RetrogeneDB ID: retro_vpac_18

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_7990:16702..17212(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000003506
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000003505
• Aliases: None
• Description: None

Sequence

>retro_vpac_18
ATGGTCAGCTCCTGCTGTGGCTCCATCTGTTCTGAGGAGGACTGTGGCCAAGGACTCTGCCAGGAGACCTGCTGCCGCCC
CAGCTGCTGCCAAACAACCTGCTGCAGGACCACCTGCTACCGCCCAAGGTGCTGTGAGTCCAGCTGCTGCCGCCCCAGAT
GCTGCATCTCCAGCTGCCAGCCCACCTGTTGCCGCCCCAGATGCTGTGAGTCCAGCTGCTGCAGACCCCAGTGCTGCCAG
TCTGTGTGCTGCCAGCCCACCTGCTGCCGCCGCAGCTGCTGTGAGTCCAGTTGCTGCAGACCCCAGTGCTGCCAGTCTGA
GTGTTGCCAGCCCACCTGCTGCCGCCCCTCCTGCTGTGGTTCCAGCTCCTGTGGCTCCAGCTGCTGCCGCACCTGCTGTT
GCCTGCGCCCAGTCTGTGGCCAGGTCTCCTGCCACACCACTTGCTATCGCCCCACCTGTGTCATCTCCACCTGCCCCCGC
CCCACGTGCTGTGCCTCCTCTTGCTTCTGA

Alignment

ORF - retro_vpac_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.9 %
• Parental protein coverage: 82.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVSSCCGFVCSEEGCSQGLCQETCCRPSCCQTTCCRTTCYRPRCCESSCCRPQCCQSLCCQPTCCQPACC
          MVSSCCG..CSEE.C.QGLCQETCCRPSCCQTTCCRTTCYRPRCCESSCCRP.CC.S..CQPTCC.P.CC
Retrocopy MVSSCCGSICSEEDCGQGLCQETCCRPSCCQTTCCRTTCYRPRCCESSCCRPRCCIS-SCQPTCCRPRCC

Parental  ISSCCRPSCCESSCCPQSCQPICCRPRCCESSCCRPRCCISS-CQPTCCHPRCCESSCCRPQCCQSVCCQ
          .SSCCRP.CC.S.CC....QP.CCR..CCESSCCRP.CC.S..CQPTCC.P.CC.SS.C...CC...CC.
Retrocopy ESSCCRPQCCQSVCC----QPTCCRRSCCESSCCRPQCCQSECCQPTCCRPSCCGSSSCGSSCCRTCCCL

Parental  PTCCRRSCCESSCCRPSCCGSSSCGSSCCRTCC
          ...C....C...C.RP.C..S......CC...C
Retrocopy RPVCGQVSCHTTCYRPTCVISTCPRPTCCASSC

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_18 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_18 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
Pongo abelii	ENSPPYG00000008436	1 retrocopy	retro_pabe_143,
Vicugna pacos	ENSVPAG00000003505	1 retrocopy	retro_vpac_18 ,