RetrogeneDB ID: retro_vpac_72

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1532:408829..410181(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1A
• Ensembl ID: ENSVPAG00000005749
• Aliases: None
• Description: tubulin, alpha 1a [Source:HGNC Symbol;Acc:20766]

Sequence

>retro_vpac_72
ATGTGTGAGTGCATCTCCATCCATATTGGCCAAGCTGGTGTCCAGATCAGCAATGCCTGCTGGGAGCTCTACTGCCTGGA
ACACGGCATCCAGCCCAATGTCCAGATGCCAAGTGACAAGACCACTGGGGGAGGAGACGACTCCTTCAACACCTTCTTCA
GTGAGACAGGCACTGGCAAGCATGTGCCTAGGGCAGTGTTCGTAGACCTGGAACCCACAGTCATTGATGTTCGCACTGGC
ACCTACTGCCAGCTCTTCCACCCTAAGCAGCTCATCACAGGCAAAGAAGATGCTGCCAGCAACTATGCCCGCAGTCACTA
CATCATTGGCAAGGAGATCATTGACCTCATCTTGGACCGAATTCGGAAACTGGCTGACCAGTGCACAGGTCTTCAGGGGT
TCCTGGTTTTCCACAGCTTTTGTGGGGGAACTGGTTCTGGGTTTACCTCCCTGCTGGTGGAATGTCTCTCTGTCCATTAT
GGCAGGAAGTCCAAGCTGGAGTTCTCCATTTACCCAGCCCCTCAGGTTTCCACAGCTATAGTTGAACCCTACAACTCCAT
CCTCACCACCCACACCACCCTGGAGCACTCTGACTGTGCTTTCATGGTAGACAATGAGGCCATCTATGACATATGTCGCA
GAAACCTCGATATTGAGCACCCAACCTGCACAAACCTGAATAGGCTGATAGGTCAAATTGTGTCCTCCGTCACCACTTCC
CTGAGGTTTGATGGAGCCCTGAATGTCAACTTGACAGAATTCCAAACCAATCTGGTACCCTATCCTCGCATCCACTTCCC
TCTGGCCACATATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTTCTGTAGCAGAGGTCACCAACGCTT
GCTTTGAGCCAGCCAACCAGATGGTGAAATGCGACCCTCGCCATGATAAATACATGGCTTGCTGCCTGTTGTACCATGGT
GACGTGGTCCCCAAAGATGTCAGTGCTGCCATTGCCACCATCAAGACAAGCGTACTATCCAGTTTGTGGACTGGTGCCCC
ACTGGCTTCAAAGTTAGTGTTAATTACCAGCCTCCCACCGTGGTACCTGGTGGAGACCTGGCCAAAGTACAGCGAGCTGT
GTGCATGCTGAGCAACACCACCGCCAGTGCTGAGGCCTGGGCTCGCCTGAACCACAAGTCTGACCTGATGTGTGCCAAGC
GTGCCTTGGTTCACGGGTACGTGGGTGAGGGCATGGAGGAAGGAGAGTTTTCTGAGGCCCGTGAGGACATGGCTGCCCTT
GAGAAGAATTATGAGGAGGTTGGTGTAGATTCTATTGAAGGAGAAGAAGAGGAAGGAGGAGAGGAACACTCA

Alignment

ORF - retro_vpac_72 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.18 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
          M.ECISIH.GQAGVQI.NACWELYCLEHGIQP..QMPSDKT.GGGDDSFNTFFSETG.GKHVPRAVFVDL
Retrocopy MCECISIHIGQAGVQISNACWELYCLEHGIQPNVQMPSDKTTGGGDDSFNTFFSETGTGKHVPRAVFVDL

Parental  EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS
          EPTVID.VRTGTY.QLFHP.QLITGKEDAA.NYAR.HY.IGKEIIDL.LDRIRKLADQCTGLQGFLVFHS
Retrocopy EPTVID-VRTGTYCQLFHPKQLITGKEDAASNYARSHYIIGKEIIDLILDRIRKLADQCTGLQGFLVFHS

Parental  FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVELYNSILTTHTTLEHSDCAFMVDNEAIY
          F.GGTGSGFTSLL.E.LSV.YG.KSKLEFSIYPAPQVSTA.VE.YNSILTTHTTLEHSDCAFMVDNEAIY
Retrocopy FCGGTGSGFTSLLVECLSVHYGRKSKLEFSIYPAPQVSTAIVEPYNSILTTHTTLEHSDCAFMVDNEAIY

Parental  DICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVNLAEFQTNLVPHPRIHFPLATYAPVISAEK
          DICRRNLDIE.PT.TNLNRLIGQIVSS.T.SLRFDGALNVNL.EFQTNLVP.PRIHFPLATYAPVISAEK
Retrocopy DICRRNLDIEHPTCTNLNRLIGQIVSSVTTSLRFDGALNVNLTEFQTNLVPYPRIHFPLATYAPVISAEK

Parental  TYQEQLSVAEITNACFEPANEMVKCDPRHGKYIACCLLYHGDVVPKDVNAAIATIKT-KRTIQFVDWCPT
          .Y.EQLSVAE.TNACFEPAN.MVKCDPRH.KY.ACCLLYHGDVVPKDV.AAIATIKT.KRTIQFVDWCPT
Retrocopy AYHEQLSVAEVTNACFEPANQMVKCDPRHDKYMACCLLYHGDVVPKDVSAAIATIKT<KRTIQFVDWCPT

Parental  GFKVGINYQPPTVVPGGDLAKVQRALCMLSNTTASAEAWACLDHKSDLMYAKRAFVHWYVGEGMEEGEFS
          GFKV..NYQPPTVVPGGDLAKVQRA.CMLSNTTASAEAWA.L.HKSDLM.AKRA.VH.YVGEGMEEGEFS
Retrocopy GFKVSVNYQPPTVVPGGDLAKVQRAVCMLSNTTASAEAWARLNHKSDLMCAKRALVHGYVGEGMEEGEFS

Parental  EAREDMAALEKDYEEVGVDSVQGEGEEEGEEYS
          EAREDMAALEK.YEEVGVDS..GE.EE.GEE.S
Retrocopy EAREDMAALEKNYEEVGVDSIEGEEEEGGEEHS

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_72 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_72 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001489	3 retrocopies	retro_btau_251, retro_btau_350, retro_btau_929,
Callithrix jacchus	ENSCJAG00000020894	2 retrocopies	retro_cjac_1209, retro_cjac_3157,
Dasypus novemcinctus	ENSDNOG00000004121	1 retrocopy	retro_dnov_43,
Equus caballus	ENSECAG00000013798	1 retrocopy	retro_ecab_223,
Homo sapiens	ENSG00000167552	1 retrocopy	retro_hsap_3313,
Nomascus leucogenys	ENSNLEG00000017836	2 retrocopies	retro_nleu_245, retro_nleu_2757,
Oryctolagus cuniculus	ENSOCUG00000027812	1 retrocopy	retro_ocun_197,
Pteropus vampyrus	ENSPVAG00000004645	2 retrocopies	retro_pvam_1283, retro_pvam_414,
Rattus norvegicus	ENSRNOG00000004559	3 retrocopies	retro_rnor_1200, retro_rnor_2006, retro_rnor_446,
Vicugna pacos	ENSVPAG00000005749	4 retrocopies	retro_vpac_157, retro_vpac_210, retro_vpac_429, retro_vpac_72 ,