RetrogeneDB ID: retro_pvam_360

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2742:114233..116219(-)
• Located in intron of: ENSPVAG00000009313

Retrocopy information

• Ensembl ID: ENSPVAG00000009314
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PAPOLA
• Ensembl ID: ENSPVAG00000013925
• Aliases: None
• Description: poly(A) polymerase alpha [Source:HGNC Symbol;Acc:14981]

Sequence

>retro_pvam_360
ATGCCGTTTCCGGTGACAACCCCGGGATCACGGCAGACCCCGCCAGCACCCAAGCACTGTGGCATCTCCTCCCCCATCAG
CTTAGCAGCCCCCAGGGAGACAGACTGCATACTGACTCAGAAATTAATCGAGACCCTGAAGCCCTTTGGGGTTTTAGAAG
AGGAAGAGGAACTGCAGCGCAGGATTTTAATTTTGGAAAAATTAAATAGTCTGGTAAAGGAATGGATACGAGAAATCAGT
GAAAGCAAGAGCCTTCCACCAGCGGTAATTGAAAATGTTGGAGGCAAAATCTTTACCTTCGGCTCTTACAGATTAGGAGT
ACACACGAAAGGTGCCGACATAGATGCCTTGTGCGTTGCACCGAGACACGTTGACCGAAGCGACTTTTTCACCTCCTTCT
ACGATAAGTTGAAACTACATGAAGAAGTAAAAGATTTAAGGGCTGTTGAGGAGGCATTTGTGCCAGTTATCAAACTGTGT
TTTGATGGGATAGAGATCGATATTTTGTTTGCAAGATTAGCCCTGCAGACTATTCCAGAAGATTTGGACCTAAGAGATGA
CAGTCTGCTTAAAAATTTAGATATTAGATGCATAAGAAGTCTTAACGGTTGCCGGGTAACCGATGAAATCTTACATCTAG
TACCAAATATCGACAACTTCAGGTTAACTCTCAGAGCCATCAAATTGTGGGCTAAATGCCACAATATCTATTCCAATATA
TTAGGTTTCCTCGGAGGTGTTTCCTGGGCTATGTTAGTGGCAAGAACTTGCCAGCTTTATCCAAATGCAGTAGCATCAAC
TCTTGTACGTAAATTTTTCTTGGTGTTTTCTGAATGGGAATGGCCAAATCCAGTGCTACTGAAAGAGCCTGAAGAACGAA
ATCTTAATTTGCCTGTGTGGGACCCGAGAGTAAATCCCAGTGATAGATACCATCTCATGCCTATAATTACACCAGCGTAC
CCACAGCAGAACTCCACATACAACGTGTCTGTTTCAACAAGGACCGTCATGATCGAGGAGTTTAAACAAGGGCTTGCTAT
CACACACGAGATTTTGCTGAGTAAGGCGGAGTGGTCCAAACTTTTTGAAGCTCCAAGCTTCTTTCAAAAGTACAAGCATT
ATATTGTACTTCTAGCGAGTGCACCAACAGAGAAACAACATCTAGAGTGGGTGGGCTTGGTGGAATCCAAAATCCGAATC
CTGGTTGGAAGCTTGGAGAAGAATGAATTCATTACACTGGCGCATGTGAATCCTCAGTCATTTCCAGCACCCAAAGAAAA
TCCTGACAAGGAAGAGTTTCGTACGATGTGGGTGATTGGGTTAGTGTTAAAAAAGCCCGAAAATTCTGAAGTTCTCAGTA
TCGACCTCACTTACGATATCCAGTCTTTCACAGATACAGTTTATAGGCAAGCAATAAATAGTAAGATGTTCGAGATGGAT
ATGAAAATTGCTGCAATGCACTTGAGAAGAAAGGAACTTCATCAGCTGCTACCTAATCACGTGCTTCCGAAAAAGAAAAC
GCAGTCGACGGAAGATGTCCGATTGACGGCTTTGAACGACAGCAGCCTCGACCTGTCTGCAGACGGTGGAAACAGCATGT
CTGTGCCTTCACCTCCTAGCGCTGCGAATACTGGCCCAGTGACCGGTGGAAACGGTCACGCCCCGGCTGTAGTGGCGGCC
TCCGGGACCAACGTGCAGGTCATTGAAGTTTCCTCGCAACAGGCAAGCCCCAGTGACAGCCCAGGGGGCGCGTCGAGTGA
AGGCGTCCCTCAGACTGCCTCACAGCCAGCCCTCTCCCCACTCCCGAAGCCCGTGATCACCAGAGTCGTTTCTTCAACAC
TTCTGGTAAATCATCCAGCCCGGCCTTCGGGGAGCGCAGCGACAAACATAGCCAACCCTATAGTAGGAGTCTAGAGGACG
TGCTCACGTCAGAGAGAAGACAGGACCGAGGCATCCAACACAGCAGAGGAACCATCTCGCAGAGAC

