RetrogeneDB ID: retro_vpac_625

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_827:201986..202732(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACAA2
• Ensembl ID: ENSVPAG00000012121
• Aliases: None
• Description: acetyl-CoA acyltransferase 2 [Source:HGNC Symbol;Acc:83]

Sequence

>retro_vpac_625
TTGGAAGGTTCTTTGTGAGCAGCATGAATAGATCAGCATGTCCAACTCCCCCATGGGAATTACTGCAGAGAATTTTGCTG
CAAAACATAAAATAAGCAGAAAAGAATGTAACAAATCCATCCCATTGTCACAGCAGAGATGGAAAGCTGCTAATGATGCT
GGTCACTTTAATAATGAGATGGTACCAATTCAGGTAAAGATGAAGAAGGGAAACAAGCAGTGCAAGTAAGAGCAGGCTTG
GTCCCAAACAAGCCTGGAGCAGCTAAATAAACTTCCTCCAGTTTTCAAGGAAGAAGGGCCAACATTGCAAGGAATGTACC
AAGCATATCTAATGTTTTCATAGCTAGTGAAGATGCTGTTAAAGGCATAACTTCACACTGGCAAGAATCGTGGGCTATTT
TGTATCTAGATGTGATCTATCTATTGTAGATAATATTGGTCTTGTCCCTGCTACCAATGAGGCACTAAAGAAAACAAGAT
TGAGTCTTGAAGACATGGATTTGGTAGAGGTGAATGAAGATTTTGGCCCCTGGAATTTAGCAGCTGAGAAGAGCTTGGAT
CTCGACCCAAGTAGAACCAACGTACAAGGAAGAGGCATTATTTGGGATCAGCCACTGGGAGGAACTGGATCAAGAATTAT
TGCACACCTGGTTCATGAATTAAGATGTGGAGGTGGAAAATATACAGTTGCATCAGCTTGCACTGGAGCTGGCCAGAGTA
TCACACTGATCACTCAGAGCACAGCC

Alignment

ORF - retro_vpac_625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.95 %
• Parental protein coverage: 64.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LEDSLWMSLTDQHIQ-TPMAITAENLAVKHKINREDCDKYALQSQQRWKAANDAGYFHNEMAPIEVKTKK
          LE.SL.....DQH.Q..PM.ITAEN.A.KHKI.R..C.K....SQQRWKAANDAG.F.NEM.PI.VK.KK
Retrocopy LEGSL*AA*IDQHVQ>SPMGITAENFAAKHKISRKECNKSIPLSQQRWKAANDAGHFNNEMVPIQVKMKK

Parental  GKQTMQVDEHPRPQTTLEQLNKLPPVFKKEGTVTAG-NASGISDGAGAVIIASEDAVK-KHNFTPLARIV
          G.......E....QT.LEQLNKLPPVFK.EG....G.N...IS.....V.IASEDAVK..HNFT.LARIV
Retrocopy GNKQCK*-EQAWSQTSLEQLNKLPPVFKEEGPTLQG<NVPSISN----VFIASEDAVK<RHNFT-LARIV

Parental  GYFVSGCDPSIM-GIGPVPAISGALKKTGLSLKDMDLVEVNEAFAPQYLAVEKSLDLDPSKTNVNGGAIA
          GYFVS.CD.SI...IG.VPA...ALKKT.LSL.DMDLVEVNE.F.P..LA.EKSLDLDPS.TNV.G..I.
Retrocopy GYFVSRCDLSIVDNIGLVPATNEALKKTRLSLEDMDLVEVNEDFGPWNLAAEKSLDLDPSRTNVQGRGII

Parental  LGHPLGGSGSRITTHLVHELRRRGGRYAVGSACIGGGQGIAVIIQSTA
          ...PLGG.GSRI..HLVHELR..GG.Y.V.SAC.G.GQ.I..I.QSTA
Retrocopy WDQPLGGTGSRIIAHLVHELRCGGGKYTVASACTGAGQSITLITQSTA

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_625 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_625 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009411	1 retrocopy	retro_amel_602,
Equus caballus	ENSECAG00000019394	1 retrocopy	retro_ecab_454,
Homo sapiens	ENSG00000167315	1 retrocopy	retro_hsap_4829,
Gorilla gorilla	ENSGGOG00000012552	1 retrocopy	retro_ggor_3011,
Myotis lucifugus	ENSMLUG00000022960	1 retrocopy	retro_mluc_654,
Nomascus leucogenys	ENSNLEG00000011576	1 retrocopy	retro_nleu_2706,
Ochotona princeps	ENSOPRG00000007567	2 retrocopies	retro_opri_1224, retro_opri_348,
Pan troglodytes	ENSPTRG00000010016	1 retrocopy	retro_ptro_3214,
Vicugna pacos	ENSVPAG00000012121	1 retrocopy	retro_vpac_625 ,