RetrogeneDB ID: retro_pvam_409

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2988:456858..457113(+)
• Located in intron of: ENSPVAG00000014105

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX19
• Ensembl ID: ENSPVAG00000002192
• Aliases: None
• Description: cytochrome c oxidase assembly homolog 19 (S. cerevisiae) [Source:HGNC Symbol;Acc:28074]

Sequence

>retro_pvam_409
ACGGCCATGAACTTTGGTTCCAAGAACTTCCAGCTGCGGCCCCGGGACCAGGGCAGCTTCCCATTGGACCATTTCGGTGA
CTGTAAAAGCTTTAAAGAGAAATTCACGAAGTGTCTCCATGAAAATAATTTGGAAAATGTTTTGTGCAGAAATGAATCAA
AAGAATATTTAGATTACAGAACGAAGAGGCAACTGATGGCACAAGAACAAATGGAAAAACTAGGATTTGGAGATTTGATT
GATAGACTATCAGAG

Alignment

ORF - retro_pvam_409 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.65 %
• Parental protein coverage: 96.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TAMNFGSKSFQPRPPDKGSFPLDHFGECKSFKEKFLKCLHDNNFENALCRKESKEYLECRMERQLMAQEP
          TAMNFGSK.FQ.RP.D.GSFPLDHFG.CKSFKEKF.KCLH.NN.EN.LCR.ESKEYL..R..RQLMAQE.
Retrocopy TAMNFGSKNFQLRPRDQGSFPLDHFGDCKSFKEKFTKCLHENNLENVLCRNESKEYLDYRTKRQLMAQEQ

Parental  LEKLGFGDLVDGKSE
          .EKLGFGDL.D..SE
Retrocopy MEKLGFGDLIDRLSE

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_409 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015253	1 retrocopy	retro_btau_671,
Homo sapiens	ENSG00000240230	1 retrocopy	retro_hsap_3300,
Gorilla gorilla	ENSGGOG00000034907	1 retrocopy	retro_ggor_1312,
Macaca mulatta	ENSMMUG00000007202	1 retrocopy	retro_mmul_2067,
Pan troglodytes	ENSPTRG00000041621	1 retrocopy	retro_ptro_2168,
Pteropus vampyrus	ENSPVAG00000002192	1 retrocopy	retro_pvam_409 ,
Tursiops truncatus	ENSTTRG00000011489	2 retrocopies	retro_ttru_1140, retro_ttru_1270,