RetrogeneDB ID: retro_ocun_1950

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:102240193..102241072(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNOT11
• Ensembl ID: ENSOCUG00000004448
• Aliases: None
• Description: CCR4-NOT transcription complex, subunit 11 [Source:HGNC Symbol;Acc:25217]

Sequence

>retro_ocun_1950
AGTGGACTTCAAGTTACCCTTGAGTGAATACCAGTCTGAGATGCTGACCTGGAGTAAAACTACCTCCCCTAGTATTCTCA
GTGACCCATACTCAGATTCTTATAATTCTGCATTTGAAAATTCAGTTGCTTAACAGATCACAGAAGCTTCAGTTAGTGGA
CCAAAACCATCTATTGAAAACCATTTTCAGCCGGTTATTCATCCACCACCTCCCCTATATATAGGTGAGGATTAACTGAC
TTGACTATATCTGACAAAGTTCCACCACACAGTTCAGTGGGATAAGTCTAGGTGTGAGAAGCCTACCACTGGTATGGAGA
TGAGTGAATAATGGTAAAAGCCTACAAAAGCCCCTTGTCTGCTCCTCAAGAAACATGTATACTTAGTGAATGATAAAGAC
CCCAATTGCGGTTACCATGATGGCCTCACTCCATCTAAGCTTCCTGATTTATTGGAGAACACCACTCCAGTCACTGTTAG
AAACATTACTGAAATTAATGAAGTGAAGTCAAATCACCAAGTATTTTTCTGTCCTGGTCAAGATGGGTATGTCCTTACAT
TCACTGGAAGTTAACAATTGACTAACTACAACTGCTGATGTGTCTTCTGCATGGATTCACCTTTATATATCAAATGGCAT
CTCTACTTTTGAACAAATTAAGGATTCATATATGCAGAATTGCTTGTTGTGTCTCATGTGTGCTTTCTCTAGTCCTTGAT
CTATAACAAAATCATTCATGTAGTTCATAAGCAGAACTTGCTTATGAAAGTACAGGCATTCTGTATTAAATTCAGTAGAC
TATGAGAATCTAGTACCCTTTCTGGTTACTGAAGCCATTAGATATTGGGGAAGCATTTTTGGAGACAAAAATGTCAAAA

Alignment

ORF - retro_ocun_1950 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.92 %
• Parental protein coverage: 58.17 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  SGLQ-LALAERQSELPTQSKASFPSILSDPDPDSSNSGFDSSVASQITEALVSGPKPPIESHFRPEFIRP
          SGLQ.L.L.E.QSE..T.SK...PSILSDP..DS.NS.F..SVA.QITEA.VSGPKP.IE.HF.P..I.P
Retrocopy SGLQ>LPLSEYQSEMLTWSKTTSPSILSDPYSDSYNSAFENSVA*QITEASVSGPKPSIENHFQP-VIHP

Parental  PPPLHICEDELAWLNPTEPDHAVQWDKSMCVKNSTGVEIKR-IMAKAFKSPLSSPQQTQLLGE-LEKDPK
          PPPL.I.ED.L..L..T...H.VQWDKS.C.K..TG.E....IM.KA.KSPLS.PQ.T..L.E...K.P.
Retrocopy PPPLYIGED*LT*LYLTKFHHTVQWDKSRCEKPTTGMEMSE<IMVKAYKSPLSAPQETCILSE<MIKTPI

Parental  LV-YHIGLTPAKLPDLVENNPLVAI-EMLLKLMQSSQITEYFSVLVNMDMSLHSMEVVNRLTTAVDLPPE
          .V.YH.GLTP.KLPDL.EN...V...E.LLKLM..SQIT.YFSVLV.M.MSLHS.EV.N.LTT..D....
Retrocopy AV<YHDGLTPSKLPDLLENTTPVTV>ETLLKLMK*SQITKYFSVLVKMGMSLHSLEVNN*LTTTADVSSA

Parental  FIHLYISNCISTCEQIKDKYMQNRLVRLVCV-FLQSLIRNKIINV---QDLFIEVQAFCIEFSRIREAAG
          .IHLYISN.IST.EQIKD.YMQN.L..L.C..FL.SLI.NKII.V...Q.L...VQAFCI.FSR..E...
Retrocopy WIHLYISNGISTFEQIKDSYMQNCLLCLMCA<FL*SLIYNKIIHVVHKQNLLMKVQAFCIKFSRL*ESST

Parental  L-FRLLKTLDTGEVPSETKMSK
          L.F.LLK.LD.GE...ETKMSK
Retrocopy L<FWLLKPLDIGEAFLETKMSK

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	0.00 RPM	17.16 RPM
SRP017611_kidney	0.00 RPM	57.47 RPM
SRP017611_liver	0.00 RPM	8.56 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1950 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1950 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1950 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000006411	7 retrocopies	retro_lafr_1004, retro_lafr_1005, retro_lafr_137, retro_lafr_355, retro_lafr_581, retro_lafr_604, retro_lafr_998,
Oryctolagus cuniculus	ENSOCUG00000004448	1 retrocopy	retro_ocun_1950 ,