RetrogeneDB ID: retro_pvam_1334

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_62778:674..1023(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VIMP
• Ensembl ID: ENSPVAG00000012873
• Aliases: None
• Description: VCP-interacting membrane protein [Source:HGNC Symbol;Acc:30396]

Sequence

>retro_pvam_1334
GCCTTGGAGACCAAACGCTCGTGCTTCTGGCACGTAATGCTGGGCTCCCTGCTGGCCGCCTGTGGCTGGCACGTCGTCCT
CAGCCTCATCCTCCTGTGCGTGGTCTCTCAGAAGCCTTCCGCCCAGCTGAGGTCCTTGAGACAGAGGCAGCTGCACCGAG
CTGTGGCTTTCACGAGACCCGGTATTGTTGGTAAATGACAAGTGAATGGAGCAGCTGCTTGTGCGAAAACGCGTGAATTA
AATGCGTGCGTTGAAAAGCATAAGGAAAAGCTAAGATATCTTGAGAGAAGGAAAAAGGAGACAGGAGATTAAAACGTGGG
GCAGCGCCTAAGAAGGAGAGTCACAAAGA

Alignment

ORF - retro_pvam_1334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.63 %
• Parental protein coverage: 62.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALETEGLRFLHVTVGSLLATYGWYIVFSCILLYVGFQKLSTRLRALRQRQLDRAAAAVEPDVVVKRQEAL
          ALET....F.HV..GSLLA..GW..V.S.ILL.V..QK.S..LR.LRQRQL.RA.A...P..V.K.Q...
Retrocopy ALETKRSCFWHVMLGSLLAACGWHVVLSLILLCVVSQKPSAQLRSLRQRQLHRAVAFTRPGIVGK*QVNG

Parental  AAARLKMQEELNAQVEKHKEKLRQLE-ETKRRQKIEMWDSMQEGKSYK
          AAA..K...ELNA.VEKHKEKLR.LE.E.KRRQ.I..W.S..EG.S..
Retrocopy AAACAKTR-ELNACVEKHKEKLRYLE>EGKRRQEIKTWGSA*EGESQR

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_1334 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007115	1 retrocopy	retro_amel_177,
Bos taurus	ENSBTAG00000000640	1 retrocopy	retro_btau_1044,
Dasypus novemcinctus	ENSDNOG00000010694	2 retrocopies	retro_dnov_207, retro_dnov_880,
Echinops telfairi	ENSETEG00000011401	1 retrocopy	retro_etel_2096,
Felis catus	ENSFCAG00000028822	1 retrocopy	retro_fcat_1524,
Pteropus vampyrus	ENSPVAG00000012873	1 retrocopy	retro_pvam_1334 ,