RetrogeneDB ID: retro_vpac_603

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_6507:90047..90646(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A36
• Ensembl ID: ENSVPAG00000008292
• Aliases: None
• Description: solute carrier family 25 (pyrimidine nucleotide carrier ), member 36 [Source:HGNC Symbol;Acc:25554]

Sequence

>retro_vpac_603
AGGGCTTTGTTTAGAAGATCAGGCCCAAATGTAACGGGGGTGGCCTCTTTCAGAGCCACAGTCTTTGCTGATTATTTGAA
CTTCAGGGAAAGGCTGAATGGTGTATTTGATCTTGATTCTATCTGATACATGATTTCAGCTACAGTGGCCTGTTTTTACT
GCCATCACAGAAATCAATCACATTTGACTAATAAATTGGTTGCAGCTTCACACAAGGAAATATGGGGAAAAGCGACTTTT
GAATGGGTGCTTTTGAATGTATTCATAAAGCGTATTAGACAGGAGGCCAAAGAGGACTTTATAGGGGCATGGCTGCTTCC
CATGGGAGCCTATCAGAGACCACTATTCGCTTGGTTATTTGTGAAATTATTAAGCAAAAAACTACTGGACCAAAGGATTA
CTCTGACAGTGGAAGATGATGAAGAGTCTGTGGAATAAATATCAGATTTTGTGGGAAATGATGCTGGTGTCACCTCAGAA
ACATGCACCACAACCACAGTGCACCATCCACAGGAGGTCGTGAGAACAAGACCATGTCAAGAGGGCCTAAAGGAGAGAGA
TTTTTTCAGATACCACGTCTGGTTGTTCACAAGGAAGGC

Alignment

ORF - retro_vpac_603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.88 %
• Parental protein coverage: 75.95 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RSLFRGLGPNLVGVAPSRAIYFAAYSNCKEKLNGLFDPDSTQVHMISAAMAGF-TAITATNPIWLIKTRL
          R.LFR..GPN..GVA..RA..FA.Y.N..E.LNG.FD.DS....MISA..A.F.TAIT..N.I.LI...L
Retrocopy RALFRRSGPNVTGVASFRATVFADYLNFRERLNGVFDLDSI*-YMISATVACF>TAITEINHI*LINW-L

Parental  QLDAR-NRGEKR--MGAFECVRKVYQTDGLRGFYRGMSASYAGISETVIHFVIYESIKQ-KLLECKIAST
          QL..R.N.G.....MGAFEC..K.Y.T.G.RG.YRGM.AS....SET.I..VI.E.IKQ.KLL...I..T
Retrocopy QLHTR>NMGKSDF*MGAFECIHKAY*TGGQRGLYRGMAASHGSLSETTIRLVICEIIKQ>KLLDQRITLT

Parental  MENEEESVKEASDFVGMMLAAATSKTC-ATTIAYPHEVVRTRLREEGTKYRS-FFQTLSLLIQEEG
          .E..EESV...SDFVG...A..TS.TC..TT...P.EVVRTR...EG.K.R..FFQ...L....EG
Retrocopy VEDDEESVE*ISDFVGND-AGVTSETCTTTTVHHPQEVVRTRPCQEGLKERD<FFQIPRLVVHKEG

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_603 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_603 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000010094	1 retrocopy	retro_ecab_234,
Felis catus	ENSFCAG00000027489	1 retrocopy	retro_fcat_1680,
Macaca mulatta	ENSMMUG00000022153	1 retrocopy	retro_mmul_2243,
Mus musculus	ENSMUSG00000032449	1 retrocopy	retro_mmus_2007,
Oryctolagus cuniculus	ENSOCUG00000002085	1 retrocopy	retro_ocun_361,
Pteropus vampyrus	ENSPVAG00000007958	1 retrocopy	retro_pvam_719,
Sus scrofa	ENSSSCG00000011669	1 retrocopy	retro_sscr_871,
Tupaia belangeri	ENSTBEG00000001759	1 retrocopy	retro_tbel_3349,
Tursiops truncatus	ENSTTRG00000003288	2 retrocopies	retro_ttru_1146, retro_ttru_947,
Vicugna pacos	ENSVPAG00000008292	1 retrocopy	retro_vpac_603 ,