RetrogeneDB ID: retro_vpac_429

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_181093:303..1218(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000005920
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_vpac_429
CCAGATCGGCAATGCCTGCTGCCGAGTGACAAGACCATTCGGGGAGGAGACGACTCCTTCAACACCTTCTTCAGTGAGAC
AGGTGCTGGCAAGCATGCGCCCAGGGCAGTGTTCGTAGACCTGGAACCCACAGTCATTGATGAAGTTCGCACTGGCACCT
ACCACCAGCCCTTCCACCCTGGGCAGCTCATCCCAGGCAAAGAAGATGCTGCCAATAACTATGCCCGCGGTCACTACACA
ATTGGCAAGGAGATCATTGACCTCGTCTTGGACCGAATTCGGAAACTGCCTGACCAGTGCACAGGTCTTCAGGGCTTCTT
GGTTTTCCACAGCTTCGGCGGGGGAACTGGTTCTGGGTTTACCTCCCTGCTGATGGAACGTCTCTCTGTCGATTATGGCA
AGAAGTCTAAGCTGGAGTTCTCCATTTACCCAGCCCCCCAGGTTTCCACAGCTGTAGTTGAGCCCTACAACTCCATCCTC
ACCACCCACACCACCCTGGAGCACTCTGACTGTGCTTCATGGTCGACAACGAGGCCATCTATGACATCTGTCATAGAAAC
CTCGATATTGAGCGCCCAACCTACACAAACCTGAATAGGTTGATAGGTCAAATTGTGTCCTCCATCACTGCTTCCCTGAG
ATTTGATGGAGCCCTGAATGTCGATCTGACAGAATTCCAGACCAACCTGGTGCCCTATCCTCGCATCCACTTCCCTCTGG
CCACATATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTTCTGTATCAGAGATCACCAAACACTTGCTT
TGAGCCAGCCAACCAGATGGTGAAATGCGACCCTCGCCATGGTAAATACATGGCTTGCTGCCTGTTGTACCGTGGTGACG
TGGTCCCCAAAGATGTCAATGCTACCATTGCCACC

Alignment

ORF - retro_vpac_429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.53 %
• Parental protein coverage: 67.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PDGQ--MPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDA
          PD.Q...PSDKTI.GGDDSFNTFFSETGAGKH.PRAVFVDLEPTVIDEVRTGTY.Q.FHP.QLI.GKEDA
Retrocopy PDRQCLLPSDKTIRGGDDSFNTFFSETGAGKHAPRAVFVDLEPTVIDEVRTGTYHQPFHPGQLIPGKEDA

Parental  ANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEF
          ANNYARGHYTIGKEIIDLVLDRIRKL.DQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEF
Retrocopy ANNYARGHYTIGKEIIDLVLDRIRKLPDQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEF

Parental  SIYPAPQVSTAVVELYNSILTTHTTLEHSDCA-FMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSI
          SIYPAPQVSTAVVE.YNSILTTHTTLEHSDCA.FMVDNEAIYDIC.RNLDIERPTYTNLNRLIGQIVSSI
Retrocopy SIYPAPQVSTAVVEPYNSILTTHTTLEHSDCA<FMVDNEAIYDICHRNLDIERPTYTNLNRLIGQIVSSI

Parental  TASLRFDGALNVNLAEFQTNLVPHPRIHFPLATYAPVISAEKTYQEQLSVAEIT-NACFEPANEMVKCDP
          TASLRFDGALNV.L.EFQTNLVP.PRIHFPLATYAPVISAEK.Y.EQLSV.EIT.N.CFEPAN.MVKCDP
Retrocopy TASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVSEIT>NTCFEPANQMVKCDP

Parental  RHGKYIACCLLYHGDVVPKDVNAAIAT
          RHGKY.ACCLLY.GDVVPKDVNA.IAT
Retrocopy RHGKYMACCLLYRGDVVPKDVNATIAT

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_429 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_429 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,