RetrogeneDB ID: retro_vpac_431

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_182805:478..1211(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000003046
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CASP6
• Ensembl ID: ENSVPAG00000009840
• Aliases: None
• Description: caspase 6, apoptosis-related cysteine peptidase [Source:HGNC Symbol;Acc:1507]

Sequence

>retro_vpac_431
GGAGTTGCTTTATCTTCAAGCATGAGAGGTCCTTCTGGACAAGAAGCTGCCGGACTGGCGGGGAACCAGCGCGGACAGAG
ACAATCTTCAGCGCAGGTTTTCAGATCTAGGATTTGAAGTGAAACGCTTTAATGATCTTAAAGCAGAAGAACTACTGCTC
AAAATTCATGAGGCATCAACCTCTAGCCATGTAGATGCCAATTGCTTTTTGTGTGTTTTCCTGAGTCACGGTGAAGGCAA
CCCCATTTACGCATATGATGCCAAAATTGAAATTCGACATTGACTGGCTTGATCAAAGGAGACAGGTGTCAGAGCCTGGT
TGGAAAACCCAAGACATTTATCATTCAGGCGTGTCGGGGAAACCAGCACTATGTGCCCGTCATTCCTTTGGATGTCGTGG
ATCGTCAGACAGATGTGCTGGATGCCAACGTAACCCAGGTGGACGCCGCCTCGGCGTGCGCACTGCGTGCCAGAGCGGAC
TTCCTCATGTGCTACTCGGTGGCAGAAGGTTGTTATTCTCATCGGGAAAACGGTGAACGGCTCATGGTACATTCAAGATT
TGTGTGAGATGCTGGGAAAATCTGGCTCCTCCTTAGAGTTCACAGAACTCCTCACACTGGTGAATAGGAGAGTTTCTCAG
CGCCAGTAGACATTTGTAAAGACCCAATGCAATTGGAAAGAGCAGGTCCCCTGCTTTGCCTCACTGCTACCTAAGAAGCT
GCTTTTCTTTCCA

Alignment

ORF - retro_vpac_431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.38 %
• Parental protein coverage: 88.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GVAL-IFNHERFFW-HLMLPDRRGTSADRDNLQRRFSDLGFEVKCFNDLKAEELLLKIHEASTSSHVDAD
          GVAL.IF.HER.FW....LPD.RGTSADRDNLQRRFSDLGFEVK.FNDLKAEELLLKIHEASTSSHVDA.
Retrocopy GVAL<IFKHERSFW<DKKLPDWRGTSADRDNLQRRFSDLGFEVKRFNDLKAEELLLKIHEASTSSHVDAN

Parental  CFLCVFLSHGEGNHVYAYDAKIEIQ-TLTGLFKGDRCQSLVGKPKIFIIQACRGNQHDVPVIPLDVVDHQ
          CFLCVFLSHGEGN..YAYDAKIEI..TLTGL.KGDRCQSLVGKPK.FIIQACRGNQH.VPVIPLDVVD.Q
Retrocopy CFLCVFLSHGEGNPIYAYDAKIEIR<TLTGLIKGDRCQSLVGKPKTFIIQACRGNQHYVPVIPLDVVDRQ

Parental  TDVPDANVTQVDAASVYTLPAGADFLMCYSVAEGYYSHRE-TVNGSWYIQDLCEMLGKFGSSLEFTELLT
          TDV.DANVTQVDAAS...L.A.ADFLMCYSVAEG.YSHRE.TVNGSWYIQDLCEMLGK.GSSLEFTELLT
Retrocopy TDVLDANVTQVDAASACALRARADFLMCYSVAEGCYSHRE>TVNGSWYIQDLCEMLGKSGSSLEFTELLT

Parental  LVNRKVSQRR-VDFCKD-PNAIG-KKQVPCFASMLTKKLHFFP
          LVNR.VSQR..VD.CKD.PNAIG.K.QVPCFAS.L.KKL.FFP
Retrocopy LVNRRVSQRQ<VDICKD<PNAIG<KEQVPCFASLLPKKLLFFP

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_431 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_431 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000002727	1 retrocopy	retro_lafr_291,
Microcebus murinus	ENSMICG00000010297	2 retrocopies	retro_mmur_709, retro_mmur_844,
Monodelphis domestica	ENSMODG00000005948	1 retrocopy	retro_mdom_1854,
Vicugna pacos	ENSVPAG00000009840	1 retrocopy	retro_vpac_431 ,