RetrogeneDB ID: retro_vpac_86

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1640:314742..315118(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIE
• Ensembl ID: ENSVPAG00000010049
• Aliases: None
• Description: peptidylprolyl isomerase E (cyclophilin E) [Source:HGNC Symbol;Acc:9258]

Sequence

>retro_vpac_86
CCCTTGGACCACATCGCCTATGAGCTGTATGCAGCCACAGTTCTAAAGACAGAAGAAAACTTTTTGCACTCTGAGCACTG
GGGAGAAAGGATTTGGTTATAAAGGTTTCTGTTTTCACAGAATTATTCCAAGATTTATGTGCCTGGGTGGTGACTTGACA
CACCATAACAGCACTGGCAGCAAGTCCACCTCTGGAGAGAAATTTGATGAGAGTTTCATCCTGAGTCATACTGGTCCTGG
CTTCTTGGCAAACACTGGGCCCAACACAAACGGTCCCCAGGTTTGGATCTGCGCTGCCAAGACTGAGGGGTTGGATGGCA
AGTATGTGGTCTTTGGCAAAGTGGGAGAGGACAAGAATATTGTGGGAGCCACAGAG

Alignment

ORF - retro_vpac_86 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.81 %
• Parental protein coverage: 54.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PAGRIQMLLRSDVVPMTAENFR-CLCTHEKGFGFKGSSFHRIIPQFMCQGGDFTNHNGTGGKSIYGKKFD
          P...I...L....V..T.ENF...L.T.EKGFG.KG..FHRIIP.FMC.GGD.T.HN.TG.KS..G.KF.
Retrocopy PLDHIAYELYAATVLKTEENFL>TLSTGEKGFGYKGFCFHRIIPRFMCLGGDLTHHNSTGSKSTSGEKF-

Parental  DENFILKHTGPGLLSMANSGPNTNGSQFFLTCDKTDWLDGKHVVFGEVTEGLDVLRQIE
          DE.FIL.HTGPG.L..AN.GPNTNG.Q......KT..LDGK.VVFG.V.E........E
Retrocopy DESFILSHTGPGFL--ANTGPNTNGPQVWICAAKTEGLDGKYVVFGKVGEDKNIVGATE

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_86 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_86 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007365	1 retrocopy	retro_cpor_560,
Myotis lucifugus	ENSMLUG00000016233	1 retrocopy	retro_mluc_339,
Tursiops truncatus	ENSTTRG00000014385	1 retrocopy	retro_ttru_1314,
Vicugna pacos	ENSVPAG00000010049	2 retrocopies	retro_vpac_261, retro_vpac_86 ,
Xenopus tropicalis	ENSXETG00000018981	1 retrocopy	retro_xtro_20,