RetrogeneDB ID: retro_vpac_645

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_9270:42100..42462(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000002816
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CRABP2
• Ensembl ID: ENSVPAG00000005002
• Aliases: None
• Description: cellular retinoic acid binding protein 2 [Source:HGNC Symbol;Acc:2339]

Sequence

>retro_vpac_645
ATGCCCAACTTCACTGGCACTTGGAAGATGCGCAGCAGCGAGAATTTCGATGAGCTGCTCAAGGCGCTGGGCGTGAGCGC
CATGCTGAGGAATGTGGCCAAGGCGGCTGCGTCCAAGCCGCACGTGGAGACCCGCCAGGATGGGGATCAGTTCTACATAA
AGACATCCACCACGGTGCGCACCACCGAGATCGACTTCAAGGTCGGAGAAGGCTTTGAGGAGGAGACAGTGGACGGACGC
AAGTGCAGGAGTTCAGCCACTTGGGAGAATGAGAGCAAGGTCCACTGCACACAAACTCTCCTCGAGGGCGACGGCCCCTA
ACCTCCTGGACCCACGAGCTGGCCAACGACGAGCTCATCCTG

Alignment

ORF - retro_vpac_645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.23 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPNFSGNWKIIRSENFKGSFQQMGVNMMLRKIAVAAASKPAVEIKQEGDTFYIKTSTTVRTTEINFKIGE
          MPNF.G.WK...SENF.......GV..MLR..A.AAASKP.VE..Q.GD.FYIKTSTTVRTTEI.FK.GE
Retrocopy MPNFTGTWKMRSSENFDELLKALGVSAMLRNVAKAAASKPHVETRQDGDQFYIKTSTTVRTTEIDFKVGE

Parental  EFEEQTVDGRPCKSLVKWESENKMVCEQRLLKGEG-PKTSWTRELTNDGELIL
          .FEE.TVDGR.C.S...WE.E.K..C.Q.LL.G.G.P.TSWT.EL.ND.ELIL
Retrocopy GFEEETVDGRKCRSSATWENESKVHCTQTLLEGDG<PLTSWTHELAND-ELIL

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_645 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_645 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000002295	1 retrocopy	retro_mmul_1110,
Sarcophilus harrisii	ENSSHAG00000015843	1 retrocopy	retro_shar_735,
Vicugna pacos	ENSVPAG00000005002	1 retrocopy	retro_vpac_645 ,