RetrogeneDB ID: retro_vpac_470

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_2266:125184..125757(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000004276
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FBXO27
• Ensembl ID: ENSVPAG00000004974
• Aliases: None
• Description: F-box protein 27 [Source:HGNC Symbol;Acc:18753]

Sequence

>retro_vpac_470
GCGCGGACCACGCCAGTCTGTCTCCTCAGCCGCTTCTGCGCGCGCAGACCGGTAAGACGCAACCTGCTGTGCAAACCTGG
GAGAGAAGAAAGCCTCCAGCAATTAATGGTGGTGCCGGATTTGGACGAACTGGCTGTGGAGGAAAACTGGGAGGTTATGC
CTAGGACTCCTTTGCAGATCTGCTTCTGGTCTCCCTACAGGTGGTATCACAAGCAGCAGCGAGTGTTGGACCTGGAGGAG
GAGGGTTTCCGGCCGGAACTTCTGGACAGTGTCAAGATTGAGGTTTGTTTCTCTGACTGGTGGACAGACCAGCAAGACAT
TAACACTATATATCAGCTAACTATCCAACTTCTAGATGCCAACCAGGTTGTCCTGGGTCATTTCTCTTCTGTGCCTTTCC
CCATCCAGCAGGGGAGAAAGACTGTCTTCTATCAGGTCAGCCATGTGTTCTCCAACCTCAAGACAGGCGTCTGCTTTGTG
TCTCTTGAACTCTGGGTCCATGAAAAGGAGTTCTGCTCCGAACATTATGGAATCTATCTGCCCGACTCCAGTGTGATTGT
GCAGGGCCGTCTG

Alignment

ORF - retro_vpac_470 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.31 %
• Parental protein coverage: 87.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADAASACLLGRFCARGPIGRNLLRNPKSKNGFQKWMRLSDGDDWSLQESR--IPGLPYLTYLLSAYRCCY
          A.....CLL.RFCAR.P..RNLL..P......Q..M...D.D.....E.....P..P......S.YR...
Retrocopy ARTTPVCLLSRFCARRPVRRNLLCKPGREESLQQLMVVPDLDELAVEENWEVMPRTPLQICFWSPYRWYH

Parental  RK-KVLDLEEEGFWPELLDSGKMEIYVSHRRTDRQGTDCIYQLIVRLLDANQAVLDHFSPKPFPIRKWRN
          ....VLDLEEEGF.PELLDS.K.E...S...TD.Q....IYQL...LLDANQ.VL.HFS..PFPI...R.
Retrocopy KQQRVLDLEEEGFRPELLDSVKIEVCFSDWWTDQQDINTIYQLTIQLLDANQVVLGHFSSVPFPIQQGRK

Parental  SVSHHVSHVFSNLKKGVRFVSFEHWMWDLEFCSEQCGVYLTNSSVIVSIRL
          .V...VSHVFSNLK.GV.FVS.E.W....EFCSE..G.YL..SSVIV..RL
Retrocopy TVFYQVSHVFSNLKTGVCFVSLELWVHEKEFCSEHYGIYLPDSSVIVQGRL

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_470 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_470 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004611	1 retrocopy	retro_cpor_1475,
Mustela putorius furo	ENSMPUG00000017748	3 retrocopies	retro_mputfur_1473, retro_mputfur_465, retro_mputfur_965,
Ictidomys tridecemlineatus	ENSSTOG00000027765	1 retrocopy	retro_itri_401,
Tupaia belangeri	ENSTBEG00000010522	1 retrocopy	retro_tbel_1067,
Tursiops truncatus	ENSTTRG00000009850	1 retrocopy	retro_ttru_1161,
Vicugna pacos	ENSVPAG00000004974	1 retrocopy	retro_vpac_470 ,