RetrogeneDB ID: retro_vpac_57

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1322:678066..678372(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBY1
• Ensembl ID: ENSVPAG00000001484
• Aliases: None
• Description: chibby homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:1307]

Sequence

>retro_vpac_57
ATGCCTTTCTTTGGGAATACATTCAGTCCGAAGAAGACGCCCCCTCGGAAGTCGGCTTCTCTCTCCAGCCTGCATAATTT
GGATCGGTCAACCTGGGAGTGGAGCTGGGTCCTGACTACGGAACCCCCACTATGAACCTGGCGGGGCAAAGCCTGAAGTT
TGAAAACGGCCAGTTGATAGCAGAGACAGGGATTAGTCGGGGTGTGGACCGGAGGGAGGCTCAGCGCCTCCGGAGACGGA
ACCAGCAGTTGGAGGAAGAAACAATCTCTTGCGGCTGAGGTGGACATCCTGCTGGACATGGTGAGC

Alignment

ORF - retro_vpac_57 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.05 %
• Parental protein coverage: 81.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPLFGNTFSPKKTPPRKSASLSNLHNLDRSTRE-VELGLDYGTPPPMNPAGKSLKFENGPWIAETGISGG
          MP.FGNTFSPKKTPPRKSASLS.LHNLDRST.E.VELG.DYGTP..MN.AG.SLKFENG..IAETGIS.G
Retrocopy MPFFGNTFSPKKTPPRKSASLSSLHNLDRSTWE<VELGPDYGTPT-MNLAGQSLKFENGQLIAETGISRG

Parental  VDRREAQRLRRRNQQLEEE-NNLLRLK-VDILLDMLS
          VDRREAQRLRRRNQQLEEE.NNLLRL..VDILLDM.S
Retrocopy VDRREAQRLRRRNQQLEEE<NNLLRLR<VDILLDMVS

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_57 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_57 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001384	2 retrocopies	retro_cfam_1396, retro_cfam_852,
Dasypus novemcinctus	ENSDNOG00000010982	1 retrocopy	retro_dnov_875,
Homo sapiens	ENSG00000100211	1 retrocopy	retro_hsap_2344,
Gorilla gorilla	ENSGGOG00000013226	1 retrocopy	retro_ggor_1781,
Myotis lucifugus	ENSMLUG00000003757	2 retrocopies	retro_mluc_1128, retro_mluc_2608,
Mustela putorius furo	ENSMPUG00000013150	1 retrocopy	retro_mputfur_1186,
Nomascus leucogenys	ENSNLEG00000015153	1 retrocopy	retro_nleu_349,
Otolemur garnettii	ENSOGAG00000028533	1 retrocopy	retro_ogar_1072,
Pan troglodytes	ENSPTRG00000014373	1 retrocopy	retro_ptro_1716,
Vicugna pacos	ENSVPAG00000001484	1 retrocopy	retro_vpac_57 ,