RetrogeneDB ID: retro_vpac_450

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_204989:669..957(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM14A
• Ensembl ID: ENSVPAG00000004486
• Aliases: None
• Description: transmembrane protein 14A [Source:HGNC Symbol;Acc:21076]

Sequence

>retro_vpac_450
ATTGGCTTTGGCTATGCAGCACTGGTTGCTTCCGGTGGGATCATTGGCTATGCAAAAGCAGGTAGTGTCCCATCCCTGGC
TGCTGGGCTCTTCTTCGGGGGTTTAGCGGGCCTGGGTGCCTATCAGCTGTCTCAGGATCCAAGGAACATTTGGGTTTTCT
TAGCTACATCTGGAACCTTGGCTGGCATCATGGGGATGAGATTCTACCACTCTGGAAAGTTTATGCCTGCAGGCTTAATT
GCGGGTGCCAGTTTGCTGATGGTCGCCAAACTTGGAATTAGTGTGTTG

Alignment

ORF - retro_vpac_450 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.25 %
• Parental protein coverage: 96.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VGFGYAALVTFGSILGYKRRGGVPSLIGGLFVGFLAGYGAYRVSNDKRDVKVSLFTAFFLATIMGVRFKR
          .GFGYAALV..G.I.GY...G.VPSL..GLF.G.LAG.GAY..S.D.R...V.L.T...LA.IMG.RF..
Retrocopy IGFGYAALVASGGIIGYAKAGSVPSLAAGLFFGGLAGLGAYQLSQDPRNIWVFLATSGTLAGIMGMRFYH

Parental  SKKIMPAGLVAGLSLMMILRLVLLLL
          S.K.MPAGL.AG.SL.M...L....L
Retrocopy SGKFMPAGLIAGASLLMVAKLGISVL

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_450 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_450 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005206	1 retrocopy	retro_btau_505,
Latimeria chalumnae	ENSLACG00000012581	1 retrocopy	retro_lcha_64,
Microcebus murinus	ENSMICG00000016339	1 retrocopy	retro_mmur_211,
Mustela putorius furo	ENSMPUG00000008935	2 retrocopies	retro_mputfur_157, retro_mputfur_586,
Sorex araneus	ENSSARG00000005516	1 retrocopy	retro_sara_307,
Tupaia belangeri	ENSTBEG00000011162	1 retrocopy	retro_tbel_1562,
Tarsius syrichta	ENSTSYG00000004269	1 retrocopy	retro_tsyr_1783,
Tursiops truncatus	ENSTTRG00000015237	1 retrocopy	retro_ttru_1442,
Vicugna pacos	ENSVPAG00000004486	1 retrocopy	retro_vpac_450 ,