RetrogeneDB ID: retro_vpac_179

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2447:4067219..4067678(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK6
• Ensembl ID: ENSVPAG00000002256
• Aliases: None
• Description: cyclin-dependent kinase 6 [Source:HGNC Symbol;Acc:1777]

Sequence

>retro_vpac_179
CTGATGGTCATCTGTGCCACAGCCTGAACTGACCAGGAGACCAAAGTGACCCTGGTATTTGAGCATGTGGACCAAAACCT
AAGGACATATCTGGACAAGGCACCCCCACCAGGCTTGCCAGTGGAGACCATCAAGGATCTGATGCACCAGTTTCTAAGAG
GCCTAGATTTCCTTCATGCCAACGGCATTGTTCACCGAGACCTGAAGCCAGAGAACATTCTGGTGACAAGTGGTGGGACA
GTCGAGCTGGCTGACTTTGGCCTGGCCAGAATCTACAGCTACCAGATGGCACTTACACCTGTGGTGGTTACACTCTGGTA
CCGTGCTCCGCAAGTTCTTCTGCAGTCTGTGTATGCAGCACCTGTGGACATGTGGAGCGTTGGCTGTATCTTTGCAGAGA
TGCTTCGTTGAAAGCCTCTGTTCTGTGGAAACTCTGAAGCTGACGAGTTAGGCAAAATC

Alignment

ORF - retro_vpac_179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.86 %
• Parental protein coverage: 57.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFDVCTVSRTDRETKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMFQLLRGLDFLHSHRVVHRDLKP
          L...C....TD.ETK.TLVFEHVDQ.L.TYLDK.P.PG.P.ETIKD.M.Q.LRGLDFLH....VHRDLKP
Retrocopy LMVICATA*TDQETKVTLVFEHVDQNLRTYLDKAPPPGLPVETIKDLMHQFLRGLDFLHANGIVHRDLKP

Parental  QNILVTSSGQIKLADFGLARIYSFQMALTSVVVTLWYRAPEVLLQSSYATPVDLWSVGCIFAEMFRRKPL
          .NILVTS.G...LADFGLARIYS.QMALT.VVVTLWYRAP.VLLQS.YA.PVD.WSVGCIFAEM.R.KPL
Retrocopy ENILVTSGGTVELADFGLARIYSYQMALTPVVVTLWYRAPQVLLQSVYAAPVDMWSVGCIFAEMLR*KPL

Parental  FRGSSDVDQLGKI
          F.G.S..D.LGKI
Retrocopy FCGNSEADELGKI

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_179 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_179 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Vicugna pacos	ENSVPAG00000002256	1 retrocopy	retro_vpac_179 ,
Vicugna pacos	ENSVPAG00000006704	4 retrocopies	retro_vpac_365, retro_vpac_437, retro_vpac_488, retro_vpac_580,