RetrogeneDB ID: retro_vpac_571

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_4839:44341..44834(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIBADH
• Ensembl ID: ENSVPAG00000012531
• Aliases: None
• Description: 3-hydroxyisobutyrate dehydrogenase [Source:HGNC Symbol;Acc:4907]

Sequence

>retro_vpac_571
AAAGCAAAGAAAAGCTCACTATCAATAGATTCCAGAGCTATCAATCCTATGGTTTTGAAAGAATTAGCTAAAGAAGTTGA
GAAAATGGGAGCAGTTTTTCTGGAGGCTCCCGTTTCTGATGGTGTAGGGAGTGGCTCAGTCTGAAAACCTAATGTTTATG
GTGGGAGGAGTCAGAGATGAATTCGCTGCTGCTCAGGAGTTGCTGGGGTATAAGGGCTGCGATGTGGTGTGTTATGGAGC
CCTTGGGACTGGGCAGACTGCAAGGCTCTGCTACAGCAGCCTGCTGTTAGCTATTTGTATGATTGGAACTGCTGAAGCTA
TGAATCTTGGAATCAGGTTAGGGCTTGACCCAAAACTATTAGCTAAAATCCTAAATATAAGCTCAAGACAGTGTTGGTCA
AGTGACATTTATAATCCTGTACCTGGAGTGATGGATGGAGTTCCCTCACCTAAGAACTGTCAGGGTGAATTCAGAATAAC
ACTCACGGCTAAG

Alignment

ORF - retro_vpac_571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.15 %
• Parental protein coverage: 65.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVKKGSLLIDSSTIDPMVSKELAKEVEKMGAVFMDAPVSGGVGA-ARSGNLTFMVGGVEDEFAAAQELLG
          K.KK.SL.IDS..I.PMV.KELAKEVEKMGAVF..APVS.GVG..A.S.NL.FMVGGV.DEFAAAQELLG
Retrocopy KAKKSSLSIDSRAINPMVLKELAKEVEKMGAVFLEAPVSDGVGS>AQSENLMFMVGGVRDEFAAAQELLG

Parental  CMGSNVVYCGAVGTGQAAKIC-NNLLLAISMIGTAEAMNLGIRLGLDPKLLAKILNMSSGRCWSSDTYNP
          ..G..VV..GA.GTGQ.A..C...LLLAI.MIGTAEAMNLGIRLGLDPKLLAKILN.SS..CWSSD.YNP
Retrocopy YKGCDVVCYGALGTGQTARLCYSSLLLAICMIGTAEAMNLGIRLGLDPKLLAKILNISSRQCWSSDIYNP

Parental  VPGVMDGVPSANNYQGGFGTTLMAK
          VPGVMDGVPS..N.QG.F..TL.AK
Retrocopy VPGVMDGVPSPKNCQGEFRITLTAK

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_571 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_571 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003153	1 retrocopy	retro_chof_1225,
Dasypus novemcinctus	ENSDNOG00000008640	2 retrocopies	retro_dnov_1465, retro_dnov_1997,
Mus musculus	ENSMUSG00000029776	1 retrocopy	retro_mmus_2360,
Oryctolagus cuniculus	ENSOCUG00000010349	1 retrocopy	retro_ocun_1896,
Sus scrofa	ENSSSCG00000016695	1 retrocopy	retro_sscr_792,
Ictidomys tridecemlineatus	ENSSTOG00000004108	1 retrocopy	retro_itri_395,
Tarsius syrichta	ENSTSYG00000014191	1 retrocopy	retro_tsyr_1136,
Vicugna pacos	ENSVPAG00000012531	1 retrocopy	retro_vpac_571 ,