RetrogeneDB ID: retro_pabe_962

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:113870444..113870690(-)
• Located in intron of: ENSPPYG00000004970

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000009141
• Aliases: None
• Description: None

Sequence

>retro_pabe_962
ATGGCCTTTACCTTGTACTCACTGCTGCAGGCAGCCCTGCTCTGTGTCAGTGCCATCGCCATGCTGCACGAAGAGAGATT
CCTCAAGAGCATTGGCTGGAGAATAGACCAGAGAATTGGTGGATTCGGGGAGGAGCCAGGAATTAAATCTCAGCTAATGA
ACCGTATTCAATCTGTAACAACTGTGATGAGAATGCCATTGATAATAGTAAATTCAATTGCAATTGTGTTACTTTTATTA
TTTGGA

Alignment

ORF - retro_pabe_962 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFTLYSLLQAALLCVNAIAVLHEERFLKNIGWGTDQGIGGFGEEPGIKSQLMNLIRSVRTVMRVPLIIV
          MAFTLYSLLQAALLCV.AIA.LHEERFLK.IGW..DQ.IGGFGEEPGIKSQLMN.I.SV.TVMR.PLIIV
Retrocopy MAFTLYSLLQAALLCVSAIAMLHEERFLKSIGWRIDQRIGGFGEEPGIKSQLMNRIQSVTTVMRMPLIIV

Parental  NSIAIVLLLLFG
          NSIAIVLLLLFG
Retrocopy NSIAIVLLLLFG

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	5.64 RPM
SRP007412_cerebellum	0.12 RPM	13.62 RPM
SRP007412_heart	0.03 RPM	7.62 RPM
SRP007412_kidney	0.10 RPM	20.48 RPM
SRP007412_liver	0.00 RPM	9.61 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_962 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_962 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_962 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1156
Pan troglodytes	retro_ptro_791
Gorilla gorilla	retro_ggor_903

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000032961	1 retrocopy	retro_btau_13,
Callithrix jacchus	ENSCJAG00000004610	1 retrocopy	retro_cjac_3333,
Echinops telfairi	ENSETEG00000000303	1 retrocopy	retro_etel_1526,
Homo sapiens	ENSG00000134049	1 retrocopy	retro_hsap_1156,
Gorilla gorilla	ENSGGOG00000027939	1 retrocopy	retro_ggor_903,
Mus musculus	ENSMUSG00000090000	1 retrocopy	retro_mmus_150,
Nomascus leucogenys	ENSNLEG00000011450	1 retrocopy	retro_nleu_2504,
Otolemur garnettii	ENSOGAG00000016626	1 retrocopy	retro_ogar_2152,
Pongo abelii	ENSPPYG00000009141	3 retrocopies	retro_pabe_2850, retro_pabe_2851, retro_pabe_962 ,
Pan troglodytes	ENSPTRG00000010002	1 retrocopy	retro_ptro_791,
Tupaia belangeri	ENSTBEG00000001443	4 retrocopies	retro_tbel_1530, retro_tbel_2783, retro_tbel_3343, retro_tbel_3429,
Tursiops truncatus	ENSTTRG00000001019	1 retrocopy	retro_ttru_1930,