RetrogeneDB ID: retro_vpac_475

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_233265:105..789(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLIC4
• Ensembl ID: ENSVPAG00000007699
• Aliases: None
• Description: chloride intracellular channel 4 [Source:HGNC Symbol;Acc:13518]

Sequence

>retro_vpac_475
GCTGGCAGTGATGGTGAAAGCATAGGAAACTGTCCCTTTTCCCAGAGGCTCTTCATGATTCTTTGGCTTAAAGGAGTTGT
GTTTAGTGTCACAACTGTTGACCTGAAAAGGAAGCCTGCAGACCTGCAGAACTTGGCTCCGGGGACCCACCCACCATTTA
TAACGTTCAGCAAGGAGGTCAAAACGGATGTAAATAAGATTGAAGAATTTCTTGAAGAAGTCTTATGCCCTCCCAAGTAC
TTAAAGCTTTCACCAAAACACCCAGAATCAAATACTGCTGGAATGGACATCTTTGCCAAATTCTCTGCATATATCAAGAA
TTCAAGGCCAGAGGCTAATGAAGCATTGGAGAGGGGTCTCTTGAAGACACTGCAGAAACTGGATGAATATCTGAATTCTC
CCCTCCCTGATGAAATTGATGAGAATAGTATGGAGGACATTAAGTTTTCCACATGTAAATTTCTGGATGGCAATGAAATG
ACACTAGCTGATTGCAACCTGCTGCCCAAACTGCACGTTGTCAAGGTGGTGGCCAAAAAATATCACAACTTTGATATTCC
AAAAGGAATGACGGGCATCTGGAGATACTTAACTAATGCTTATAGTAGGGATGAGTTCACCAATACCTGCCCCAGTGATA
AGGAGGTTGAAATAGCATATAGTGATGTCGCCAAAAGACTTACC

Alignment

ORF - retro_vpac_475 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.37 %
• Parental protein coverage: 99.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGSDGESIGNCPFSQRLFMILWLKGVVFSVTTVDLKRKPADLQNLAPGTHPPFITFNNEVKTDVNKIEEF
          AGSDGESIGNCPFSQRLFMILWLKGVVFSVTTVDLKRKPADLQNLAPGTHPPFITF..EVKTDVNKIEEF
Retrocopy AGSDGESIGNCPFSQRLFMILWLKGVVFSVTTVDLKRKPADLQNLAPGTHPPFITFSKEVKTDVNKIEEF

Parental  LEEVLCPPKYLKLSPKHPESNTAGMDIFAKFSAYIKNSRPEANEALERGLLKTLQKLDEYLNSPLPDEID
          LEEVLCPPKYLKLSPKHPESNTAGMDIFAKFSAYIKNSRPEANEALERGLLKTLQKLDEYLNSPLPDEID
Retrocopy LEEVLCPPKYLKLSPKHPESNTAGMDIFAKFSAYIKNSRPEANEALERGLLKTLQKLDEYLNSPLPDEID

Parental  ENSMEDVKFSTRKFLDGNEMTLADCNLLPKLHIVKVVAKKYRNFDIPKGMTGIWRYLTNAYSRDEFTNTC
          ENSMED.KFST.KFLDGNEMTLADCNLLPKLH.VKVVAKKY.NFDIPKGMTGIWRYLTNAYSRDEFTNTC
Retrocopy ENSMEDIKFSTCKFLDGNEMTLADCNLLPKLHVVKVVAKKYHNFDIPKGMTGIWRYLTNAYSRDEFTNTC

Parental  PSDKEVEIAYSDVAKRLT
          PSDKEVEIAYSDVAKRLT
Retrocopy PSDKEVEIAYSDVAKRLT

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_475 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_475 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 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007591	10 retrocopies	retro_chof_1284, retro_chof_1401, retro_chof_1446, retro_chof_1654, retro_chof_2177, retro_chof_2673, retro_chof_784, retro_chof_789, retro_chof_808, retro_chof_947,
Callithrix jacchus	ENSCJAG00000020833	2 retrocopies	retro_cjac_1713, retro_cjac_461,
Cavia porcellus	ENSCPOG00000004010	1 retrocopy	retro_cpor_1490,
Homo sapiens	ENSG00000169504	2 retrocopies	retro_hsap_4143, retro_hsap_4678,
Gorilla gorilla	ENSGGOG00000005586	2 retrocopies	retro_ggor_1579, retro_ggor_2783,
Macropus eugenii	ENSMEUG00000008789	1 retrocopy	retro_meug_780,
Macaca mulatta	ENSMMUG00000002416	2 retrocopies	retro_mmul_1183, retro_mmul_2488,
Mus musculus	ENSMUSG00000037242	2 retrocopies	retro_mmus_2259, retro_mmus_945,
Nomascus leucogenys	ENSNLEG00000008997	3 retrocopies	retro_nleu_1457, retro_nleu_1785, retro_nleu_2168,
Otolemur garnettii	ENSOGAG00000014620	1 retrocopy	retro_ogar_2672,
Pongo abelii	ENSPPYG00000001715	3 retrocopies	retro_pabe_219, retro_pabe_3466, retro_pabe_3632,
Pan troglodytes	ENSPTRG00000000350	3 retrocopies	retro_ptro_2816, retro_ptro_3107, retro_ptro_396,
Pteropus vampyrus	ENSPVAG00000005838	1 retrocopy	retro_pvam_812,
Ictidomys tridecemlineatus	ENSSTOG00000002184	1 retrocopy	retro_itri_52,
Tarsius syrichta	ENSTSYG00000008978	1 retrocopy	retro_tsyr_252,
Vicugna pacos	ENSVPAG00000007699	1 retrocopy	retro_vpac_475 ,