RetrogeneDB ID: retro_vpac_219

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2941:28377..28941(+)
• Located in intron of: ENSVPAG00000003374

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNE1
• Ensembl ID: ENSVPAG00000001390
• Aliases: None
• Description: cyclin E1 [Source:HGNC Symbol;Acc:1589]

Sequence

>retro_vpac_219
GAGATGAAATTGTTGCCATTAATCATTATGAAGGCACTTAAGTGGCATTAAGGTCCCCTAACCATTGTGTCCCGGCTGAA
TGTATACATGCAGATTGTGTATCTAAATGATTTTTATGAAGTGCTCCTGTCACAGTATCCTCAGCAAATTTCCAAACAGA
CTGCAGAGCTTTTAGATCTCCGTGTCCTGGATGTTGGCCACTTAGAATTTTCCTATGGTTTGCTTGCTGCTTCTGCCTTG
TATCATTTCTCTTCATCAGAACTGATGCAAAATCTTTCAGGGTGTCAGTGGTGTGATACAGAGAAGTGTGTCAAGTGGAT
GGTTCCATTTGCCATGGTTATAAGGGAGCCAGGAAGTTAAAAACTTAAGCACTTCAAGGGGAATTTCTGAAGATGCACAT
AGCATCCAGACCCTATAAACAGCTTGGATTTGCTGGACAAAGCACAAGCAAAGAAAGCCATATTGTCTGAAGAAAATAGG
ATTTCTCCTCTCCCCACGGAGTCCTCACCTCCTCCCACCCCCAAACAGAGCAGTAAGAAGCAGAGCGGTGGGCAGGGAAC
AGCA

Alignment

ORF - retro_vpac_219 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.96 %
• Parental protein coverage: 53.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EILTMELIIMKALKWHLSPLTIVSWLNVYMQVAYLNDFYEVLLPQYPQQVFIQIAELLDLCVLDVGCLEF
          E.....LIIMKALKWH..PLTIVS.LNVYMQ..YLNDFYEVLL.QYPQQ...Q.AELLDL.VLDVG.LEF
Retrocopy EMKLLPLIIMKALKWH*GPLTIVSRLNVYMQIVYLNDFYEVLLSQYPQQISKQTAELLDLRVLDVGHLEF

Parental  PYGVLAASALYHFSSSELMQKVSGYQWCDIEKCVKWMVPFAMVIRETGSSKLKHF-RGVPAEDAHNIQT-
          .YG.LAASALYHFSSSELMQ..SG.QWCD.EKCVKWMVPFAMVIRE.GS.KLKHF.RG...EDAH.IQT.
Retrocopy SYGLLAASALYHFSSSELMQNLSGCQWCDTEKCVKWMVPFAMVIREPGS*KLKHF>RGI-SEDAHSIQT<

Parental  HINSLDLLDKAQAKKAI-SEENRISPLPSGVLTPP---QSSKKQSSEQETA
          .INSLDLLDKAQAKKAI.SEENRISPLP.....PP...QSSKKQS..Q.TA
Retrocopy PINSLDLLDKAQAKKAILSEENRISPLPTESSPPPTPKQSSKKQSGGQGTA

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_219 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_219 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001857	2 retrocopies	retro_cjac_3786, retro_cjac_3996,
Oryctolagus cuniculus	ENSOCUG00000009143	1 retrocopy	retro_ocun_676,
Otolemur garnettii	ENSOGAG00000006217	2 retrocopies	retro_ogar_3309, retro_ogar_930,
Sus scrofa	ENSSSCG00000002855	1 retrocopy	retro_sscr_232,
Vicugna pacos	ENSVPAG00000001390	1 retrocopy	retro_vpac_219 ,