RetrogeneDB ID: retro_pvam_513

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3533:38484..38913(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAMP7
• Ensembl ID: ENSPVAG00000000829
• Aliases: None
• Description: vesicle-associated membrane protein 7 [Source:HGNC Symbol;Acc:11486]

Sequence

>retro_pvam_513
GCCATTCTTTCTGCTGTCATTGCCAGGGGAACCACCATCCTTGCCAAACACTCTTGGTGTGGAGGAAACTTCCTGGAGGC
GACAGAGTAGATTCTGGCTCAGATACCTTCTGAAAATAACAAACTAATGTACTTACACAGCAACTATTTGTTTCATTACA
TCTGCCAAGACAGGATTGTGTACCTTTGTATCACTGCTAATGATTTTGAATGTTCCAGAGCCTTTAATTTTCTGAATGAG
ATAAAGAAGAGATTCCAGACCACTTATGGTTCAAGAGCACAGACAGCACTTCCATATGCCATGAGTAGTAATTTCTCAAG
TGTCTTGGCCGCACAGCTGAAGCATCATTGTCAGAATAAGGGCCTAGACAAACTGATGGAGACTCAAGCTCAAGTGGATG
AACTGAAAGGAATCATGGTCAGAAACATA

Alignment

ORF - retro_pvam_513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.81 %
• Parental protein coverage: 55.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHSNYLFHYICQDRIVYLCITDDDFE
          AIL.AV.ARGTTILAKH.WCGGNFLE.TE.ILA.IPSENNKL.Y.HSNYLFHYICQDRIVYLCIT..DFE
Retrocopy AILSAVIARGTTILAKHSWCGGNFLEATE*ILAQIPSENNKLMYLHSNYLFHYICQDRIVYLCITANDFE

Parental  RSRAFNFLNEIKKRFQTTYGSRAQTALPYAMNSEFSSVLAAQLKHHSENKGLDKVMETQAQVDELKGIMV
          .SRAFNFLNEIKKRFQTTYGSRAQTALPYAM.S.FSSVLAAQLKHH..NKGLDK.METQAQVDELKGIMV
Retrocopy CSRAFNFLNEIKKRFQTTYGSRAQTALPYAMSSNFSSVLAAQLKHHCQNKGLDKLMETQAQVDELKGIMV

Parental  RNI
          RNI
Retrocopy RNI

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_513 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000051412	1 retrocopy	retro_mmus_2131,
Oryctolagus cuniculus	ENSOCUG00000001270	1 retrocopy	retro_ocun_842,
Pteropus vampyrus	ENSPVAG00000000829	1 retrocopy	retro_pvam_513 ,
Ictidomys tridecemlineatus	ENSSTOG00000025036	1 retrocopy	retro_itri_720,
Tursiops truncatus	ENSTTRG00000010643	1 retrocopy	retro_ttru_66,