RetrogeneDB ID: retro_vpac_568

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_476:411760..412248(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DAZAP2
• Ensembl ID: ENSVPAG00000001156
• Aliases: None
• Description: DAZ associated protein 2 [Source:HGNC Symbol;Acc:2684]

Sequence

>retro_vpac_568
CAATATCTAATGCAGCCAACCTAGCCCCTGGAGCCTCCTGGGAATCCTGTGTACACTCAGACCTTGCATTTTCCCCAGGC
TCCACCCCATACTGATGCTAGACCTGCTAGCTCAGAGCTCTATCTGTTGTCTGAGTTTGTGCACTAAGAGGCTGCCACAG
CCCCCACCATGTCAGCTATAGTTCCTGGCACTTCACTGTATCTTCCCATGACCTTGTCTGTGGCTGTTGGACCTTTAATT
TTCACAATGCTCATAGTTTATTATCCAGTTGGTTCCACCTGTCCACCTGGTGCAACAGTGCTGGAGGAAGGAGGGTATAA
TTCAGGTGCCATATTTGGAACTGGCTCTACTACTGGCAACATCTCTCCTCCTCCAGATGCCTTCCTAATGCTGCTCAGCT
GACAGACATGCAAGGAGCCAATGTACTTGTAACTCAGCAGAAGGGAAACTTCTTCATGGGTGGTTCAGATGGGGGCTACA
GCATCTGG

Alignment

ORF - retro_vpac_568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QYPTQPTYPVQPPGNPVYPQTLHLPQAPPYTDAPPAYSELYRPS-FVHPGAATVPTMSAAFPGASLYLPM
          QY..QPT.P..PPGNPVY.QTLH.PQAPP.TDA.PA.SELY..S.FVH..AAT.PTMSA..PG.SLYLPM
Retrocopy QYLMQPT*PLEPPGNPVYTQTLHFPQAPPHTDARPASSELYLLSEFVH*EAATAPTMSAIVPGTSLYLPM

Parental  AQSVAVGPLGSTIPMAYYPVGPIYPPGSTVLVEGGYDAGARFGAGATAGNIPPPPPG-CPPNAAQLAVMQ
          ..SVAVGPL..T....YYPVG...PPG.TVL.EGGY..GA.FG.G.T.GNI.P.PP..C.PNAAQL..MQ
Retrocopy TLSVAVGPLIFTMLIVYYPVGSTCPPGATVLEEGGYNSGAIFGTGSTTGNISP-PPD<CLPNAAQLTDMQ

Parental  GANVLVTQRKGNFFMGGSDGGYTIW
          GANVLVTQ.KGNFFMGGSDGGY.IW
Retrocopy GANVLVTQQKGNFFMGGSDGGYSIW

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_568 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_568 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	ENSCHOG00000000298	1 retrocopy	retro_chof_85,
Dasypus novemcinctus	ENSDNOG00000009306	1 retrocopy	retro_dnov_1772,
Equus caballus	ENSECAG00000007313	1 retrocopy	retro_ecab_286,
Myotis lucifugus	ENSMLUG00000009959	1 retrocopy	retro_mluc_351,
Mus musculus	ENSMUSG00000000346	1 retrocopy	retro_mmus_1073,
Sorex araneus	ENSSARG00000003823	1 retrocopy	retro_sara_632,
Tupaia belangeri	ENSTBEG00000013232	1 retrocopy	retro_tbel_3228,
Vicugna pacos	ENSVPAG00000001156	2 retrocopies	retro_vpac_314, retro_vpac_568 ,