RetrogeneDB ID: retro_pvam_1150

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_3304:148650..149186(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCD2
• Ensembl ID: ENSPVAG00000010822
• Aliases: None
• Description: programmed cell death 2 [Source:HGNC Symbol;Acc:8762]

Sequence

>retro_pvam_1150
AGATTGAGACATAAGCGGACTTATACACAATCAGATAATTTGGACAATACTGCTCCACACCACAACTCCCTTTTTCCAGA
ATTTGAAATCATAATAGAAACAGAAGAGGTGATTACACCTGAACTTGCAGAAAAAGATGAATCAGAGATTATAGGGAGCA
TGGGAAGAACCTGGGGAAGAATCGGATTCCATGGCAAAAGAAGAATCCAGGGAAGATAATTTTTTCTACAAGTTTACAAC
TGAAATAGCCTTGGAACCAGAACGGATTCTCAGATGTGGCAGAGAGATTGCCCCCATCTGGATCTTTGGTGAAAAGATCC
CTCAAGAAAAAGACATTCCAGATTGACCCTGTGGTGCCAAGATAATGTTTGAATTCCAGGTCATGCCTCAGCTGCTCAAC
TACCTAAAGGTGGACAGACTGCTCAGGAATATCCATTGGGGGCGTCCTGCCCATCTTCATCTGTGCCAAAAGCTGTAGAC
TGGGCACTGGCTACACAAAGGAATTTGTTTGCAAGCAAGATATAACAGATACACCT

Alignment

ORF - retro_pvam_1150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.64 %
• Parental protein coverage: 52.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLGHKQACTQSGDLDNTLPDHNFLFPEFEIIIETEDEITPEDV-EKEDESEIVGSMGEVPEEELDSMAKH
          RL.HK...TQS..LDNT.P.HN.LFPEFE.II....E........K.......G...E.P.EE.DSMAK.
Retrocopy RLRHKRTYTQSDNLDNTAPHHNSLFPEFE-IIIETEEVITPEL>QKKMNQRL*GAWEE-PGEESDSMAKE

Parental  ESREDTIFQNFKTKIAQEPEQILRYGRGIAPIWVSGENIPQEQDIPDCPCGAKRIFEFQVMPQLLNYLKA
          ESRED..F..F.T.IA.EPE.ILR.GR.IAPIW..GE.IPQE.DIPD.PCGAK..FEFQVMPQLLNYLK.
Retrocopy ESREDNFFYKFTTEIALEPERILRCGREIAPIWIFGEKIPQEKDIPD*PCGAKIMFEFQVMPQLLNYLKV

Parental  DRLGRSVDW-GVLAVYTCAESCRLGTGYTEEFVWKQEIADTP
          DRL.R...W.GVL....CA.SCRLGTGYT.EFV.KQ.I.DTP
Retrocopy DRLLRNIHW>GVLPIFICAKSCRLGTGYTKEFVCKQDITDTP

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_1150 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 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017075	2 retrocopies	retro_amel_1329, retro_amel_1404,
Callithrix jacchus	ENSCJAG00000020634	1 retrocopy	retro_cjac_3946,
Equus caballus	ENSECAG00000016819	1 retrocopy	retro_ecab_533,
Felis catus	ENSFCAG00000007037	2 retrocopies	retro_fcat_305, retro_fcat_749,
Homo sapiens	ENSG00000071994	1 retrocopy	retro_hsap_4305,
Gorilla gorilla	ENSGGOG00000028229	2 retrocopies	retro_ggor_2876, retro_ggor_899,
Microcebus murinus	ENSMICG00000007474	1 retrocopy	retro_mmur_108,
Macaca mulatta	ENSMMUG00000019916	1 retrocopy	retro_mmul_1137,
Mustela putorius furo	ENSMPUG00000007227	2 retrocopies	retro_mputfur_621, retro_mputfur_707,
Nomascus leucogenys	ENSNLEG00000000295	2 retrocopies	retro_nleu_1458, retro_nleu_2633,
Otolemur garnettii	ENSOGAG00000014002	2 retrocopies	retro_ogar_2090, retro_ogar_2288,
Pongo abelii	ENSPPYG00000017193	2 retrocopies	retro_pabe_3505, retro_pabe_958,
Pan troglodytes	ENSPTRG00000018828	2 retrocopies	retro_ptro_2915, retro_ptro_788,
Pteropus vampyrus	ENSPVAG00000010822	1 retrocopy	retro_pvam_1150 ,
Sus scrofa	ENSSSCG00000025312	2 retrocopies	retro_sscr_303, retro_sscr_450,