RetrogeneDB ID: retro_vpac_157

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2225:238051..239183(-)
• 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_157
TTGCATGAGTGCATCTCCATCCGTGTTGGCCAGGCTGGTGCCCAGATCGGTAATGCCTGCTGGAAGCTCTACTGCCTGGA
ACACGGCATCCAGCCCGATGGCCTGATGCCAAGTGACAAGACCTCTGGGGGAGAAGACAACTCCTTCAACACCTTCAGTG
AGACAGGCGCTGGCAACCATCTGCCCAGGGCAGTGTTTGTCGACCTGGAACCTACAGTCATTGATGAAGTTCGCACTGGC
ACCTACCGCCAGCTCTTCCACCCTGAGCAGCTCATCACGGGCAAAGAAGATGCTGCCAGTAACTATGCCCGCGGTCACTA
CACCATTGGCAAGGAGATCATTGACCTTGTTGTGGACCAAATTCGGAAACTGGCTGACCAGTGCACAGGTCTTCAGGGCT
TCTTGGTTTTCCACAGCTTTGGTGGGGGAACTGGTTCTGGGTTGACCTCCCTGCTGATGGAACGTCTCTCTGTTGATTAT
GGCAAGAAGTCCAAGCTGGAGTTCTCCATTTACCCAGACCATCAGGTTTCCACAGCTGTAGTTGAGCCCTACAGCTCCAT
CCTCACCACCCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAACGAGGTCATCTATGGCATCTGTCGTA
GAAACCTCGATATTGAGCGCCCAACCTACACAAACCTGAATAGGCTGATAGGTCAAATTGTATCCTCAACCACTGCTTCC
CTGAGGTTTGATGGAGCCCTGAATGTCGATCTAATAGAATTCCAAACCAACCTGGTACCCTACCCTCTCATCCACTTCCC
TCTGGCCACATATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTTCTGTAGCAGAGATCACCACTTGCT
TTGAGCCAGCCAACCAGAGAGTGAAAAGTGACCCTCACCATGGTAAACACATGGCCTGCTGCCTGTTGTACCGTGGTGAC
GTGGTCCCCAAAGATGTCAGTGCTGCCATTGCCACCATCAAGACCAAGCGTTATCATCCAGTTTGTGGACTGGTGCCCCA
CTGGCTTCAAAGTTGGCATTAATTACCAGCCTCCCACCGTGGTACCTGGTGGAGACCTGGCCAAAGTACAGTGAGCTGTG
TGCATGCTGAGC

Alignment

ORF - retro_vpac_157 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.68 %
• Parental protein coverage: 83.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
          ..ECISI.VGQAG.QIGNACW.LYCLEHGIQPDG.MPSDKT.GG.D.SFNTF.SETGAG.H.PRAVFVDL
Retrocopy LHECISIRVGQAGAQIGNACWKLYCLEHGIQPDGLMPSDKTSGGEDNSFNTF-SETGAGNHLPRAVFVDL

Parental  EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS
          EPTVIDEVRTGTYRQLFHPEQLITGKEDAA.NYARGHYTIGKEIIDLV.D.IRKLADQCTGLQGFLVFHS
Retrocopy EPTVIDEVRTGTYRQLFHPEQLITGKEDAASNYARGHYTIGKEIIDLVVDQIRKLADQCTGLQGFLVFHS

Parental  FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVELYNSILTTHTTLEHSDCAFMVDNEAIY
          FGGGTGSG.TSLLMERLSVDYGKKSKLEFSIYP..QVSTAVVE.Y.SILTTHTTLEHSDCAFMVDNE.IY
Retrocopy FGGGTGSGLTSLLMERLSVDYGKKSKLEFSIYPDHQVSTAVVEPYSSILTTHTTLEHSDCAFMVDNEVIY

Parental  DICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVNLAEFQTNLVPHPRIHFPLATYAPVISAEK
          .ICRRNLDIERPTYTNLNRLIGQIVSS.TASLRFDGALNV.L.EFQTNLVP.P.IHFPLATYAPVISAEK
Retrocopy GICRRNLDIERPTYTNLNRLIGQIVSSTTASLRFDGALNVDLIEFQTNLVPYPLIHFPLATYAPVISAEK

Parental  TYQEQLSVAEITNACFEPANEMVKCDPRHGKYIACCLLYHGDVVPKDVNAAIATIKTKR-TIQFVDWCPT
          .Y.EQLSVAEIT..CFEPAN..VK.DP.HGK..ACCLLY.GDVVPKDV.AAIATIKTKR..IQFVDWCPT
Retrocopy AYHEQLSVAEIT-TCFEPANQRVKSDPHHGKHMACCLLYRGDVVPKDVSAAIATIKTKR>IIQFVDWCPT

Parental  GFKVGINYQPPTVVPGGDLAKVQRALCMLS
          GFKVGINYQPPTVVPGGDLAKVQ.A.CMLS
Retrocopy GFKVGINYQPPTVVPGGDLAKVQ*AVCMLS

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_157 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_157 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,