Alignment

ORF - retro_pvam_360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.54 %
• Parental protein coverage: 90.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPFPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCLLTQKLIETLKPFGVFEEEEELQRRILILGKLNS
          MPFPVTT.GS.QT.P..KH.GI.SPISLAAP.ETDC.LTQKLIETLKPFGV.EEEEELQRRILIL.KLNS
Retrocopy MPFPVTTPGSRQTPPAPKHCGISSPISLAAPRETDCILTQKLIETLKPFGVLEEEEELQRRILILEKLNS

Parental  FVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQ
          .VKEWIREISESK.LP..VIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKL.
Retrocopy LVKEWIREISESKSLPPAVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLH

Parental  EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI
          EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI
Retrocopy EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI

Parental  LHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWE
          LHLVPNIDNFRLTLRAIKLWAK.HNIYSNILGFLGGVSWAMLVARTCQLYPNA.ASTLV.KFFLVFS.WE
Retrocopy LHLVPNIDNFRLTLRAIKLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAVASTLVRKFFLVFSEWE

Parental  WPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDE
          WPNPVLLK.PEE.NLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTR.VM.EEFKQGLAIT.E
Retrocopy WPNPVLLKEPEERNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRTVMIEEFKQGLAITHE

Parental  ILLSKGEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
          ILLSK.EWSKLFEAP.FFQKYKHYIVLLASAPTEKQ.LEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
Retrocopy ILLSKAEWSKLFEAPSFFQKYKHYIVLLASAPTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQS

Parental  FPAPKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKR
          FPAPKENPDKEEFRTMWVIGLV.KK.ENSE.LS.DLTYDIQSFTDTVYRQAINSKMFE.DMKIAAMH..R
Retrocopy FPAPKENPDKEEFRTMWVIGLVLKKPENSEVLSIDLTYDIQSFTDTVYRQAINSKMFEMDMKIAAMHLRR

Parental  KQLHELLPNHVLQKKKKHSTEGVRLTPLNDSSLDLSMDSDNSMSVPSPTSAMKTSPLNSSGSSQGRNSPA
          K.LH.LLPNHVL.KKK..STE.VRLT.LNDSSLDLS.D..NSMSVPSP.SA..T.P....G........A
Retrocopy KELHQLLPNHVLPKKKTQSTEDVRLTALNDSSLDLSADGGNSMSVPSPPSAANTGPV-TGGNGHAPAVVA

Parental  PAVTAASVTNIQATEVSVPQVNSSESSGGTSSESIPQTATQPAISSPPKPTVSRVVSSTRLVNPPPRPSG
          ...T...V........S........SS.G.......Q.A..P.....PKP...RVVSST.LVN.P.RPSG
Retrocopy ASGTNVQVIEVSSQQASPSDSPGGASSEGV-PQTASQPALSPL----PKPVITRVVSSTLLVNHPARPSG

Parental  NATTKIPNTVVGVKRRSSPHKEESPKKTKTEEDETIED
          .A.T.I.N..VGV.R..S...E.......T.E.....D
Retrocopy SAATNIANPIVGV*RTCSRQREDRTEASNTAEEPSRRD

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_360 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 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014142	1 retrocopy	retro_amel_517,
Bos taurus	ENSBTAG00000004054	1 retrocopy	retro_btau_1078,
Canis familiaris	ENSCAFG00000017783	1 retrocopy	retro_cfam_1783,
Callithrix jacchus	ENSCJAG00000006512	2 retrocopies	retro_cjac_1763, retro_cjac_543,
Homo sapiens	ENSG00000090060	1 retrocopy	retro_hsap_30,
Gorilla gorilla	ENSGGOG00000006287	1 retrocopy	retro_ggor_202,
Myotis lucifugus	ENSMLUG00000010922	1 retrocopy	retro_mluc_1396,
Macaca mulatta	ENSMMUG00000018610	1 retrocopy	retro_mmul_1675,
Monodelphis domestica	ENSMODG00000012887	2 retrocopies	retro_mdom_1714, retro_mdom_1916,
Mustela putorius furo	ENSMPUG00000003054	1 retrocopy	retro_mputfur_1375,
Mus musculus	ENSMUSG00000021111	1 retrocopy	retro_mmus_37,
Nomascus leucogenys	ENSNLEG00000000625	1 retrocopy	retro_nleu_2771,
Otolemur garnettii	ENSOGAG00000004611	1 retrocopy	retro_ogar_987,
Pongo abelii	ENSPPYG00000006128	1 retrocopy	retro_pabe_3113,
Pan troglodytes	ENSPTRG00000006704	1 retrocopy	retro_ptro_2595,
Pteropus vampyrus	ENSPVAG00000013925	1 retrocopy	retro_pvam_360 ,
Vicugna pacos	ENSVPAG00000006464	1 retrocopy	retro_vpac_378,