RetrogeneDB ID: retro_vpac_277

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_356:589819..590194(-)
• Located in intron of: ENSVPAG00000007961

Retrocopy information

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

Parental gene information

• Parental gene symbol: TBCA
• Ensembl ID: ENSVPAG00000001561
• Aliases: None
• Description: tubulin folding cofactor A [Source:HGNC Symbol;Acc:11579]

Sequence

>retro_vpac_277
TCACGGTTACCCCGGCTCTCTGCCCCTCCTTCCCGCGGTGCTCGAGGGACCATGGCCGATCCTCGCATGAGGCAGATCAA
GATCAAAACCGGCGCGGTGAAGCGATTGGTCAAAGAAAAAATGATGTATGAAAAAGAAGCAAAACAACAAGAAGAAAAGA
TTGAAAAACTGAAAGCCGAAGATGGTGAAAATTATGCTATTAAAAAGCAGGCGGAGATCCTGCAAGAGTCCCGCATGATG
ATCCCAGATTGCCAGCGCAGGTTGGAAGCTGCATACAGTGACCTTCTGCAATTATTAGAGAGTGAAAAAGACTTGGAAGA
AGCTGTGGAATATAAGGAGGCACGTGTAGTACTGGATTCAGTGAAGTTAGAAGCC

Alignment

ORF - retro_vpac_277 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.2 %
• Parental protein coverage: 93.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRLPRLSAPPSRGARGTMADPRVRQIKIKTGVVKRLVKEKMMYEKEAKQQEEKIEKMKAEDGENYAIKKQ
          SRLPRLSAPPSRGARGTMADPR.RQIKIKTG.VKRL..................EK.KAEDGENYAIKKQ
Retrocopy SRLPRLSAPPSRGARGTMADPRMRQIKIKTGAVKRLXXXXXXXXXXXXXXXXXXEKLKAEDGENYAIKKQ

Parental  AEILQESRMMIPDCQRRLEAAYSDLLQLLESEKDLEEAVEYKEARVVLDSVKLEA
          AEILQESRMMIPDCQRRLEAAYSDLLQLLESEKDLEEAVEYKEARVVLDSVKLEA
Retrocopy AEILQESRMMIPDCQRRLEAAYSDLLQLLESEKDLEEAVEYKEARVVLDSVKLEA

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_277 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_277 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014223	4 retrocopies	retro_acar_11, retro_acar_130, retro_acar_142, retro_acar_195,
Choloepus hoffmanni	ENSCHOG00000002112	2 retrocopies	retro_chof_1592, retro_chof_304,
Callithrix jacchus	ENSCJAG00000019848	4 retrocopies	retro_cjac_114, retro_cjac_2160, retro_cjac_2173, retro_cjac_2974,
Loxodonta africana	ENSLAFG00000005316	1 retrocopy	retro_lafr_1212,
Macaca mulatta	ENSMMUG00000011853	1 retrocopy	retro_mmul_229,
Procavia capensis	ENSPCAG00000011849	1 retrocopy	retro_pcap_394,
Rattus norvegicus	ENSRNOG00000048342	1 retrocopy	retro_rnor_140,
Vicugna pacos	ENSVPAG00000001561	1 retrocopy	retro_vpac_277 ,