RetrogeneDB ID: retro_ocun_1589

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018706:106944..107886(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNOT6
• Ensembl ID: ENSOCUG00000011083
• Aliases: None
• Description: CCR4-NOT transcription complex, subunit 6 [Source:HGNC Symbol;Acc:14099]

Sequence

>retro_ocun_1589
TGTCGTATGCTATAATGTGATAAATATGCGACCTGAGAATTCTATGGCTACTGTCCATCATGGGCACTAAATTCGGACTA
CAGGAAAAAGGCCCTTATTCAAGAAATCTTGAGCTGCAGTGCTGATATCATAAGCCTTAAGGAGATTGAAATGGAACAGT
ATTACAGTTTTTTCTGGTATAACTGAAAAAAAAAGTGGCTATCATGGATTCTTTAGCCCTATGTTTTGATCTAGGACAAT
GTCAGACCAAAAAAGAAAGCATGTTGATGCTGTGAAATATTCTTCAAGATCAAAAAATTTAACTTGGTTCAGAAACACAC
TGTTGAATTTAATCAGCTAGTAATGGCAAATTCATAAGGGTCTGAAACAATGCTGAACAGAATCATGAAAAAAGATAACA
TTGGAGTTGCAGTACTTCGCATAGAATTGATTGAAGTATCATCTGGAAAGGCACATCATGGCACACAACTCATTCTCATG
GCAAATGCTCATATACACTGGGATCCAGAGTACTCCAATATGAAGTTGGTACAAACTATGATGTTCCTCTCCAAAGTGAA
GAACATTATCGATGAAGCCTTTCAAAGCCTCAGATCTAAGGTACTAGGAGAATTCGTAACTATTCCACTTGTGTTATGTG
CCAACCTTAATTCTTTGCCAGACTCTGCTGTTGTGGAATATTTGAGAACTGGTTGAGTAGAAACAAATCATAAAGACTTT
AAGGACTGAGGTAGAATGAAAGTCTTACAAACTTCAGCTATTAGTAATGGGAAGAACGGAACAACCAACAGAAGGATCAC
TCATGGTTTCAAGTTGAAGAGTGCCTATGAGAGTGGCGTGATGCCTTACACAAATTATACATTTGATTTCTTCAGAAGGT
TTTGATATTGAATCTTCTATTCTAAACCTCAGTTGAACACTGGGACCTTTAGACCACCACTG

Alignment

ORF - retro_ocun_1589 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.9 %
• Parental protein coverage: 56.63 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CYNVLCDKYATRQLYGYCPSWALNWDYRKKAIIQEILSCNADIISLQEVETEQYYSFFL-VELKERGYNG
          C....CDKYAT...YGYCPSWALN.DYRKKA.IQEILSC.ADIISL.E.E.EQYYSFF.....K..GY.G
Retrocopy CRML*CDKYAT*EFYGYCPSWALNSDYRKKALIQEILSCSADIISLKEIEMEQYYSFFW>ITEKKSGYHG

Parental  FFSPKSRARTMSEQERKHVDG-CAIFFKVEKFTLIQKHTVEFNQLAMANSEGSEAMLNRVMTKDNIGVAV
          FFSP....RTMS.Q.RKHVD..C.IFFK..KF.L.QKHTVEFNQL.MANS.GSE.MLNR.M.KDNIGVAV
Retrocopy FFSPMF*SRTMSDQKRKHVDA<CEIFFKIKKFNLVQKHTVEFNQLVMANS*GSETMLNRIMKKDNIGVAV

Parental  LLELRKELIEMSSGKAHLGTEKQLILVANAHMHW-PEYSDVKLVQTMMFLSEVKNIIDKASRSLRSNVLG
          ...LR.ELIE.SSGKAH.GT..QLIL.ANAH.HW.PEYS..KLVQTMMFLS.VKNIID.A..SLRS.VLG
Retrocopy ---LRIELIEVSSGKAHHGT--QLILMANAHIHWDPEYSNMKLVQTMMFLSKVKNIIDEAFQSLRSKVLG

Parental  EFGTIPLVLCADLNSLPDSGVVEYLSTGGVETNHKDFKEL-RYNESLTNFSCNGKNGTTNGRITHGFKLK
          EF.TIPLVLCA.LNSLPDS.VVEYL.TG.VETNHKDFK...R.....T....NGKNGTTN.RITHGFKLK
Retrocopy EFVTIPLVLCANLNSLPDSAVVEYLRTG*VETNHKDFKD*GRMKVLQTSAISNGKNGTTNRRITHGFKLK

Parental  SAYESGLMPYTNYTFDFKGIIDY-IFYSKPQLNTLGILGPL
          SAYESG.MPYTNYTFDF.....Y.IFYSKPQLNT.....PL
Retrocopy SAYESGVMPYTNYTFDFFRRF*Y*IFYSKPQLNTGTFRPPL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.06 RPM	14.46 RPM
SRP017611_kidney	0.00 RPM	12.47 RPM
SRP017611_liver	0.00 RPM	7.94 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1589 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1589 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1589 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000019325	1 retrocopy	retro_ecab_962,
Microcebus murinus	ENSMICG00000013018	1 retrocopy	retro_mmur_1392,
Oryctolagus cuniculus	ENSOCUG00000011083	1 retrocopy	retro_ocun_1589 ,