RetrogeneDB ID: retro_pvam_857

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_13749:29700..30424(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNPPD1
• Ensembl ID: ENSPVAG00000010786
• Aliases: None
• Description: cyclin Pas1/PHO80 domain containing 1 [Source:HGNC Symbol;Acc:25220]

Sequence

>retro_pvam_857
ATGGATTGGCATCTCTACACTGACCTTTGAAAGATCTTGAGGTGCTGAGCTGGCTAGAGAGCTATGTGGCTAAAAAGAAT
GGATGGAGATGGGGCTGGTACATCTAAGCAGACCTGCATGTACTGCTGGAGTCATCAGCCTGGAAGCTGGCCCTGGGCTC
GCTCTGCTAGCAGCTGGTAAAGTTGTCCTACCTGTTAGCTATGGCATATATGAGTAGTGTGGCCCTGGCTGTGGCATCGG
TGGCTGTAGTACACCAGCCCTTAGGGCTGCACTGCAGCACCCCATGTGGCCCCCTGGACCTTGGACTGACTTTCAGGTAC
TTCTTGGAACCCTGCATACCTTCTCCCATGCCACACTGCCTGCCTTCTCCTGCCAATGTTTCCAGCTGCCTGGAATGTGA
TGTAATATTGCCTTTACTCTGGGGCAGTCTTCTGGCATCACTGACATCCAACCTTTGCCTCCCCTAGATCCTCCTGCCCC
TCTCACTCTTCTCTATAACTGTGCCCTTTGCCAGAAGCTCCAGAAAGACACCCCCACAACCTGCTGCGCCTGCCACCTCC
CCCACCATACCATCTGCACTGGGCCCCCCAGCTTCTTGTACCATCCCCATGGCTTGCCTCCGCACTGGCCCTGGAGCCCG
ATGACCTGTCTACTCCCACAGCTCCAACAGTGTTTCCTTTTCAGCATCATGGAGCTGGCCCACCTCAAGTCTTTCATTTT
TCCC

Alignment

ORF - retro_pvam_857 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.44 %
• Parental protein coverage: 58.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDWRLYTD-PREIFEVLSWLESSVAQQ-GRRRGWYTYTDLCVLLEQPACQLALGSLCQQLAKLSCLVAMA
          MDW.LYTD.P....EVLSWLES.VA...G.R.GWY...DL.VLLE..A..LALGSLC.QL.KLS.L.AMA
Retrocopy MDWHLYTD<PLKDLEVLSWLESYVAKKNGWRWGWYI*ADLHVLLESSAWKLALGSLC*QLVKLSYLLAMA

Parental  YVSSVALAMASVAVIHQSLGLSCSPPPGPPDLGLASRCLLEPCIHSPVPQCLSPSANASTCLEGDVGLRS
          Y.SSVALA.ASVAV.HQ.LGL.CS.P.GP.DLGL..R..LEPCI.SP.P.CL...AN.S.CLE.DV.L..
Retrocopy YMSSVALAVASVAVVHQPLGLHCSTPCGPLDLGLTFRYFLEPCIPSPMPHCLPSPANVSSCLECDVILPL

Parental  LWGSLLASLTP-PPLPPPDPPAPPTLLHNCPLCQKLRKDSP-SCHACHHPNHTVRTGPSSPWYHSHGLAP
          LWGSLLASLT...PLPP.DPPAP.TLL.NC.LCQKL.KD.P..C.ACH.P.HT..TGP.S..YH.HGL.P
Retrocopy LWGSLLASLTS<QPLPPLDPPAPLTLLYNCALCQKLQKDTPTTCCACHLPHHTICTGPPSFLYHPHGLPP

Parental  PWSWSPMPPLLPQPQQCSLFRIMELARLKSFIFP
          .W.WSPM..LLPQ.QQC.LF.IMELA.LKSFIFP
Retrocopy HWPWSPMTCLLPQLQQCFLFSIMELAHLKSFIFP

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_857 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000015328	1 retrocopy	retro_mdom_538,
Pteropus vampyrus	ENSPVAG00000010786	1 retrocopy	retro_pvam_857 ,
Rattus norvegicus	ENSRNOG00000018325	1 retrocopy	retro_rnor_2150,