RetrogeneDB ID: retro_pabe_3133

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:40295247..40295554(-)
• Located in intron of: ENSPPYG00000017605

Retrocopy information

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

Parental gene information

• Parental gene symbol: VMA21
• Ensembl ID: ENSPPYG00000020820
• Aliases: None
• Description: Vacuolar ATPase assembly integral membrane protein VMA21 [Source:UniProtKB/Swiss-Prot;Acc:Q5RDV3]

Sequence

>retro_pabe_3133
ATGGAGCACCCAGATAAAGTGGCACTGAACGCACTGCAGCCTCCTAAGTTCAGAAAAGAAAGCTCATTAGCATCTACACT
GAAGATGCTCCTGTTCTTCACAGCTTTAATGATCACTGTTCCTACTGGGTTATTTATATTTCACAACTAAATCTTATATA
TTTGGAGGCACCCTTGGGATGTCCAATAGGGACAGCTGTTTTTATGCTGCTATTGTTGCAGTGGTCACCGGCCATGTGGT
GTTGGCCCTCTTTATGTATGTGGCCTGGAATGAAGGCTCATGACAGTGGCATGAAGGCAAACAGGAT

Alignment

ORF - retro_pabe_3133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MERPDKAALNALQPPEFRNESSLASTLKTLLFFTALMITVP-IG-LYFTTKSYIFEGALGMSNRDSYFYA
          ME.PDK.ALNALQPP.FR.ESSLASTLK.LLFFTALMITVP..G.LYFTTKSYIF.G.LGMSNRDS.FYA
Retrocopy MEHPDKVALNALQPPKFRKESSLASTLKMLLFFTALMITVP>LGYLYFTTKSYIFGGTLGMSNRDSCFYA

Parental  AIVAVVAVHVVLALFVYVAWNEGSRQWREGKQD
          AIVAVV..HVVLALF.YVAWNEGS.QW.EGKQD
Retrocopy AIVAVVTGHVVLALFMYVAWNEGS*QWHEGKQD

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	0.06 RPM	27.37 RPM
SRP007412_cerebellum	0.00 RPM	43.41 RPM
SRP007412_heart	0.00 RPM	11.05 RPM
SRP007412_kidney	0.00 RPM	22.24 RPM
SRP007412_liver	0.03 RPM	16.56 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3133 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3133 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3133 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3724
Macaca mulatta	retro_mmul_1693

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006296	1 retrocopy	retro_btau_1106,
Callithrix jacchus	ENSCJAG00000003916	1 retrocopy	retro_cjac_150,
Dasypus novemcinctus	ENSDNOG00000008426	1 retrocopy	retro_dnov_504,
Homo sapiens	ENSG00000160131	1 retrocopy	retro_hsap_3724,
Macaca mulatta	ENSMMUG00000009034	1 retrocopy	retro_mmul_1693,
Mus musculus	ENSMUSG00000073131	2 retrocopies	retro_mmus_116, retro_mmus_3675,
Nomascus leucogenys	ENSNLEG00000013711	1 retrocopy	retro_nleu_1971,
Oryctolagus cuniculus	ENSOCUG00000015201	1 retrocopy	retro_ocun_443,
Pongo abelii	ENSPPYG00000020820	1 retrocopy	retro_pabe_3133 ,
Rattus norvegicus	ENSRNOG00000049744	1 retrocopy	retro_rnor_2843,
Ictidomys tridecemlineatus	ENSSTOG00000011179	1 retrocopy	retro_itri_500,