RetrogeneDB ID: retro_vpac_489

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_24156:3934..4434(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: U2AF1
• Ensembl ID: ENSVPAG00000002856
• Aliases: None
• Description: U2 small nuclear RNA auxiliary factor 1 [Source:HGNC Symbol;Acc:12453]

Sequence

>retro_vpac_489
GCCGTGAGCGATGTCGAGATGCAGGAGCACTATGATGAGTTTTTTGAGGAGATTTTCACGGAGATGGAGAAGTACGGAGA
GGTGAAGGAGATGAACGTCTGTGACAACCTTGGAGAGCACCTCGTCGGGAATGTGTACGTGAAGTTTCGCCGTGAAGGGG
ATGCAGAAAAGGCCGTGATTGACTTGAACAACCGCTGGCTTAACGGGCAGCCTATCCATGCCGAGCTCTCCCCTGTGACC
GACTTCAGAGAAGCCTGCTGCCGGCAGTACGAGATGGGGGAGTGCACGCGAGGAGGCTTCTGCAACTTCATGCATCTGAA
GCCCATTTCTCGGGAGCTGCGGCGGGAGTTGTACGGGCGCCGTCGCAAGAAACATAGGTCGAGGTCCCGGTCCCGGGAGC
GTCGCTCTCGGTCGAGAGACGCGGTCGAGGTGGCGGCGGCGGCGGGGGACGGGAGCGCGACAGAAGGCGGTCGCGAGATG
GGGAGAGATCGAGGCGGTTC

Alignment

ORF - retro_vpac_489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.44 %
• Parental protein coverage: 76.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNG
          AVSDVEMQEHYDEFFEE.FTEME.KYGEV.EMNVCDNLG.HLVGNVYVKFRRE.DAEKAVIDLNNRW.NG
Retrocopy AVSDVEMQEHYDEFFEEIFTEME-KYGEVKEMNVCDNLGEHLVGNVYVKFRREGDAEKAVIDLNNRWLNG

Parental  QPIHAELSPVTDFREACCRQYEMGECTRGGFCNFMHLKPISRELRRE-YGRRRKKHRSRSRSRERRSRSR
          QPIHAELSPVTDFREACCRQYEMGECTRGGFCNFMHLKPISRELRRE.YGRRRKKHRSRSRSRERRSRSR
Retrocopy QPIHAELSPVTDFREACCRQYEMGECTRGGFCNFMHLKPISRELRRELYGRRRKKHRSRSRSRERRSRSR

Parental  D-RGRGGGGGGGGGGRERDRRRSRDRERSGRF
          D.RGRGGGGGGG...RERDRRRSRD.ERS.RF
Retrocopy D<RGRGGGGGGG---RERDRRRSRDGERSRRF

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_489 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_489 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
Microcebus murinus	ENSMICG00000013835	1 retrocopy	retro_mmur_614,
Otolemur garnettii	ENSOGAG00000016504	1 retrocopy	retro_ogar_241,
Pan troglodytes	ENSPTRG00000013952	2 retrocopies	retro_ptro_1000, retro_ptro_549,
Tupaia belangeri	ENSTBEG00000000453	2 retrocopies	retro_tbel_2115, retro_tbel_963,
Vicugna pacos	ENSVPAG00000002856	1 retrocopy	retro_vpac_489 ,