RetrogeneDB ID: retro_vpac_378

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_13972:42195..43994(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000004027
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PAPOLA
• Ensembl ID: ENSVPAG00000006464
• Aliases: None
• Description: poly(A) polymerase alpha [Source:HGNC Symbol;Acc:14981]

Sequence

>retro_vpac_378
TTGCAGCACAGGAATTTAATTTTGGAGAAATTAAATAATCTGGTAAAGGAAAGGTTTGAGAAATCAGTGAAAGCAAGAGC
CATTTTTCAAGCTATAATGAAAATGTTGGAGGGAAGATCTTTACATTCGGTTCTTACAGGTTAGGAGTGCATACCAAAGG
GGCCGATATCGACGCGCTGTGCGTTGCACCGAGACATGTTGATCGAAGCGACTTTTTCACCTCCTTCTATGATAAATTGA
AACTACATGAAGAAGTGAAAGACTTAAGGGCTGTTGAGGAAGCATTTGTTCCAGTTATCAAACTGTGTTTTGATGGGATA
GAGATTGATATTTTGTTTGCGAGATTAGCACTGCAGACTATTCCAGAAGATCTGGACCTAAGAGATGACAGTCTGCTTAA
AAATTTAGATATTAGATGCATAAGAAGTCTTAACGGTTGCCGGGTAACTGATGAAATTTTACACCTAGTACCGAACATTG
ACAACTTCAGGTTAACTCTGAGGGCCATCAAGTTGTGGGCCAAATGCCACAATATCTATTCCAATATATTAGGTTTCCTA
GGAGGTGTGTCCTGGGCTATGCTAGTAGCAAGAACTTGCCAGCTTTATCCAAATGCAATAGCGTCAACTCTTGTGCGTAA
ATTTTTCTTGGTGTTTTCTGAATGGGAATGGCCAAATCCAGTGCTGCTGAAAGAGCCTGAAGAACGGAATCTTAATCTGC
CTGTATGGGACCCAAGAGTAAATCCTAGTGACAGGTACCATCTCATGCCTATAATCACACCAGCATACCCGCAGCAGAAC
TCCACGTACAACGTGTCTGTTTCAACAAGGATGGTCATGATTGAGGAGTTCAAACAGGGACTTGCTATCACACATGAAAT
TTTGCTGAGTAAAGCAGAGTGGTCCAAACTTTTTGAAGCGCCAAGCTTCTTTCAAAAGTACAAGCATTATATTGTACTAC
TAGCAAGTGCACCAACCGAAAAACAGCACCTAGAATGGGTGGGCTTGGTGGAATCAAAAATCCGAATCCTGGTCGGAAAC
TTGGAGAAGAATGAATTTATTACACTGGCACATGTGAATCCTCAGTCATTTCCAGCACCCAAAGAAAATCCTGACAAAGA
AGAATTTCGTACAATGTGGGTGATTGGGTTAGTGTTAAAAAAGCCAGAAAACTCTGAAGTTCTCAGTATTGATCTCACCT
ATGATATCCAGTCTTTCACTGATACGGTGTATAGGCAAGCGATAAATAGTAAGATGTTTGAGATGGATATGAAAATTGCT
GCAATGCATTTAAGAAGAAAGGAACTTCATCAGCTGCTACCTAATCATGTGCTTCAGAGAAAGAACACGCATCCGCTGGA
AGGAGTCAGATTGGCAGCTTTGAATGACGGCAGCCTCGATTTGTCTGTACACAGTGAAAACAGCATGTCTGTGTCTTCAC
TTCCTGGCTCAGTGAAGACTGGCCCAACGACTGGCAGCACTCAGGGCAGAAACAGCCCTGCCCTGGCTGTGATGGCAGCC
TCTGTGGCCAACGTGCAGGTTACTGAAGTTTCCGTGCGACAAGCAGACCCCAGTGAAAGCCCCGGGAGTGCATCCAGTGA
AGGCACTTCTCAGACTGCCTTGCAGCCAGCGGTTTCTTCACCACTGAAGCCCATGGTCACCAGAGTTGTTTCTTCAGCCC
GACTGGTAAATCATCCACCCAGGCCTTCAGGGAGTGCAGCAACAAACATAGCTAATCCTATAGTAGGAATCTAGAGGACG
CTTGAGCATCACAAAGAAGAAAGGACCAAGGACAGAAGG

Alignment

ORF - retro_vpac_378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.25 %
• Parental protein coverage: 81.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQRRILILGKLNNLVKEWIR-EISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDR
          LQ.R.LIL.KLNNLVKE....EISESK....S..ENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDR
Retrocopy LQHRNLILEKLNNLVKERFE<EISESKSHFSSYNENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDR

Parental  SDFFTSFYEKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIR
          SDFFTSFY.KLKL.EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIR
Retrocopy SDFFTSFYDKLKLHEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIR

Parental  CIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIAS
          CIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAK.HNIYSNILGFLGGVSWAMLVARTCQLYPNAIAS
Retrocopy CIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAIAS

Parental  TLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMV
          TLV.KFFLVFS.WEWPNPVLLK.PEE.NLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMV
Retrocopy TLVRKFFLVFSEWEWPNPVLLKEPEERNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMV

Parental  MVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLE
          M.EEFKQGLAIT.EILLSKAEWSKLFEAP.FFQKYKHYIVLLASAPTEKQ.LEWVGLVESKIRILVG.LE
Retrocopy MIEEFKQGLAITHEILLSKAEWSKLFEAPSFFQKYKHYIVLLASAPTEKQHLEWVGLVESKIRILVGNLE

Parental  KNEFITLAHVNPQSFPAPKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKM
          KNEFITLAHVNPQSFPAPKENPDKEEFRTMWVIGLV.KK.ENSE.LS.DLTYDIQSFTDTVYRQAINSKM
Retrocopy KNEFITLAHVNPQSFPAPKENPDKEEFRTMWVIGLVLKKPENSEVLSIDLTYDIQSFTDTVYRQAINSKM

Parental  FEVDMKIAAMHVKRKQLHQLLPNHVLQKKKKHSTEGVRLTPLNDSSLDLSMDSDNSMSVPSPTSAMKTSP
          FE.DMKIAAMH..RK.LHQLLPNHVLQ.K..H..EGVRL..LND.SLDLS..S.NSMSV.S.....KT.P
Retrocopy FEMDMKIAAMHLRRKELHQLLPNHVLQRKNTHPLEGVRLAALNDGSLDLSVHSENSMSVSSLPGSVKTGP

Parental  LNSSGSSQGRNSPAPAVTAASVTNIQATEVSAPQVNSSESSGGTASESIPQTATQPAISPPPKPTVSRVV
          ....GS.QGRNSPA.AV.AASV.N.Q.TEVS..Q...SES.G...SE...QTA.QPA.S.P.KP.V.RVV
Retrocopy --TTGSTQGRNSPALAVMAASVANVQVTEVSVRQADPSESPGSASSEGTSQTALQPAVSSPLKPMVTRVV

Parental  SSTRLVNPAPRPSGNAAAKIPNPIVGVKRTSSPHKEESPKKTR
          SS.RLVN..PRPSG.AA..I.NPIVG..RT...HKEE..K..R
Retrocopy SSARLVNHPPRPSGSAATNIANPIVGI*RTLEHHKEERTKDRR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq

Vicugna pacos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_vpac_378 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_378 was not experimentally validated.

Homology

Retrocopy orthology:

Vicugna pacos 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 ,