RetrogeneDB ID: retro_vpac_116

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1891:444412..444814(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000009975
• Aliases: None
• Description: None

Sequence

>retro_vpac_116
AGGGATTCCTTTCCTGCTGATCATCCTTAAGCTAGAAGAGTGACAAAACTGAGTTGGATGAGATAAGCCACAGGGGTAGA
GCTTCAGTGGCCCTGTTTATGGGGAGGAGTTGGAGCTGGAGCGAATCCTGTGGCTGCGGCCTGGGAAGCGGGATCGCCGT
TTCACGGAGGGGGGGGCCTGCGCCGAGGGGAACGTGATCTTCTCCGCCTCCGTGGGGGTGACCGGCGCCTCAAGGGAGGT
GGTAGCAGCATTCTCCTGGGAGGGCTGAATCGCCTGGAAGGTGGCCGAGGCCAGGGGGCCAGCACAGCAGTGACAGTGAT
CGCCTGGCCATCGATTTGTCCTCCGCCCATGCGCTTCAGCGCCTTATGGGCCTCGTCTAGATTCTCAAACTCCGCATATG
CA

Alignment

ORF - retro_vpac_116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.94 %
• Parental protein coverage: 76.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RDSFPTDHLSARKVTKLSRMYKSQG-ELQW-PAYREELELERLLWRRRPGERDRRRTGDLRRGERDLL-L
          RDSFP.DH..AR.VTKLS.M....G.ELQW.P.Y.EELELER.LW..RPG.RDRR.T......E.....L
Retrocopy RDSFPADHP*ARRVTKLSWMR*ATGVELQW>PVYGEELELERILW-LRPGKRDRRFTXXXXCAEGNVI<L

Parental  IR--GGDRRHMGGGGSILLGGLNRLGGGLGQGVSTAVAVISWPSICPPPSICFSAFSASSGFSNSTYA
          .R..GGDRR..GGG.SILLGGLNRL.GG.GQG.STAV.VI.WPSICPPP...FSA..ASS.FSNS.YA
Retrocopy LRLRGGDRRLKGGGSSILLGGLNRLEGGRGQGASTAVTVIAWPSICPPP-MRFSALWASSRFSNSAYA

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_116 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_116 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004876	3 retrocopies	retro_chof_1586, retro_chof_1986, retro_chof_2273,
Homo sapiens	ENSG00000167970	1 retrocopy	retro_hsap_3023,
Tursiops truncatus	ENSTTRG00000008219	1 retrocopy	retro_ttru_1557,
Vicugna pacos	ENSVPAG00000009975	1 retrocopy	retro_vpac_116 ,