RetrogeneDB ID: retro_vpac_314

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_729:249846..250300(+)
• Located in intron of: ENSVPAG00000006107

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_314
CAGCCAGCTTTCTTTGCGCGGCATCCTGGGAATCTGGTGTACCCTCAAACATTGCATCAGCGTCAGGCTCTGCCCTGTAC
CCAGAGGTCTGTTGTCCGAGCTTTGTGCACCCAGGGGCTGCCGCAGTCCCCATGGTGTCAGCTGCTTTTCCTGGCACCTC
ACAGTACCTTCCCATGGCGCAGTCTGTGGCTGTTGGCCTCTAGGCTCCACAGTCCTCACAGCTTAGTGTCTGGTTGGCCC
CGTCTCTCCAGCTGGTTCAGTGGTGCCAGTGAAAGGAGGGAGTGATGCGGGTGCCAGATTCGGAGCTGAGGCCACTGCTG
GCAGCATTCCTCCTCCACCCCCAGGATGTCCTCCCAGGGCTGCTCAGCTTGCAGTCAGGCAGGGAGCTGTTGTCCTCGTA
ACTCAGCAGAAGGCAGACTTCATGGGTGGTTCAGAGGGTGGCTGCACCATCTGG

Alignment

ORF - retro_vpac_314 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.81 %
• Parental protein coverage: 93.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QPPGNPVYPQTLHLPQAPPYTDAPPA-YSELYRPSFVHPGAATVPTMSAAFPGASLYLPMAQSVAVG-PL
          QP......P..L..PQ......A.P..Y.E...PSFVHPGAA.VP..SAAFPG.S.YLPMAQSVAVG.PL
Retrocopy QPAFFARHPGNLVYPQTLHQRQALPC<YPEVCCPSFVHPGAAAVPMVSAAFPGTSQYLPMAQSVAVG<PL

Parental  GSTIPMAYYPVGPIYPPGSTVLVEGGYDAGARFGAGATAGNIPPPPPGCPPNAAQLAVMQGANVLVTQRK
          GST...A...VGP..P.GS.V.V.GG.DAGARFGA.ATAG.IPPPPPGCPP.AAQLAV.QGA.VLVTQ.K
Retrocopy GSTVLTA*CLVGPVSPAGSVVPVKGGSDAGARFGAEATAGSIPPPPPGCPPRAAQLAVRQGAVVLVTQQK

Parental  GNFFMGGSDGGYTIW
          ...FMGGS.GG.TIW
Retrocopy AD-FMGGSEGGCTIW

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_314 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_314 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,