RetrogeneDB ID: retro_vpac_356

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_11598:1924..2402(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000001819
• Aliases: None
• Description: None

Sequence

>retro_vpac_356
GTTGGTGCCTGGGTGCTTCATGGGCCCACTGGCCCAAAGGGAGACCCTGGCAGCTCGGGCCAGTGGGGATGAGGGGCCTG
CCAGGTCTGCAGGGCCCCCAAAGGAGCCCTGGCCAGGCCGGAGCTGTGGGTGCCCCTAGAGAGAGGGGACCTCCAGGCCC
TCCAGGGCCACTTAGGCCCCTGGACCCCCAACCCCTGTTAGACCACAATCTGCCTGGATCTCCCAGCAAGAGGACCCATT
TCTGTCCAACACCTTCACTGAGACCAGCAGCCACTGGCTCATGGGCCCTCCTGGACCTCCTGGTCCCATTGGCATCCCTG
GGAGTTTTGCACACATGGGACCCTCAGGCCCCTCTGGACTCAAAGGAATCTTCAGCCCCCCAGGAGGGAAGGGCGAGAGA
GGACTGTGTGGGGAGCTGGCTCCTCAAGGCTCCATGGGGCAGTGGGGAAATCCCGGCCCCAGAGGAGACCCTGGTGAG

Alignment

ORF - retro_vpac_356 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.1 %
• Parental protein coverage: 59.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VGAWVLHGPTGPKGD-PGSL-PVGMRDLPGLQGPQRSPGQAGAVGAPRERGPPG-LPGPL-APGPPTPVR
          VGAWVLHGPTGPKGD.P..L.PVGMR.LPGLQGPQRSPGQAGAVGAPRERGPPG.L.G.L.APGPPTPVR
Retrocopy VGAWVLHGPTGPKGD<PWQLGPVGMRGLPGLQGPQRSPGQAGAVGAPRERGPPG>LQGHL>APGPPTPVR

Parental  PQSAWISQQEEPFLSNTFTETSSHWLMGPPGPPGPIGIPGSFAHMGPSGPSGLKGIFSHPGGKGERXXXX
          PQSAWISQQE.PFLSNTFTETSSHWLMGPPGPPGPIGIPGSFAHMGPSGPSGLKGIFS.PGGKGER....
Retrocopy PQSAWISQQEDPFLSNTFTETSSHWLMGPPGPPGPIGIPGSFAHMGPSGPSGLKGIFSPPGGKGERGLCG

Parental  XXXXXXXXXXXGEPGPKGDPGQ
          ...........G.PGP.GDPG.
Retrocopy ELAPQGSMGQWGNPGPRGDPGE

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_356 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_356 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Vicugna pacos	ENSVPAG00000001819	2 retrocopies	retro_vpac_356 , retro_vpac_504,