RetrogeneDB ID: retro_vpac_211

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2868:1893040..1893387(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RALA
• Ensembl ID: ENSVPAG00000002810
• Aliases: None
• Description: v-ral simian leukemia viral oncogene homolog A (ras related) [Source:HGNC Symbol;Acc:9839]

Sequence

>retro_vpac_211
GACTCACCTGGGCAGGAGGACTACTCTGCAATTAGAGACAACTTCTTCCACAGTGGGAGGGTTTCCTCTGTGTTTTCTCT
ATTACAGAAATTGAATCTTTTGCAGCCACAGCTGGTCTCAGGGAGCAGATGTTCAGAGTGAAAGAAGATGAGAATGTTTC
ATTTTTGCTGGTTGGTTACAAATCAGATTTAGGAGATAAAACGAAGGTTTATGTAAAGGAGGCGAAAACCAGAGCCAGTC
ACTGGAATGTTAACGATGTGGAAACATCTGCTAAAATGCCAGCTAATGTCAACAAGGTATTTTTTGATTTAATGAGGGAA
TTTCAAGCCAGAAAATAGGAGACGTCG

Alignment

ORF - retro_vpac_211 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.07 %
• Parental protein coverage: 56.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DTAGQEDYAAIRDNYFRSG-EGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQ
          D..GQEDY.AIRDN.F.SG.EGFLCVFSITE.ESFAATA..REQ..RVKEDENV.FLLVG.KSDL.DK..
Retrocopy DSPGQEDYSAIRDNFFHSG<EGFLCVFSITEIESFAATAGLREQMFRVKEDENVSFLLVGYKSDLGDKTK

Parental  VSVEEAKTRADQWNVNYVETSAKTRANVDKVFFDLMREIRARKMEDS
          V.V.EAKTRA..WNVN.VETSAK..ANV.KVFFDLMRE..ARK.E.S
Retrocopy VYVKEAKTRASHWNVNDVETSAKMPANVNKVFFDLMREFQARK*ETS

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_211 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_211 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 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007630	1 retrocopy	retro_cjac_3313,
Dasypus novemcinctus	ENSDNOG00000017413	1 retrocopy	retro_dnov_573,
Homo sapiens	ENSG00000006451	2 retrocopies	retro_hsap_1136, retro_hsap_3707,
Macropus eugenii	ENSMEUG00000000259	1 retrocopy	retro_meug_1638,
Macaca mulatta	ENSMMUG00000016059	2 retrocopies	retro_mmul_1706, retro_mmul_882,
Nomascus leucogenys	ENSNLEG00000003055	1 retrocopy	retro_nleu_935,
Pongo abelii	ENSPPYG00000017619	3 retrocopies	retro_pabe_3148, retro_pabe_3208, retro_pabe_945,
Pan troglodytes	ENSPTRG00000019108	1 retrocopy	retro_ptro_2511,
Sus scrofa	ENSSSCG00000029741	1 retrocopy	retro_sscr_634,
Ictidomys tridecemlineatus	ENSSTOG00000020292	2 retrocopies	retro_itri_1314, retro_itri_1315,
Vicugna pacos	ENSVPAG00000000931	2 retrocopies	retro_vpac_283, retro_vpac_408,
Vicugna pacos	ENSVPAG00000002810	1 retrocopy	retro_vpac_211 ,
Vicugna pacos	ENSVPAG00000010033	1 retrocopy	retro_vpac_491,