RetrogeneDB ID: retro_vpac_278

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_3593:1111678..1112280(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000000095
• Aliases: None
• Description: None

Sequence

>retro_vpac_278
AGTCTTCATTATAACCTCATGGTGGTATCCCAGGATGGAACTGTGCAATCACAGTTTTCTGCTGAGGGACACTTGGATGG
TCAGGCCTTCCTATGCTGTGACTGTGAGACAGGCGGGTAGAGCCCTGGGGGCTGTGGGCAGAAGTAGTCCTAGGAGCAGA
GACATGGGACACACAGTCCAAGGACTTGACTAAGAATGGGAAGGGCCTCAGAAAATTTCAGGCAGAAATCATGGCCCTGC
AGGAGGAGAAAGGAAGTTTGCATTCTTCCCAGAAGATTCAGGGCTGTGAGATCCAAGAAGACAACCATGCCAGGGGCTTC
AGTTGTTTCTAATATCGTGGGGAGCTCTTCCCCTCCTATCACCCAAAGCCCTATGGATGGGAAATGCCCTGGTCTTTGAC
TTGGACCTGGACTATGGAAATAGAGAAGTCCCAGGACATAGATGGATATAAAAGGAAGGATTACTGGGTCTGTGTGCAGG
GAGAGCTTTGTGGAAGACTGCAGAAATATCTGAAATCCTAAATGGGCTTCACAGAGAGAATAGTGCCCCCAGCAGTGAAC
ATGACCAGCAGCATGGCCTTGGAGGGCATGGTCACCCTGACA

Alignment

ORF - retro_vpac_278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.92 %
• Parental protein coverage: 64.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLHYSLTVLCQDGFVQPSFSAEGRLDGQAFLHYDSGKG-RAEPQGPWAED-FAAETWDTEIKDLTENGRD
          SLHY.L.V..QDG.VQ..FSAEG.LDGQAFL..D...G.R.EP.G.WAE....AETWDT..KDLT.NG..
Retrocopy SLHYNLMVVSQDGTVQSQFSAEGHLDGQAFLCCDCETG<RVEPWGLWAEVVLGAETWDTQSKDLTKNGKG

Parental  LRQLLAETMSLQEEKGGLHSLQETVGCEIREDGQARGFRSICYDGKLFLSCHLETHGCRVPQSLDQTLAM
          LR...AE.M.LQEEKG.LHS.Q...GCEI.ED..ARGF....Y.G.LF.S.H....G...P.SL..T..M
Retrocopy LRKFQAEIMALQEEKGSLHSSQKIQGCEIQEDNHARGFSCF*YRGELFPSYHPKPYGWEMPWSLTWTWTM

Parental  EIKKSWDTDGFQSKHYRAHVQGDFV-RLQSYVESRMGFTDRTVPPAVNVTLSQALEGRVNLS
          EI.KS.D.DG...K.Y...VQG....RLQ.Y..S.MGFT.R.VPPAVN.T.S.ALEG.V.L.
Retrocopy EIEKSQDIDGYKRKDYWVCVQGELCGRLQKYLKS*MGFTERIVPPAVNMTSSMALEGMVTLT

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_278 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_278 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Vicugna pacos	ENSVPAG00000000095	1 retrocopy	retro_vpac_278 ,