACT
CCCACTGCGTCGTGAAGGAGTATTTTGTGGCTCCCCAGGTAATATCTCTTTGCCAAAGCTGAATGAACAAGAGCCTTTCT
CACACAGC

Alignment

ORF - retro_pabe_3181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.89 %
• Parental protein coverage: 80.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QGSGRITAEVIEHLERLALVDFGSREAVARLEKAIAFADRLRAVDTDG-VEPMESVLEDRRLYLRSDNVV
          Q.SGRI..EVIE.LE.L..VDFGS.EAV.RLE.AI.FA..L...DTDG.VEPMESVLE.R.LYLRS.NVV
Retrocopy QASGRIMTEVIEPLEPLVPVDFGSHEAVVRLERAIVFAHGLHPMDTDG<VEPMESVLEGRCLYLRSNNVV

Parental  EGNCADELLQNSHRVVEEYFVAP-PGNISLPKLDEKEPFLHS
          EGNCA.ELLQNSH.VV.EYFVAP.PGNISLPKL.E.EPF.HS
Retrocopy EGNCAEELLQNSHCVVKEYFVAP<PGNISLPKLNEQEPFSHS

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	0.94 RPM
SRP007412_cerebellum	0.24 RPM	1.46 RPM
SRP007412_heart	0.03 RPM	0.33 RPM
SRP007412_kidney	0.00 RPM	0.93 RPM
SRP007412_liver	0.00 RPM	0.80 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3181 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3181 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3181 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3902
Pan troglodytes	retro_ptro_2655

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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,