RetrogeneDB ID: retro_ocun_1659

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018747:40519..41152(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9orf41
• Ensembl ID: ENSOCUG00000017017
• Aliases: None
• Description: chromosome 9 open reading frame 41 [Source:HGNC Symbol;Acc:23435]

Sequence

>retro_ocun_1659
TGGAGTGAAAGTGGCAAAACAGACAGGATGTCTGCTAGCAGCCAATCATTAAAGAAATATTAAAAAATTTTCCAAAATAG
AGATGAGATCCTCTGAAAGAAAATACTCCAGTACATGGTGTTGGACTAGGAAGATAGACCTGGGAATATCAATGCTAGGT
TTTGCTTCTCAAGGAATTAATATAATCTTTTTCTGCTTTTTCCCTCACCATTATACTCAATGGATGCTCTGAAATTAATA
AATATATACTATATACTGGGTCCAACAGATTAACAACATATCAGCTGATCGGATTAGACTTACCTTTTTTCTCTGATCTT
GACTCCCATCATCTTCCCCTTGTTTGTAACTTTTCTTTGAATGTAACAGCTTTTCTGGAGATTTATTCAAAATTCAATAC
CTGGAACTATATTGCTATGTGCTTCTTCATAGATACTGCTCACCATGTAATGGATTACATTGATATGAGATGGAAAATAT
TTAAAACAGCTGGAATTTGGATCAATCCAGGGCATCTTCTGCATTACTCTGAAAATGGTAGCAAATGAACTTTTCATAGA
ATTGAGCTACAAGGATACAAATATTGTCATTCTGCAATATGAATTCCAAGTAGAGATGAAAAAACAATCTATC

Alignment

ORF - retro_ocun_1659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.28 %
• Parental protein coverage: 53.37 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  WSETGKAER-DACYQPIIKEILKNFPKERWDPSKVTILVPGAGLGRLAWE-IAMLGYACQG-NEWSFFML
          WSE.GK..R.D.C.QPIIKEILKNFPK.R.DP.K....V.G.GLGR..WE.I.MLG.A.QG.N....F.L
Retrocopy WSESGKTDR<DVC*QPIIKEILKNFPK*R*DPLKENTPVHGVGLGR*TWE<ISMLGFASQG<N*YNLFLL

Parental  FSS-NFVLNRCSEINKYRLYP-WIHQFSNNRRSADQIRPIFF-PDVDPHSLPPGSNFSMTAGDFQEIYSE
          F.S....LN.CSEINKY.LY..W..Q..N...SAD.IR..FF..D.D.H.LP...NFS.....F.EIYS.
Retrocopy FPS<TIILNGCSEINKYILYT<WVQQINNI--SADRIRLTFF>SDLDSHHLPLVCNFSLNVTAFLEIYSK

Parental  CNTWDCIATCFFIDTAHNVIDYIDTIWKILKPGGIWINLGPLLYHFEN-LANELSIELSYEDIKNVVLQY
          .NTW..IA.CFFIDTAH.V.DYID..WKI.K..GIWIN.G.LL...EN..ANEL.IELSY.D...V.LQY
Retrocopy FNTWNYIAMCFFIDTAHHVMDYIDMRWKIFKTAGIWINPGHLLHYSEN>VANELFIELSYKDTNIVILQY

Parental  GFQVEVEKESV
          .FQVE..K.S.
Retrocopy EFQVEMKKQSI

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	9.49 RPM
SRP017611_kidney	0.10 RPM	14.29 RPM
SRP017611_liver	0.00 RPM	5.32 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1659 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1659 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1659 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000024726	2 retrocopies	retro_mmus_1013, retro_mmus_3359,
Oryctolagus cuniculus	ENSOCUG00000017017	4 retrocopies	retro_ocun_1659 , retro_ocun_1737, retro_ocun_1827, retro_ocun_921,
Ictidomys tridecemlineatus	ENSSTOG00000000385	5 retrocopies	retro_itri_1389, retro_itri_1652, retro_itri_1653, retro_itri_1654, retro_itri_1843,