RetrogeneDB ID: retro_vpac_556

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_43552:3642..4492(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000006037
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OXCT1
• Ensembl ID: ENSVPAG00000002550
• Aliases: None
• Description: 3-oxoacid CoA transferase 1 [Source:HGNC Symbol;Acc:8527]

Sequence

>retro_vpac_556
ATGCCCCTGTGCAAAGCCGCCAGAACCTCAGGGGTGGAGGTGGAAGAAGTCGTGGATGCGGGGTCTTTTGCCCCAGAAGA
CATCCAGGTTCCTGACATTTATGTAGATCGTGTCATCCGGCGGGGGGAAATATGAGAAAAGAATTGAGTGTGTAACCATT
CGGAAAGAGGAAGATGAAAGGAGCAAGTCTACGGATGATGTAAGGACACAGATCATCAAGTGGGCAGCTCTGGAATTTGA
GGACGGCATGTATGCCAATTGGGCGTTGGGACCCCTCCTCTGGCCACCAGCTACATCAGCCCCAATATGACCGTTCATCT
TCACAGTGAACATGGAATCCTGGTCCTGGGTCTGTTTCCACCAAAAGATGGGGTGAATGCAGATCTCATCAACATGGGCA
AGTAAACAGCCACCCTTCTTCCTGGGGGTGTTTTTTCTCCAGCAATGTATCATATGCCACGATCTGAGGGGGCCACATCC
ACCTAACCTTCCTAGGAGCCATACAGGTTTCCAAGCATGGTCACCTGGCTAACTGAATGACACCTGGCAAGAAGGTGAGA
GGAATGGGGGGTGCGATGGACCTGGTGTCCAGCACCAAGACCAGAGTGGTGGTCCCCATGGAGCACTGCACCAAGGCCAA
GAGCCCAAAATCTTGGAGAAATGCACAATGCCACTGACTGGGAAGCGGTGCGTGGACCGCATCATCACTGAGAAGGCCGT
GTTTCACGTGCACAAGAAGAGAGGACTGACTCTGATTGAGTTCTGGGACGGCCTGATGGTGGAGGACATCCAGAGGAGCA
CGGGGAGCATCATTGCCCTCTCCCCGAATCTCAGACCCATGCAGCAGGTC

Alignment

ORF - retro_vpac_556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.89 %
• Parental protein coverage: 54.93 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LPMCKAAETTIVEVEEIVDIGSFAPEDIHIPKIYVHRLIK-GEKYEKRIERISIRKEEDVKTKSVKPGDN
          .P.CKAA.T..VEVEE.VD.GSFAPEDI..P.IYV.R.I..G.KYEKRIE...IRKEED...KS....D.
Retrocopy MPLCKAARTSGVEVEEVVDAGSFAPEDIQVPDIYVDRVIR>GGKYEKRIECVTIRKEEDERSKST---DD

Parental  VRERIIKRAALEFEDGMYAN-LGIGIPLLASNFISPNMTVHLQSENGVLGLGPYPLQNEVDADLINAGKE
          VR..IIK.AALEFEDGMYAN.LG.G.P.LA...ISPNMTVHL.SE.G.L.LG..P....V.ADLIN.GK.
Retrocopy VRTQIIKWAALEFEDGMYAN<LGVGTPPLATSYISPNMTVHLHSEHGILVLGLFPPKDGVNADLINMGK*

Parental  TVTVLPGAF-YFSSDES-AMIRGGHVNLTMLGAMQVSKYGDLANWMIPEKMVKGMDGAMDLVSSVQT-YE
          T.T.LPG....FSS..S.A.I.GGH..LT.LGA.QVSK.G.LAN.M.P.K.V.GM.GAMDLVSS..T...
Retrocopy TATLLPGGV<FFSSNVSYATI*GGHIHLTFLGAIQVSKHGHLAN*MTPGKKVRGMGGAMDLVSSTKTRVV

Parental  VTMKH-AKGNAHK-IMEKCTLPLTGKQCVNRIITEKAVFDVDSKKGLTLIELWEGLTVDDIKKSTGCDFA
          V.M.H..K....K.I.EKCT.PLTGK.CV.RIITEKAVF.V..K.GLTLIE.W.GL.V.DI..STG...A
Retrocopy VPMEHCTKAKSPK<ILEKCTMPLTGKRCVDRIITEKAVFHVHKKRGLTLIEFWDGLMVEDIQRSTGSIIA

Parental  VSPKLMPMRQI
          .SP.L.PM.Q.
Retrocopy LSPNLRPMQQV

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_556 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_556 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 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033186	2 retrocopies	retro_btau_1243, retro_btau_1302,
Dipodomys ordii	ENSDORG00000016318	1 retrocopy	retro_dord_282,
Equus caballus	ENSECAG00000018312	1 retrocopy	retro_ecab_511,
Homo sapiens	ENSG00000083720	1 retrocopy	retro_hsap_14,
Gorilla gorilla	ENSGGOG00000025087	1 retrocopy	retro_ggor_378,
Myotis lucifugus	ENSMLUG00000009431	1 retrocopy	retro_mluc_194,
Nomascus leucogenys	ENSNLEG00000016656	1 retrocopy	retro_nleu_2438,
Oryctolagus cuniculus	ENSOCUG00000009231	1 retrocopy	retro_ocun_672,
Otolemur garnettii	ENSOGAG00000009909	2 retrocopies	retro_ogar_2773, retro_ogar_2781,
Pongo abelii	ENSPPYG00000015428	2 retrocopies	retro_pabe_336, retro_pabe_478,
Pan troglodytes	ENSPTRG00000016829	1 retrocopy	retro_ptro_140,
Rattus norvegicus	ENSRNOG00000043094	2 retrocopies	retro_rnor_2177, retro_rnor_2256,
Ictidomys tridecemlineatus	ENSSTOG00000008271	1 retrocopy	retro_itri_747,
Tarsius syrichta	ENSTSYG00000013641	1 retrocopy	retro_tsyr_1455,
Tursiops truncatus	ENSTTRG00000004331	1 retrocopy	retro_ttru_875,
Vicugna pacos	ENSVPAG00000002550	1 retrocopy	retro_vpac_556 ,