RetrogeneDB ID: retro_vpac_595

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_620:3524..4088(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MXI1
• Ensembl ID: ENSVPAG00000003400
• Aliases: None
• Description: MAX interactor 1, dimerization protein [Source:HGNC Symbol;Acc:7534]

Sequence

>retro_vpac_595
CTGCAGCATTCAAAGACCCCACGGATGTTGAGCCTGGCACAGAAACATAGCAGCGGGAGCAGCAGCACCAGCACTGCCAA
CAGGTCTACACGCAATGAGCTGGAAAAGAATCGACGAGCTCATCTTCGCCTGGGTTTAGGACGCTTAAAAGTTCTGATTC
CGCTAGGACCAGACTGCGCCAGGCACACAACGCTAGGTTTGCCCAACAAAGCCAAAGCACACATCAAGAAACTTGAAGAA
GCTGAAAGGAAGAGCCAGCACCAGCAGCTAGAGAACTTGGAAGGAGAACAGAGACTTCTGAAGCCGTGACTGGAACAGCT
GCAGGGTCCTCAGGAGATGGAACGAATACGAATGGACAGCATTGGATCGACTATTTCTTCAGATCATTCTGCTTCAGAGT
GAGAGGAGATTGAAGTGGGTGTTGAAAGCACAGAGTTCTTCCATGACGAAGTGGACAGTATCAGTACCACCAGCATCAGT
GACATCGATGACCACCACAGCCCGCAGAGTGTCGGGAGTGAGGAGGGTTACTCCAGTTCCAGTGTCAAACTTTCATTCAC
TTCC

Alignment

ORF - retro_vpac_595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.7 %
• Parental protein coverage: 92.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQHSKTPRRLSRAQKHSSGSSNTSTANRSTHNELEKNRRAHLRLCLERLKVLIPLGPDCTRHTTLGLLNK
          LQHSKTPR.LS.AQKHSSGSS.TSTANRST.NELEKNRRAHLRL.L.RLKVLIPLGPDC.RHTTLGL.NK
Retrocopy LQHSKTPRMLSLAQKHSSGSSSTSTANRSTRNELEKNRRAHLRLGLGRLKVLIPLGPDCARHTTLGLPNK

Parental  AKAHIKKLEEAERKSQHQ-LENLEREQRFLKRRLEQLQGPQEMERIRMDSIGSTISSDRSDSEREEIEVD
          AKAHIKKLEEAERKSQHQ.LENLE.EQR.LK..LEQLQGPQEMERIRMDSIGSTISSD.S.SE.EEIEV.
Retrocopy AKAHIKKLEEAERKSQHQQLENLEGEQRLLKP*LEQLQGPQEMERIRMDSIGSTISSDHSASE*EEIEVG

Parental  VESTEFSHGEVDNISTTSISDIDDHSSLQSIGSDEGYSSASVKLSFTS
          VESTEF.H.EVD.ISTTSISDIDDH.S.QS.GS.EGYSS.SVKLSFTS
Retrocopy VESTEFFHDEVDSISTTSISDIDDHHSPQSVGSEEGYSSSSVKLSFTS

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_595 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_595 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006556	2 retrocopies	retro_chof_1350, retro_chof_1817,
Cavia porcellus	ENSCPOG00000022901	1 retrocopy	retro_cpor_574,
Dasypus novemcinctus	ENSDNOG00000002479	2 retrocopies	retro_dnov_1336, retro_dnov_668,
Mus musculus	ENSMUSG00000025025	1 retrocopy	retro_mmus_1948,
Vicugna pacos	ENSVPAG00000003400	2 retrocopies	retro_vpac_483, retro_vpac_595 ,