RetrogeneDB ID: retro_ocun_1612

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018717:1294813..1295349(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OAZ2
• Ensembl ID: ENSOCUG00000017341
• Aliases: None
• Description: ornithine decarboxylase antizyme 2 [Source:HGNC Symbol;Acc:8096]

Sequence

>retro_ocun_1612
AGTATTTTGCCTTTGACTAACTGTCCCCAGCTCCAGTGCTGTAGGCACATTGTTCCAGGGCCTTTGTGTTGCCCTGATAG
CTGCCACCTACTGTTGAATATCCTCAGTAAGTGAGGGGATGCAGGAATCTTTCTCTCTGAGCTCTACTAAAGGACGAGAA
GCTCACTACGACCCAGGACCTCCCTGTGAACAATGGAAACTCTCACATTATCCACTGCTGGTACAAGGCCAGCAAAGCAA
ATGTCTTCCGGGATGCAGTCCTGTTCACCAGAGACTATTTGTAGAAATGCCAGATGTATGAGCAGTTGATGGCAGCAAGG
AAGGACTGCTAGCACGGCTTGACTTTGCTGCAGAGAAGGTGAAAATAAACCATGTCTTCCTCTGCTTCAGGGAGGACCAG
GAAGAAAGAACAGTACTCCTGAAGACCTTCAGCTTCTTGGGCTTTGAGACTGTACATTCAGGTCACCCCTTGTCTCTTCT
TGGCCAGACTGGCTGTTCATGGTTTACACCAGGACCAGAATTTGTCCAGTGAGGAC

Alignment

ORF - retro_ocun_1612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.83 %
• Parental protein coverage: 96.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SILPLSNCPQLQCCRHIVPGPLWC-DAPHPLSKIPGGRG-GGRDPSLSALIYKDEKLTVTQDLPVNEGKP
          SILPL.NCPQLQCCRHIVPGPL.C.D..H.L..I....G.G.R..SL.AL..KDEKLT.TQDLPVN.G..
Retrocopy SILPLTNCPQLQCCRHIVPGPLCCPDSCHLLLNILSK*G<GCRNLSL*ALL-KDEKLTTTQDLPVNNGNS

Parental  HIVHFRYEVTEVKVSSWDAVLSS-QSLFVEIPDGLLADGSKEGLLALLEFAEEKMKVNYVFICFRKGRED
          HI.H..Y......V...DAVL...Q.LFVE.PD....DGSKEGLLA.L.FA.EK.K.N.VF.CFR...E.
Retrocopy HIIHCWYKASKANVFR-DAVLFT<QRLFVEMPDV*AVDGSKEGLLARLDFAAEKVKINHVFLCFREDQEE

Parental  RAPLLKTFSFLGFEIVRPGH-PCVPARPDVMFMVYP-LDQNLSDED
          R..LLKTFSFLGFE.V..GH.P.V...PD..FMVY...DQNLS.ED
Retrocopy RTVLLKTFSFLGFETVHSGH<PLVSSWPDWLFMVYT<QDQNLSSED

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	93.21 RPM
SRP017611_kidney	0.00 RPM	46.83 RPM
SRP017611_liver	0.00 RPM	14.95 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1612 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1612 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000007344	1 retrocopy	retro_mmur_1013,
Myotis lucifugus	ENSMLUG00000022795	2 retrocopies	retro_mluc_1003, retro_mluc_2416,
Mus musculus	ENSMUSG00000040652	2 retrocopies	retro_mmus_1343, retro_mmus_2305,
Oryctolagus cuniculus	ENSOCUG00000017341	1 retrocopy	retro_ocun_1612 ,
Ochotona princeps	ENSOPRG00000009548	2 retrocopies	retro_opri_1184, retro_opri_145,
Tupaia belangeri	ENSTBEG00000008091	1 retrocopy	retro_tbel_2493,
Tursiops truncatus	ENSTTRG00000011834	1 retrocopy	retro_ttru_502,