RetrogeneDB ID: retro_vpac_574

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_5031:80899..81313(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOJ
• Ensembl ID: ENSVPAG00000004859
• Aliases: None
• Description: ras homolog family member J [Source:HGNC Symbol;Acc:688]

Sequence

>retro_vpac_574
AGCGTCACCATAGGGGGCAAGCAGTACCTCCTGGGACTCTGTGACACAGTCAGACAGGAAGACTATGATCATCTGAGGCC
TTTATCTTGTCCAATGACTGATGTCTTCCTTATATGCTTCTCTGTGGTGAATCCAGCCTCATTTCAAAATGTGAAAGAGG
AGTGGGTACCAGAACTTAAAGGAATACGCACCACATGCACCCTTTTTATTAATAGGAACCTAGATTGATCTCCGAGATGA
CCCCAAAACTTCAGCAAGACTGAATGATATGAAAGAGATACTTACATATGTGGAACAAGGACAGAAACCAGCAAAAGAGA
GGTGCGTGCTGCTCTGTGGAATGTTCAGCTTTAACCCAGAAGGCATTGAAGACTGTTCTGATGAGCTGTAGGAGCCATTT
TAACTCCAAAGAAA

Alignment

ORF - retro_vpac_574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.74 %
• Parental protein coverage: 90.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TVTVRGKQHLLGLYDT-RQEDYNQLRPLSYPNTDVFLICFSVVNPASYHNIQEEWVPE-LKDCMPHVPYV
          .VT..GKQ.LLGL.DT.RQEDY..LRPLS.P.TDVFLICFSVVNPAS..N..EEWVPE.LK...PH.P..
Retrocopy SVTIGGKQYLLGLCDTVRQEDYDHLRPLSCPMTDVFLICFSVVNPASFQNVKEEWVPE>LKEYAPHAPFL

Parental  LIGTQIDLRDDPKTLARLLYMKEKPLTYEHGVKLAKAIGAQCYLECS--ALTQKGLKAVFDE-AILTIFH
          LIGT.IDLRDDPKT.ARL..MKE.....E.G.K.AK.....C.L.C........G.....DE.A...I..
Retrocopy LIGT*IDLRDDPKTSARLNDMKEILTYVEQGQKPAK---ERCVLLCGMFSFNPEGIEDCSDE<AVGAILT

Parental  PKK
          PKK
Retrocopy PKK

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_574 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_574 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001761	2 retrocopies	retro_dnov_192, retro_dnov_927,
Gorilla gorilla	ENSGGOG00000007948	1 retrocopy	retro_ggor_22,
Pan troglodytes	ENSPTRG00000006424	4 retrocopies	retro_ptro_1643, retro_ptro_2091, retro_ptro_2971, retro_ptro_910,
Vicugna pacos	ENSVPAG00000004859	2 retrocopies	retro_vpac_574 , retro_vpac_588,
Vicugna pacos	ENSVPAG00000006919	3 retrocopies	retro_vpac_13, retro_vpac_451, retro_vpac_542,