RetrogeneDB ID: retro_vpac_519

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_29442:5926..6211(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL8B
• Ensembl ID: ENSVPAG00000012114
• Aliases: None
• Description: ADP-ribosylation factor-like 8B [Source:HGNC Symbol;Acc:25564]

Sequence

>retro_vpac_519
TCAGTGGGCTTCAACTTGACGAAAGTAGCTAAAGGTAACATCACAATAAAGAGTTGGAACATAGGAGGACAGCCCTGCTT
CTAGAGCATGTGGGAACGATACTGCAGAGGAGTCAGGGCTGTTGTTTACATGATAGATGCTGCAGATCTCGAAAAGAGAG
AATCCTCTTGAAGTGAACTACATAATCTTCTAGATAAACCACAGTTACAAGGAATTCCAATACTAGTTCTTGGAAGCAAG
AGAGATCTTCCTAATGTCTTGGATGAGAAAGAGCTAATTGAGAAA

Alignment

ORF - retro_vpac_519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.95 %
• Parental protein coverage: 65.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TVGFNMRKVTKGNVTIKIWDIGGQPRFRSMWERYCRGVNAIVYMIDAADREKIEASRNELHNLLDKPQLQ
          .VGFN..KV.KGN.TIK.W.IGGQP.F.SMWERYCRGV.A.VYMIDAAD.EK.E.S..ELHNLLDKPQLQ
Retrocopy SVGFNLTKVAKGNITIKSWNIGGQPCF*SMWERYCRGVRAVVYMIDAADLEKRESS*SELHNLLDKPQLQ

Parental  GIPVLVLGNKRDLPNALDEKQLIEK
          GIP.LVLG.KRDLPN.LDEK.LIEK
Retrocopy GIPILVLGSKRDLPNVLDEKELIEK

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_519 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_519 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007757	2 retrocopies	retro_chof_1196, retro_chof_2630,
Callithrix jacchus	ENSCJAG00000015842	2 retrocopies	retro_cjac_1120, retro_cjac_470,
Homo sapiens	ENSG00000134108	1 retrocopy	retro_hsap_361,
Gallus gallus	ENSGALG00000008314	1 retrocopy	retro_ggal_25,
Gorilla gorilla	ENSGGOG00000004952	1 retrocopy	retro_ggor_373,
Microcebus murinus	ENSMICG00000000244	2 retrocopies	retro_mmur_1220, retro_mmur_1239,
Mustela putorius furo	ENSMPUG00000017035	2 retrocopies	retro_mputfur_1390, retro_mputfur_541,
Oryctolagus cuniculus	ENSOCUG00000014090	2 retrocopies	retro_ocun_1942, retro_ocun_751,
Pongo abelii	ENSPPYG00000013694	1 retrocopy	retro_pabe_343,
Tarsius syrichta	ENSTSYG00000001724	1 retrocopy	retro_tsyr_2150,
Vicugna pacos	ENSVPAG00000003224	4 retrocopies	retro_vpac_281, retro_vpac_328, retro_vpac_6, retro_vpac_78,
Vicugna pacos	ENSVPAG00000003891	1 retrocopy	retro_vpac_459,
Vicugna pacos	ENSVPAG00000012114	2 retrocopies	retro_vpac_495, retro_vpac_519 ,