RetrogeneDB ID: retro_pvam_881

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_14726:14713..15571(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMAD2
• Ensembl ID: ENSPVAG00000007760
• Aliases: None
• Description: SMAD family member 2 [Source:HGNC Symbol;Acc:6768]

Sequence

>retro_pvam_881
TTGGTGCTGCTGCACACTGACATCTTAATAAAACTACCACATGTGAATGATTACACCCACTTCATTCCTGCAAACAATAC
TTTTCCAGTGGGAATTGAGCCACAGAGTAGCTATACCCTAAAAATGCCACCTCTTGTATATATCAGTGAAGATAGAGAAA
TAAGCGATCAACTGTTGAACCAAAGTATGGATACAAGGTCTCCAGCAGAACTATCTCCTACTACTCTTCCCCTGTTAATC
ATAGTTTGGATTTGCAGCCAGTTACTTACTCAGAACCTGCATTTTGGTGTTCAATAGGACATTATGAATTAAACTAGAGA
GTTGGAGAGAACTTTCATACATCATAGCCCTCACTCACTGTAGATGGCTTCACAGATCCATCAAATTCAGAAAGGTTCTG
CTTAGATTTACTCTCCAGTGTCAACCAAAATGCTATAGTAGAAATGAAAAGAAGACATATAGAAATAGTAGTGTGCTTGT
ATTCCATAGGTGGGGAAATTTTTGCTGAGTGCCTAAGTAATAGTGTAATCTTTGTGCAGAGCCCCAATTGTAATAAGAGA
TATGGCTGACACCCTGCAATAACGTGTAAAATTCCACTAGGCTATAATCTGAAAATCTTCGACAATCAGAAATTTGCTGC
TCTTCTGGCTCAGTCTGTTAATCATGGTTTTAAGTGATATATCAGCCAACTAGAAAGTGCTCCATAGAATGAATTTTGTG
AAAGGGTGGGAAGCAGAATACCAAAGGCACATGGTAATAAGCACTTTTTACTGAATTGAACTTCACTTGAATGGACCTCT
ACAGTGGTTGAACAAAGTATTAAACCAGAAGGGATCCCTTTCAGCGCATTGCTCAACA

Alignment

ORF - retro_pvam_881 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.45 %
• Parental protein coverage: 61.46 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LVPRHTEILTELPPLDDYTHSIPENTNFPAGIEPQSNYIPETPPPGYISEDGETSDQQLNQSMDTGSPAE
          LV..HT.IL..LP...DYTH.IP.N..FP.GIEPQS.Y....PP..YISED.E.SDQ.LNQSMDT.SPAE
Retrocopy LVLLHTDILIKLPHVNDYTHFIPANNTFPVGIEPQSSYTLKMPPLVYISEDREISDQLLNQSMDTRSPAE

Parental  LSPTTL-SPVNHSLDLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNSERFCLGLLS
          LSPTTL.SPVNHSLDLQPVTYSEPAFWCSI..YELN.RVGE.FH.S.PSLTVDGFTDPSNSERFCL.LLS
Retrocopy LSPTTL<SPVNHSLDLQPVTYSEPAFWCSIGHYELN*RVGENFHTS*PSLTVDGFTDPSNSERFCLDLLS

Parental  NVNRNATVEMTRRHIGRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNN
          .VN.NA.VEM.RRHI...V.LY.IGGE.FAECLS.S.IFVQSPNCN.RYG.HPA..CKIP.G.NLKIF.N
Retrocopy SVNQNAIVEMKRRHIEIVVCLYSIGGEIFAECLSNSVIFVQSPNCNKRYG*HPAITCKIPLGYNLKIFDN

Parental  QEFAALLAQSVNQGFE-AVYQLTRMCTI-RMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQ
          Q.FAALLAQSVN.GF....YQ.TR.C.I.RM.FVKGW.AEY.R..V.ST...IELHLNGPLQWL.KVL.Q
Retrocopy QKFAALLAQSVNHGFK<VIYQPTRKCSI<RMNFVKGWEAEYQRHMVISTFY*IELHLNGPLQWLNKVLNQ

Parental  MGSPSVRCSS
          .GS.S..CS.
Retrocopy KGSLSAHCST

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_881 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
Callithrix jacchus	ENSCJAG00000004630	1 retrocopy	retro_cjac_1145,
Pteropus vampyrus	ENSPVAG00000007760	1 retrocopy	retro_pvam_881 ,