RetrogeneDB ID: retro_pabe_114

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:19683534..19683762(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000011652
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000006209
• Aliases: None
• Description: None

Sequence

>retro_pabe_114
ATGCCCAAGTGCCCCGCGTGCGACAAGGTGTACTTCGCCGAGAGGGTGACCTCTCTAGGCAAGGACTGGCATCGGCCCTG
CCTGAAGTGTGAGAAATGTGGGAAGACGCTGACCTCCGGGGGCCACGCTGAGCATGACAGCAAACCCTACTGCTACTACC
CCTGCTACGCCGCCATGTTTGGGCCTAAAGGCTTTGGGCGGGGTGGATCCGAGAGACACACTTTCAAG

Alignment

ORF - retro_pabe_114 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERVTSLGKDWHRPCVKCEKCGKTLTSGGHAEHEGKPYCNHPCYAAMFGPKGFGRGGAESHTFK
          ERVTSLGKDWHRPC.KCEKCGKTLTSGGHAEH..KPYC..PCYAAMFGPKGFGRGG.E.HTFK
Retrocopy ERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHDSKPYCYYPCYAAMFGPKGFGRGGSERHTFK

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	0.33 RPM	1.82 RPM
SRP007412_cerebellum	0.12 RPM	0.85 RPM
SRP007412_heart	1.35 RPM	6.98 RPM
SRP007412_kidney	1.43 RPM	6.53 RPM
SRP007412_liver	0.67 RPM	4.10 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_114 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_114 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_114 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047229	1 retrocopy	retro_btau_488,
Callithrix jacchus	ENSCJAG00000019788	1 retrocopy	retro_cjac_163,
Dipodomys ordii	ENSDORG00000001365	1 retrocopy	retro_dord_70,
Homo sapiens	ENSG00000213145	1 retrocopy	retro_hsap_2550,
Gorilla gorilla	ENSGGOG00000027381	1 retrocopy	retro_ggor_3,
Macropus eugenii	ENSMEUG00000001631	1 retrocopy	retro_meug_93,
Macaca mulatta	ENSMMUG00000007158	2 retrocopies	retro_mmul_1479, retro_mmul_553,
Pongo abelii	ENSPPYG00000004790	2 retrocopies	retro_pabe_2199, retro_pabe_2347,
Pongo abelii	ENSPPYG00000006209	1 retrocopy	retro_pabe_114 ,
Pan troglodytes	ENSPTRG00000033768	1 retrocopy	retro_ptro_43,
Pteropus vampyrus	ENSPVAG00000014240	1 retrocopy	retro_pvam_1304,
Rattus norvegicus	ENSRNOG00000027990	2 retrocopies	retro_rnor_2590, retro_rnor_2599,
Sarcophilus harrisii	ENSSHAG00000000807	1 retrocopy	retro_shar_341,
Tursiops truncatus	ENSTTRG00000004063	1 retrocopy	retro_ttru_1367,