RetrogeneDB ID: retro_ocun_888

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:23809383..23809837(-)
• Located in intron of: ENSOCUG00000015901

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNC
• Ensembl ID: ENSOCUG00000003309
• Aliases: None
• Description: cyclin C [Source:HGNC Symbol;Acc:1581]

Sequence

>retro_ocun_888
GCAGGGAGCTTCTGTCACAACTCCCACTATTCGCAATGGATTTTGGATAAACAAGATCTGCTGAAGGAGCATCAAAAGGA
TTTAAAGTTTCTCTCAGAGGAGTATTGAGAGTTACAGGCTTTTTTTTGGTACAAATATTATCCAAGGATTTAAGTGAACA
TCTTAAATTAAGACAACAGGTTATTGCCACTGCTGCAGTCTATTTTAAGGGATTCTATGCCAGGTATTCTCGGAAAAGTA
TACAGCCCATATTAATGGCTCCAACTTGTGTTTTTTGGCACCCAAAGTAGAAGAATTTGGAGTAGCCTCAAATACAAGAT
TAATTTCTGCTGCTGCATCTTTATTAGAAACCAGATTTTCATATGCCTTTCCAAAGGAATTCTCTTCCAGGATGAATCAT
CAATTAGAATGTGAATTCTGTCTTTCAGAACTAATTCACTGTTGTTTGATAATA

Alignment

ORF - retro_ocun_888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.42 %
• Parental protein coverage: 53.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AGNFWQSSHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQ-IFF-TNVIQA-LGEHLKLRQQVIATATVY
          AG.F...SHY.QWILDKQDLLKE.QKDLKFLSEE.Y..LQ..FF.TN.IQ..L.EHLKLRQQVIATA.VY
Retrocopy AGSFCHNSHYSQWILDKQDLLKEHQKDLKFLSEE-Y*ELQ>LFFGTNIIQG>LSEHLKLRQQVIATAAVY

Parental  FKRFYARYSLKSIDPVLMAPTCVF-LASKVEEFGVVSNTRLISAATSVLKTRFSYAFPKEFPYRMNHILE
          FK.FYARYS.KSI.P.LMAPTCVF.LA.KVEEFGV.SNTRLISAA.S.L.TRFSYAFPKEF..RMNH.LE
Retrocopy FKGFYARYSRKSIQPILMAPTCVF<LAPKVEEFGVASNTRLISAAASLLETRFSYAFPKEFSSRMNHQLE

Parental  CEFYLLELMDCCLIV
          CEF.L.EL..CCLI.
Retrocopy CEFCLSELIHCCLII

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	13.25 RPM
SRP017611_kidney	0.00 RPM	16.42 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_888 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_888 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_888 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008954	1 retrocopy	retro_amel_1828,
Canis familiaris	ENSCAFG00000003525	1 retrocopy	retro_cfam_1774,
Dasypus novemcinctus	ENSDNOG00000011999	3 retrocopies	retro_dnov_1153, retro_dnov_216, retro_dnov_2243,
Dipodomys ordii	ENSDORG00000008393	2 retrocopies	retro_dord_230, retro_dord_75,
Myotis lucifugus	ENSMLUG00000012815	1 retrocopy	retro_mluc_1582,
Oryctolagus cuniculus	ENSOCUG00000003309	2 retrocopies	retro_ocun_1753, retro_ocun_888 ,
Ochotona princeps	ENSOPRG00000012972	2 retrocopies	retro_opri_1026, retro_opri_151,
Sus scrofa	ENSSSCG00000004353	1 retrocopy	retro_sscr_760,
Tupaia belangeri	ENSTBEG00000017525	1 retrocopy	retro_tbel_677,