RetrogeneDB ID: retro_pvam_460

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3254:166165..166343(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COA5
• Ensembl ID: ENSPVAG00000001578
• Aliases: None
• Description: cytochrome c oxidase assembly factor 5 [Source:HGNC Symbol;Acc:33848]

Sequence

>retro_pvam_460
GGCGTGCAAGGGGCCCTGGGCACCCGTCTGCTTCAGGAGGGCTGTGTGCTTCAGAAAGGAAAAGCCCCTCCACAGTGTCC
CAAGGAACAAAACACCAAAGTTTTTGCAATATCCACTTTTTAAATGTAGAATATCAATGTTGGATGCCAGACCAAAGTTC
AGAGGAAGAAAAGGATAT

Alignment

ORF - retro_pvam_460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.67 %
• Parental protein coverage: 79.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GVKEDLGACLLQSDCVLQEGKSPRQCLKEGNCKA-LKYSFFECKRSMLDARSRFRGRKGY
          GV...LG..LLQ..CVLQ.GK.P.QC.KE.N.K..L.Y..F.C..SMLDAR..FRGRKGY
Retrocopy GVQGALGTRLLQEGCVLQKGKAPPQCPKEQNTKV>LQYPLFKCRISMLDARPKFRGRKGY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_460 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007139	1 retrocopy	retro_cjac_1382,
Cavia porcellus	ENSCPOG00000009263	1 retrocopy	retro_cpor_270,
Equus caballus	ENSECAG00000004183	1 retrocopy	retro_ecab_295,
Echinops telfairi	ENSETEG00000013626	1 retrocopy	retro_etel_757,
Felis catus	ENSFCAG00000004424	1 retrocopy	retro_fcat_201,
Homo sapiens	ENSG00000183513	1 retrocopy	retro_hsap_204,
Gorilla gorilla	ENSGGOG00000006019	1 retrocopy	retro_ggor_278,
Myotis lucifugus	ENSMLUG00000013167	2 retrocopies	retro_mluc_1336, retro_mluc_1760,
Monodelphis domestica	ENSMODG00000001197	1 retrocopy	retro_mdom_1413,
Nomascus leucogenys	ENSNLEG00000001998	1 retrocopy	retro_nleu_1854,
Ochotona princeps	ENSOPRG00000002972	3 retrocopies	retro_opri_1198, retro_opri_1203, retro_opri_391,
Pongo abelii	ENSPPYG00000012085	1 retrocopy	retro_pabe_435,
Pan troglodytes	ENSPTRG00000012267	1 retrocopy	retro_ptro_340,
Pteropus vampyrus	ENSPVAG00000001578	1 retrocopy	retro_pvam_460 ,
Sorex araneus	ENSSARG00000006275	1 retrocopy	retro_sara_61,