RetrogeneDB ID: retro_pvam_623

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_4086:163312..163689(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000001230
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPIF
• Ensembl ID: ENSPVAG00000001713
• Aliases: None
• Description: peptidylprolyl isomerase F [Source:HGNC Symbol;Acc:9259]

Sequence

>retro_pvam_623
GCTCTGAGCACAGGGAAGAAAGGATTTGGTTATAAAGGTTCTCGTTTTCACAGAATTATTCTGGGATTTATGTGCCAGGG
TGGTGACTTCACACACCGTACGGGCACTGGCGGCAAATCCATCCATGGGGAGAAATGTGATGATGAGAATTTCATCCTGA
AGCACGTGGGTCCCGGCATCTTGTTCATGGCGAACACTGGACCAACACAAACAGTTCCTGGCTTTGCACGGGCATGGCCA
AGACCGAATGCCTGGATCGCACGCGTGTGGCCTTTGGCAAGGCGAAAAAGGGCACGCCAACCGCGGAAGCCGTGGGACGC
TTTGGGTCCAGCAATGACAAGACCAGCGAGAAGGGCACCACTTCTGTCTGCGGACGA

Alignment

ORF - retro_pvam_623 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.69 %
• Parental protein coverage: 61.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGP-N
          AL.TG.KGFGYKGS.FHR.I..FMCQ.GDFT...GTGGKSI.G....DENF.LKHVGPG.L.MAN.GP.N
Retrocopy ALSTGKKGFGYKGSRFHRIILGFMCQGGDFTHRTGTGGKSIHGEKCDDENFILKHVGPGILFMANTGP<N

Parental  TNGSQFFICTIKTDWLDGKHVVFGHVKEGMDVVKKIESFGSKNGKTSKKIVITDCGQ
          TN.S.......KT..LD...V.FG..K.G.........FGS.N.KTS.K.....CG.
Retrocopy TNSSWLCTGMAKTECLDRTRVAFGKAKKGTPTAEAVGRFGSSNDKTSEKGTTSVCGR

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_623 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 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000008796	3 retrocopies	retro_ecab_507, retro_ecab_649, retro_ecab_732,
Homo sapiens	ENSG00000108179	1 retrocopy	retro_hsap_1436,
Microcebus murinus	ENSMICG00000007086	8 retrocopies	retro_mmur_1266, retro_mmur_218, retro_mmur_515, retro_mmur_568, retro_mmur_605, retro_mmur_694, retro_mmur_769, retro_mmur_87,
Nomascus leucogenys	ENSNLEG00000010567	1 retrocopy	retro_nleu_70,
Procavia capensis	ENSPCAG00000009406	1 retrocopy	retro_pcap_275,
Pan troglodytes	ENSPTRG00000002669	1 retrocopy	retro_ptro_979,
Pteropus vampyrus	ENSPVAG00000001713	2 retrocopies	retro_pvam_380, retro_pvam_623 ,
Tupaia belangeri	ENSTBEG00000015457	1 retrocopy	retro_tbel_1906,
Xenopus tropicalis	ENSXETG00000018981	1 retrocopy	retro_xtro_20,