RetrogeneDB ID: retro_vpac_180

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_245:1300310..1300589(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNIH4
• Ensembl ID: ENSVPAG00000012521
• Aliases: None
• Description: cornichon homolog 4 (Drosophila) [Source:HGNC Symbol;Acc:25013]

Sequence

>retro_vpac_180
GTGGTGGCGTTGGTCTCTCTGCTCGGCTGTTACACGCTCATCTTCCTCTCAGTGTGCTTCATAATTACAGAGTCTTGTTT
AGAGTGTGATTACGTTCATGTGAGATCATGTTACTCGAAACTGAACCAGTGGGTGATCCAGAAGGGGCTGGCCATACCGT
TATCACTGTATTAATGCTCATTTCATTGCACTGCTTCATCTTCCTTCACAACCTGCCTGTCGCCATTTGGAATATAATAC
CAGTTCATTAAGGTGCCAAGTGGTAACACGGGAGCATTT

Alignment

ORF - retro_vpac_180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.53 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVFVFSLLDCCALIFLSVYFI-TLSDLECDYINARSCCSKLNKWVI-PEVVGHTIITVLMLISLHWFIFL
          VV...SLL.C..LIFLSV.FI.T.S.LECDY...RSC.SKLN.WVI.PE..GHT.ITVLMLISLH.FIFL
Retrocopy VVALVSLLGCYTLIFLSVCFIITESCLECDYVHVRSCYSKLNQWVI<PEGAGHTVITVLMLISLHCFIFL

Parental  LNLPVATWNI-YRLIMVPSGNMGVF
          .NLPVA.WNI.Y..I.VPSGN.G.F
Retrocopy HNLPVAIWNI>YQFIKVPSGNTGAF

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_180 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_180 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 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006544	1 retrocopy	retro_chof_327,
Callithrix jacchus	ENSCJAG00000008013	1 retrocopy	retro_cjac_2474,
Cavia porcellus	ENSCPOG00000007310	1 retrocopy	retro_cpor_777,
Dasypus novemcinctus	ENSDNOG00000007093	1 retrocopy	retro_dnov_1669,
Homo sapiens	ENSG00000143771	1 retrocopy	retro_hsap_3656,
Gorilla gorilla	ENSGGOG00000005708	1 retrocopy	retro_ggor_2470,
Myotis lucifugus	ENSMLUG00000003134	1 retrocopy	retro_mluc_1314,
Macaca mulatta	ENSMMUG00000009936	1 retrocopy	retro_mmul_1796,
Nomascus leucogenys	ENSNLEG00000013549	1 retrocopy	retro_nleu_514,
Ochotona princeps	ENSOPRG00000001589	1 retrocopy	retro_opri_749,
Pongo abelii	ENSPPYG00000000183	1 retrocopy	retro_pabe_3003,
Pan troglodytes	ENSPTRG00000002025	1 retrocopy	retro_ptro_2481,
Pteropus vampyrus	ENSPVAG00000014034	1 retrocopy	retro_pvam_692,
Ictidomys tridecemlineatus	ENSSTOG00000027396	2 retrocopies	retro_itri_1502, retro_itri_1552,
Vicugna pacos	ENSVPAG00000012521	2 retrocopies	retro_vpac_180 , retro_vpac_215,