RetrogeneDB ID: retro_vpac_197

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2739:169599..170644(+)
• Located in intron of: ENSVPAG00000002872

Retrocopy information

• Ensembl ID: ENSVPAG00000002879
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCNI
• Ensembl ID: ENSVPAG00000011865
• Aliases: None
• Description: cyclin I [Source:HGNC Symbol;Acc:1595]

Sequence

>retro_vpac_197
CAGGTGAATGTGCCAAAAATGCCTACAAATCAGAATGTTTCTCCATCCCGGAGAGATGAAGTGATTCAGTGGCTGGCCAA
ACTCAAGTACCAATTCAGTCTTTACCCAGAAACATATGCACTGGCTAGTAGTCTTTTGCACAGATTCTTAGCTACTGTGA
AGGCCCACCCAAAGCACTTGAGTTGTAGTGCAATCGAATGTTTTTTCCTGGCTGCCAAGACTGTTGAGGAGGATGAGAGA
ATTCCAGCACTGAAGTTGTTGGCAAGAGATAGTTTCTGTGGATGTTCTTCATCTGAAATTCTGAGGATGGAGAGAATTAT
TCTGGATAAGCTGAGCTGGGATCTTCACCCAGCCACACCACTGGATTTTCATCACATTTTCCATGCCATTGCAGTGTCAG
CTAGGCCTCAGTTACTTTTTAGTTTGCCAAACTGAGCTCATCTCAACATTTGGCTGTCCTCACCAAGCAACTACTTCACT
GTATGGCCTGCAACCAACTTCTGCAATTCAAAGGATCCATGCTTGCTCTGGCCATGATTAGTCTGGAAGTGGAGAAACTC
ATTCCTGATTGGCTTCCTCTTAGAATTGAACTGCTTCAGAAAGCACAGATGGATAGCTCCCAGCTGACCCGCTGTCGGGA
GCCATGGCACATCACCTTTCTACTCTGCAGTCCTCCCTGCCTCTAAATTCTGTTTATGTCTACTGTTCCCTCAAGCATGC
CCTGGTGACCTGTGACAAAGGAGTGTTCAGATTACATCCCTCCTCTGCCCCAGGCCCAGAGTTCTCCAAGGACAACAGCA
AACCAGAAGTGCCAGTCAGAGGTCCAGCGCCTTCTACCATCATCTCCCAGCTCGAATGGGTGCAAGCATACCTCTGCTGA
ATGCAAAGTAGAGGAAATGAAAGTGAACACCTTCTACGATGAGATCAAATGGCTCTGTAATGAAGATAATGCTTCAGAAA
ATGTGCGTTCTGTGTATGGCACTGATTTATCAAGGCAAGAGGGACATGCTTCCTTTGTCTACCTTTGCAGCCTGTTTCTG
TCATG

Alignment

ORF - retro_vpac_197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.32 %
• Parental protein coverage: 92.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KVNVPKMPTNQNVSPSQRDEVIQWLAKLKYQFNLYPETFALASSLLDRFLATVKAHPKYLSCIAISCFFL
          .VNVPKMPTNQNVSPS.RDEVIQWLAKLKYQF.LYPET.ALASSLL.RFLATVKAHPK.LSC.AI.CFFL
Retrocopy QVNVPKMPTNQNVSPSRRDEVIQWLAKLKYQFSLYPETYALASSLLHRFLATVKAHPKHLSCSAIECFFL

Parental  AAKTVEEDERIPGLKVLARDSFCGCSSSEILRMERIILDKLNWDLHTATPLDFLHIFHAIAVSTRPQLLF
          AAKTVEEDERIP.LK.LARDSFCGCSSSEILRMERIILDKL.WDLH.ATPLDF.HIFHAIAVS.RPQLLF
Retrocopy AAKTVEEDERIPALKLLARDSFCGCSSSEILRMERIILDKLSWDLHPATPLDFHHIFHAIAVSARPQLLF

Parental  SLP-KLSPSQHLAVLTKQLLHCMACNQLLQFKGSMLALAMISLEMEKLIPDWLPLTIELLQKAQMDSSQL
          SLP.KLS.SQHLAVLTKQLLHCMACNQLLQFKGSMLALAMISLE.EKLIPDWLPL.IELLQKAQMDSSQL
Retrocopy SLP<KLSSSQHLAVLTKQLLHCMACNQLLQFKGSMLALAMISLEVEKLIPDWLPLRIELLQKAQMDSSQL

Parental  IHCRE-LVAHHLSTLQSSLPLNSVYVYRPLKHTLVTCDKGVFRLHPSSAPGPDFSKDNSKPEVPVRGTA-
          ..CRE...AHHLSTLQSSLPLNSVYVY..LKH.LVTCDKGVFRLHPSSAPGP.FSKDNSKPEVPVRG.A.
Retrocopy TRCRE<AMAHHLSTLQSSLPLNSVYVYCSLKHALVTCDKGVFRLHPSSAPGPEFSKDNSKPEVPVRGPA<

Parental  AFCHHLPA-ANGCKHTSAKRKVEEMEVDDFYDGIKRLYNEDNASENVGSVCGTDLSRQEGHAS-PCPPLQ
          AF.HHLPA..NGCKHTSA..KVEEM.V..FYD.IK.L.NEDNASENV.SV.GTDLSRQEGHAS..C.PLQ
Retrocopy AFYHHLPA<SNGCKHTSAECKVEEMKVNTFYDEIKWLCNEDNASENVRSVYGTDLSRQEGHAS<LCLPLQ

Parental  PVSVM
          PVSVM
Retrocopy PVSVM

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_197 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_197 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014768	1 retrocopy	retro_cjac_1311,
Echinops telfairi	ENSETEG00000000952	1 retrocopy	retro_etel_1137,
Loxodonta africana	ENSLAFG00000029218	1 retrocopy	retro_lafr_295,
Macaca mulatta	ENSMMUG00000019904	1 retrocopy	retro_mmul_2529,
Mus musculus	ENSMUSG00000063015	2 retrocopies	retro_mmus_1211, retro_mmus_2730,
Tarsius syrichta	ENSTSYG00000009907	1 retrocopy	retro_tsyr_834,
Vicugna pacos	ENSVPAG00000008340	1 retrocopy	retro_vpac_351,
Vicugna pacos	ENSVPAG00000011865	1 retrocopy	retro_vpac_197 ,