RetrogeneDB ID: retro_vpac_468

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_2260:37078..38151(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTR3
• Ensembl ID: ENSVPAG00000009479
• Aliases: None
• Description: ARP3 actin-related protein 3 homolog (yeast) [Source:HGNC Symbol;Acc:170]

Sequence

>retro_vpac_468
GGACGGTAGCAAGCGTGTAGGGGGGATTGCGGCACCAGGCATACAAAACTAGAGTATGCTTGAAATACAGACCCACAGTT
TATCATCCCTGCTTGTACTACCATTAAGGAGTCAGCACAAGTGGGCGCTCAGGCTCAAAGGAGGGGTGATGAAAGGTGCT
GACATCCTAGAATTCCTCACTGGGGATGAAGCAGTAGAAAAACCTGCATATGCAACCAAGTGGCCGACCCGCCGCGGTGT
CTTGGGAGATCGGGACTTGATGGAAAGGTCTGCGGAGCAAGTGATCTTTTACACATTTAAGGGCAGAACCTGAGGCCATT
ATTTTCTCTTGACGGAGCCTCCACTGAGCGCTTCAGGAAACAGGGAGCGCACCGCTGACTAGCGTGTGAGCCCTTCGGCG
CTGCAGGCTTGCCCTCTGCTGCCCAGGCCGCTCTTGCCGTCGCTGCTTCCGGGGCCCCAGGACAAGGAGGAGAACGGACG
CGCACGGGGACGGGGACAGACGGTGGGGACGGTGGCACTCACGTCTTCCCTGTGGCTGAAGGGTATGTGACTGGCAGCTG
TATCAGCACATTCCAATCGCAGGACAAGACAGCATGTATTTTATTTGGCAGTTACTGAGAGACCGAGAAGTAGGAATTCC
CCCAGAGCAGTCCTTGGAAACTGCTACGGCAGTACAGGAGCGCTGTACTTGAGTCTGCCCAGATTTAGTAAAAGAATTTG
ACAAGTATGATACAGACGGATCAAAGTGGATTAAACAGTATACTGGATCAACGCTGTCTCAGAGAAAGAATTTTCCATTG
ATGTTGGGTAGGAGAGATTCTTGGGACCTGAAATTCTTTTTCGTCCAGAGTTTGCTAACCCAGACTTTACTCACCCATCT
CAGAAGTTGTAGATGGAGTGATTCAGAATTGTCCTGTGATGTCAGACGCCCTCTCTACGAGAGTATTGTCCTCTCTGGAG
ATTCAACCGTGCTCAGGGACTTTGGATGATGCTTGCAAAGAGATTTGAAAAGAACTGTAGATGCCAGGCTGAAATTAAAT
GAGGAATTGGGTGGTGGTAGACTGAAGCCAAAA

Alignment

ORF - retro_vpac_468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.3 %
• Parental protein coverage: 85.89 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  GRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRR-VMKGVDDLDFFIGDEAIEKPT
          GR..AC..DCGT..TKL.YA.NT.PQFIIP.C..IKESA.VG.QAQRR.VMKG.D.L.F..GDEA.EKP.
Retrocopy GR*QACRGDCGTRHTKLEYA*NTDPQFIIPACTTIKESAQVGAQAQRR>VMKGADILEFLTGDEAVEKPA

Parental  YATKWPIRHGIVEDWDLMERFMEQVIF-KYLRAEPE-DHYFLLTEPPLNTPENREYTAE-IMFESFNVPG
          YATKWP.R.G...D.DLMER..EQVIF...LRAEPE..HYFLLTEPPL....NRE.TA.....E.F...G
Retrocopy YATKWPTRRGVLGDRDLMERSAEQVIF>THLRAEPE<GHYFLLTEPPLSASGNRERTAD<LACEPFGAAG

Parental  LYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCI-KHIPIAGRDITYFIQQL
          L..A.QA.LA.AAS....Q.GERT.TGT..D.GDG.THV.PVAEGYV.GSCI..HIPIAG.D..YFI.QL
Retrocopy LPSAAQAALAVAASGAPGQGGERTRTGTGTDGGDGGTHVFPVAEGYVTGSCI<QHIPIAGQDSMYFIWQL

Parental  LRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWIKQYTG-INAISKKEFSIDVGYERF
          LRDREVGIPPEQSLETA.AV.ER...VCPDLVKEF.KYDTDGSKWIKQYTG.INA.S.KEFSIDVG.ERF
Retrocopy LRDREVGIPPEQSLETATAVQERCT*VCPDLVKEFDKYDTDGSKWIKQYTG<INAVSEKEFSIDVG*ERF

Parental  LGPEIFFHPEFANPDFT-QPISEVVDEVIQNCPI-DVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVD
          LGPEI.F.PEFANPDFT..PISEVVD.VIQNCP..DVRRPLY..IVLSG.ST..RDFG..LQRDLKRTVD
Retrocopy LGPEILFRPEFANPDFT<SPISEVVDGVIQNCPV<DVRRPLYESIVLSGDSTVLRDFG*CLQRDLKRTVD

Parental  ARLKLSEELSGGRLKPK
          ARLKL.EEL.GGRLKPK
Retrocopy ARLKLNEELGGGRLKPK

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_468 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_468 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003401	1 retrocopy	retro_btau_672,
Callithrix jacchus	ENSCJAG00000014091	4 retrocopies	retro_cjac_3602, retro_cjac_3813, retro_cjac_385, retro_cjac_4005,
Homo sapiens	ENSG00000115091	2 retrocopies	retro_hsap_1391, retro_hsap_4694,
Gorilla gorilla	ENSGGOG00000011346	1 retrocopy	retro_ggor_2921,
Mustela putorius furo	ENSMPUG00000010717	1 retrocopy	retro_mputfur_1275,
Mus musculus	ENSMUSG00000026341	1 retrocopy	retro_mmus_3653,
Nomascus leucogenys	ENSNLEG00000011619	2 retrocopies	retro_nleu_1077, retro_nleu_2364,
Pongo abelii	ENSPPYG00000012798	1 retrocopy	retro_pabe_3647,
Pan troglodytes	ENSPTRG00000012388	2 retrocopies	retro_ptro_3118, retro_ptro_955,
Vicugna pacos	ENSVPAG00000009479	1 retrocopy	retro_vpac_468 ,