RetrogeneDB ID: retro_pvam_1014

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_2255:86186..86732(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAVCR1
• Ensembl ID: ENSPVAG00000008858
• Aliases: None
• Description: hepatitis A virus cellular receptor 1 [Source:HGNC Symbol;Acc:17866]

Sequence

>retro_pvam_1014
TGGGTAGCCTTCACAAGCCTCATACTACTTTGGACAGAATGCTGTAGCTTTTCATGGACAAGTGAGTGGAGTGGTTGGTC
AGCTTGTCATGCTTCCCTGTACCTACTCACCAGCTAGTGAAGTGACAACCATGTGCTAGAGCCAACGGATGTGTTCATGG
TATAAACGCTCAAATCAACTCATCAGGATTAATGGATACAATGCCACCTTTCAAAGGAATACGCACTATGAGCTAAATGA
ATCATTTCAAAAGGGAATGTGTCTTTAACCATAAAGAATGAAGCCCAGTGTGATAGTGGTATGTACTATTGATGTGTTGA
GCACTCGGGGTGGTTTAATGATTTGAAAATCAACATATTATTTACCAGTGTTCCAATATCACCTATGATCTTCACCTCCA
CTCTTATTAGGACAGCACCCACGAGGAACCTCAAGACAGTTCCACCTAGGGTCACCAGTGTTCCAACAACACCTAGGGTC
TTCACCTCTGCTTCTACAATGCCAACATCCATGCAGAACCTTAAGACATAAACTACTTCATCTTCT

Alignment

ORF - retro_pvam_1014 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.08 %
• Parental protein coverage: 62.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WLAFTSLILLWTD-AVVSQVQVSGVVGQPVTLPCTYSTASEITTMCWGRGGCPRSLCSNQLIWTDGYRVT
          W.AFTSLILLWT..AV....QVSGVVGQ.V.LPCTYS.ASE.TTMC.....C.....SNQLI...GY..T
Retrocopy WVAFTSLILLWTE>AVAFHGQVSGVVGQLVMLPCTYSPASEVTTMC*SQRMCSWYKRSNQLIRINGYNAT

Parental  FQKDMRYELNG-IIPKGNVSLTIKNAQQSDSGTYCCRIEHSGWFNDKKVNILLEIKPPKTTSVPTSPRVS
          FQ....YELN..II.KGNVSLTIKN..Q.DSG.Y....EHSGWFND.K.NIL.....P......TS....
Retrocopy FQRNTHYELNE<IISKGNVSLTIKNEAQCDSGMYY*CVEHSGWFNDLKINILF-TSVPISPMIFTSTLIR

Parental  TSAPTTSATTLSLTTENISSSP--VQTTETQPTTPQKTITSLQSNS
          T.APT....T...........P.......T.PT..Q...T...S.S
Retrocopy T-APTRNLKTVPPRVTSVPTTPRVFTSASTMPTSMQNLKT*TTSSS

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_1014 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000008858	1 retrocopy	retro_pvam_1014 ,