RetrogeneDB ID: retro_pvam_342

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2650:54206..54954(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDIP1
• Ensembl ID: ENSPVAG00000016131
• Aliases: None
• Description: cell death-inducing p53 target 1 [Source:HGNC Symbol;Acc:13234]

Sequence

>retro_pvam_342
CCTCCTTATCCTGGAGGCCCCACAGACCCCTTCTGGGGGAGAAAAGTGGAGCCTTGCCTACCTCAGGCCGTACCTCTCCA
GCTGTGATGCAGCCTACATTGGGCTTATTGCTGCCCCCTGAAGACATTGGCCCCCCCACCCTACGAGCCCCCTAGGTCAC
CCAGTGCCCCAATCTGGCTTCATTCCCCCCAAATGTGAATGCATATGGCGCCCATATGTCTCCAGGTTTCTACCGTCCTC
CAGAACCCCACTCACCCATGGGTGACTACTGGCCGGGGCCTACCCACCAGGGCCCTACCCTGACCCTGGGAGCCACACTG
CTATGGTCCTGGTCCCTTCGGGGGCTGCCACCATGGTGACAGTGTTACAGAAGAAACCTTTGAGGGCATACCCATATAGA
TGGTGTGTTCCCACTGCCAGCAGGCCCATCACCACCAAGATCTCTACAAGACTGGCGTAATCTCATGCTGGGTATTGTTT
GCTGCTTCATGGAGCATGGTCTAGGCTGCTGCTTGTTTCCCTTGCCTCATCAACGACTTCAAGGATGGGACGTACACGTG
CCCCAGCTGCAAAGCTACATCTACATGTACAAGTGCATATGCTAACCGAGCCAGGACTGGACTCCCTGCTGTCAGTCTGG
CCCCATGTGTTTTGCTTCCAGTACTCAGTGGCTCGTGTCCCCACTCCAACTTAAGGATAGAAGCCATTCCACTGGTCCCC
TGGAAATCTTGTCCTCTTTGCTTTGCCC

Alignment

ORF - retro_pvam_342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.9 %
• Parental protein coverage: 96.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 11

Retrocopy - Parental Gene Alignment:

Parental  PPYPGGPT-APLLEDKSGAPPAPGSTSPAVMQPPPGTSLPPADIG-PPPYE-PLDHSVPQPGFI-PPHVN
          PPYPGGPT..PLL..KSGA.P..G.TSPAVMQP..G..LPP.DIG.PPPYE.PL.H.VPQ.GFI.PP.VN
Retrocopy PPYPGGPT<RPLLGEKSGALPTSGRTSPAVMQPTLGLLLPPEDIG>PPPYE>PLGHPVPQSGFI>PPNVN

Parental  ADGSYMPPGFYPPPGPHPPMGYYPPGP-YPPGPYPGPGGHTATVLVPSGAATTVTVLQ-GEIFEGAPVQT
          A.G..M.PGFY.PP.PH.PMG.Y.PGP.YPPGPYP.PG.HTA.VLVPSGAAT.VTVLQ..E.FEG.P...
Retrocopy AYGAHMSPGFYRPPEPHSPMGDYWPGP<YPPGPYPDPGSHTAMVLVPSGAATMVTVLQ<EETFEGIPI*M

Parental  VCPHCQQA-ITTKIS-YEIGLMNFVLGFFCCFMGCDLGCCLIPCLINDFKDVTHTCPSCK-TSTRTSVCA
          VC.HCQQA.ITTKIS.Y..G.......F...........C..PCLINDFKD.T.TCPSCK.TST.TS..A
Retrocopy VCSHCQQA>ITTKIS<YKTGVISCWVLFAASWSMV*AAAC-FPCLINDFKDGTYTCPSCKATSTCTSAYA

Parental  NGARTD-SPC-QSGPTCFAPHAQW-SCPHSHLGVEAIPP-SPGSLVIFALP
          N.ART...PC.QSGP.CFA...QW.SCPHS.L..EAIP..SPG.LV.FALP
Retrocopy NRARTG<TPCCQSGPMCFASSTQW>SCPHSNLRIEAIPL>SPGNLVLFALP

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_342 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000009213	1 retrocopy	retro_pvam_261,
Pteropus vampyrus	ENSPVAG00000016131	1 retrocopy	retro_pvam_342 ,