RetrogeneDB ID: retro_pvam_171

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1737:506512..507308(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C5orf15
• Ensembl ID: ENSPVAG00000012421
• Aliases: None
• Description: chromosome 5 open reading frame 15 [Source:HGNC Symbol;Acc:20656]

Sequence

>retro_pvam_171
ATGGCCGCTGTTGCCCAAGGGAGGATGGCTGGGGCTGTGTAAGCAAAGCTGCTGCCTAGGCTGGGCATCCAGGTTCCCAG
AGGTTTGGCGCGGCCGCTGGTCCCTGGTGTTCTTGGTTGCATCCGCCACCATGTCCAGTGATCAATCTCCAACTGTTTCA
CCGAGCCAAACTGTACTCAAGCCAGACGTTTCTACTCCGAATATGAGTGCTGTTTTAACTCATGAAAACCAAACCAAACC
ATCTATTTCCCAGATCAGCATCACTCTCCCTCCCACAGCTAGTACAAAGAAAAGTGGAGAGGAATCTGCGGCCCCTCATC
CCTCACCTATGATTTCTCTGTCCGGAAAGGAAGCTGATAACAATGAAGACCCTAGCATGGAAGAGGAAGACTTCTTCACG
CCGAATAGTTCTCCGTCCACCGCCAAAGACACTCTAGACAAGGGAGATTACAGAGAACCAGACTACGACTGGACCACCAA
CCCCAGGGACGATGAGTCCAGTGAGGCGTTGGAAGGAAACAGGGGCTACCTGGAAATCGAACAGTAAGATCTTTTAAGAC
CCCATCCTCAAATATAGCAGAGGAATATAGTCATTTCATTTTTCATCTTATTATTTTTGATTTTTGCATTGCTGTTGTTT
ACATTACATATCACAACAAAAGGAAGATTTTTCCTTCTGGTTCAAAGCAGGAAATGGCGTGATGGTCTTTGTCCCAAAAC
AGTGGAATATCATCGTCTAGACCAGAATGTTAATGAGGCAATGTCTTCTCTGAAGATTACCAATGATTATATTTTT

Alignment

ORF - retro_pvam_171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAVAQRRMSGAVQAKLPPKLGIQVPGGLARPLV-LVLLLVSATMSSDQSLAVSPSQTVLKPDVSTPNMS
          MAAVAQ.RM.GAV.AKL.P.LGIQVP.GLARPLV.LV.L..SATMSSDQS..VSPSQTVLKPDVSTPNMS
Retrocopy MAAVAQGRMAGAV*AKLLPRLGIQVPRGLARPLV>LVFLVASATMSSDQSPTVSPSQTVLKPDVSTPNMS

Parental  AVLTRENQTKPSISQISTTLPPTTSTEKSGGASAAPHLSPTTSLSREEVVNNEDPSMEEEDLLTLNSSPS
          AVLT.ENQTKPSISQIS.TLPPT.ST.KSG..SAAPH.SP..SLS..E..NNEDPSMEEED..T.NSSPS
Retrocopy AVLTHENQTKPSISQISITLPPTASTKKSGEESAAPHPSPMISLSGKEADNNEDPSMEEEDFFTPNSSPS

Parental  TAKDTLDNGDYGEPDYDWTTNPRDDESSEALEEN-RGYLEIEQSVRSFKTPSSNIEEEDSHFFFHLIIFA
          TAKDTLD.GDY.EPDYDWTTNPR.D..S....E.....L.....VRSFKTPSSNI.EE.SHF.FHLIIF.
Retrocopy TAKDTLDKGDYREPDYDWTTNPR-DDESSEALEG<KQGLPGNRTVRSFKTPSSNIAEEYSHFIFHLIIFD

Parental  FCIAVVYITYHNKRKIF-LLVQSRKWRDGLCSKTVEYHRLDQNVNEAMPSLKITNDYIF
          FCIAVVYITYHNKRKIF.LLVQSRKWRDGLC.KTVEYHRLDQNVNEAM.SLKITNDYIF
Retrocopy FCIAVVYITYHNKRKIF>LLVQSRKWRDGLCPKTVEYHRLDQNVNEAMSSLKITNDYIF

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_171 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
Gorilla gorilla	ENSGGOG00000021947	1 retrocopy	retro_ggor_416,
Nomascus leucogenys	ENSNLEG00000008019	1 retrocopy	retro_nleu_1021,
Pongo abelii	ENSPPYG00000015780	1 retrocopy	retro_pabe_295,
Pan troglodytes	ENSPTRG00000017234	1 retrocopy	retro_ptro_324,
Pteropus vampyrus	ENSPVAG00000012421	1 retrocopy	retro_pvam_171 ,