RetrogeneDB ID: retro_pabe_869

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:86198920..86199199(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDRG1
• Ensembl ID: ENSPPYG00000010897
• Aliases: None
• Description: p53 and DNA damage-regulated protein 1 [Source:RefSeq peptide;Acc:NP_001124674]

Sequence

>retro_pabe_869
ATGCTGTTACCTGATGCAGAGCAAGTTCTGCGGTACCTGTTCGAGGTGGAGGAGCTTGTTGAGGAGGTGCTGGTGGACAA
GCAGCAGATTGTGGATGTGGACACCAAAAGGAATAAAATACCAGAGGGCCTGAGAGCCCTGCAGAATGGTCTCAGCCTCT
CTGAAGATGTGGTTTTCCTCAGGAACATGTTTGTCAAGATGCCTCACCCTCAGGTAAAGGAAAAGATTAAGAAAAATCGG
GATCATCTGGATAAAGAAATAGAAATAATCCAAAAACAA

Alignment

ORF - retro_pabe_869 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.28 %
• Parental protein coverage: 70.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLSPEAERVLRYLVEVEELAEEVLADKRQIVDLDTKRNQNREGLRALQKDLSLSEDVMVCFGNMFIKMPH
          ML.P.AE.VLRYL.EVEEL.EEVL.DK.QIVD.DTKRN...EGLRALQ..LSLSEDV.V...NMF.KMPH
Retrocopy MLLPDAEQVLRYLFEVEELVEEVLVDKQQIVDVDTKRNKIPEGLRALQNGLSLSEDV-VFLRNMFVKMPH

Parental  PETKEMMKKDQDHLDKEIEKLRKQ
          P..KE..KK..DHLDKEIE...KQ
Retrocopy PQVKEKIKKNRDHLDKEIEIIQKQ

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	15.32 RPM
SRP007412_cerebellum	0.00 RPM	20.31 RPM
SRP007412_heart	0.00 RPM	7.65 RPM
SRP007412_kidney	0.00 RPM	13.69 RPM
SRP007412_liver	0.00 RPM	8.48 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_869 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_869 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_869 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1037
Pan troglodytes	retro_ptro_707
Gorilla gorilla	retro_ggor_818
Macaca mulatta	retro_mmul_824

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020766	1 retrocopy	retro_cjac_3320,
Homo sapiens	ENSG00000088356	1 retrocopy	retro_hsap_1037,
Gorilla gorilla	ENSGGOG00000024924	1 retrocopy	retro_ggor_818,
Macropus eugenii	ENSMEUG00000003915	1 retrocopy	retro_meug_1967,
Myotis lucifugus	ENSMLUG00000007377	1 retrocopy	retro_mluc_348,
Macaca mulatta	ENSMMUG00000000973	1 retrocopy	retro_mmul_824,
Nomascus leucogenys	ENSNLEG00000009712	1 retrocopy	retro_nleu_910,
Oryctolagus cuniculus	ENSOCUG00000016709	1 retrocopy	retro_ocun_1047,
Ochotona princeps	ENSOPRG00000006403	1 retrocopy	retro_opri_630,
Pongo abelii	ENSPPYG00000010897	1 retrocopy	retro_pabe_869 ,
Pan troglodytes	ENSPTRG00000013368	1 retrocopy	retro_ptro_707,