RetrogeneDB ID: retro_vpac_638

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_89736:3066..3390(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCTP
• Ensembl ID: ENSVPAG00000011704
• Aliases: None
• Description: phosphatidylcholine transfer protein [Source:HGNC Symbol;Acc:8752]

Sequence

>retro_vpac_638
TGCAATGGACAGGCAGTGGCCTACTGGTAAGTGGATTTCCCTAGCCCTCTTTCTAACAGAGGGTATGTCTACGGGCGGCA
GCAACAAGACCTGGACTTTGAAGGGCAGCAGGTCCATGTCATCCTGGCCCAGAGCACCTCCATGCCACAGTTTCTGGAAA
AATCGGGAGTGATCCAGGTGAAGCATTACAAGCAGAAGATAGCGATCCACAGTGATGGCAAAAGGGGGAGCAAAGTTTTC
ATTTGTTGTTCGCATAAACCTAGGTAGCCCAATTCCATCCCGGATCATAAATTGGGCTGCCAGAATGGAGTTCCTAACTT
CCTA

Alignment

ORF - retro_vpac_638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.91 %
• Parental protein coverage: 50.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CNGQAVVYWQVKYPFPLSDRDYVYVRQRQELDFEGQKVHVILAQSTSVPQFPEKSGVIRVKQYKQRLAIQ
          CNGQAV.YW.V..P.PLS.R.YVY.RQ.Q.LDFEGQ.VHVILAQSTS.PQF.EKSGVI.VK.YKQ..AI.
Retrocopy CNGQAVAYW*VDFPSPLSNRGYVYGRQQQDLDFEGQQVHVILAQSTSMPQFLEKSGVIQVKHYKQKIAIH

Parental  SDGKRGSKVFMYYFDNP-GGQIPSWLVNWAAK-NGVPNFL
          SDGKRGSKVF......P.G..IPS...NWAA..NGVPNFL
Retrocopy SDGKRGSKVFICCSHKP>GSPIPSRIINWAAR<NGVPNFL

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_638 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_638 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000002870	1 retrocopy	retro_mmur_44,
Vicugna pacos	ENSVPAG00000011704	1 retrocopy	retro_vpac_638 ,