RetrogeneDB ID: retro_ocun_1889

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:60123260..60123877(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000004774
• Aliases: None
• Description: None

Sequence

>retro_ocun_1889
AGTTCCAGCACTGAGGACAGCAGCCCCAGCAGTGTGGCTTTGGTGTCATTCAGAGAAGGTAATCCCACAGAGATGACTTC
ATCTCCTTGGCTCTGGGGAAGCAAGAGCATTGGAATGCTGTCTATGAGAGAGAACTACAAACTTTGCAGGAATATGGAGA
TACAAAAGAAATCTGGTTTGGAGAAGAGAGTGTGACTTGACTAATAAGATGATGAAGAAACAGAATATTCCACTGGATGC
AACCAGTGCTTCATATTGGAATTGGATATAGTGTTTTCCTGGTTGAACCTGCAAAATTTGGTTTCAGTAATATTATTGGC
ATTGAGTACTCTCCTTCAGCAATTCAGATTTCTGGAAGTATCCTAGAGAAAGAAGGGCTATCTAACTTTAAGTTGAAGGT
ATAAGATTTTTGAATCTTTCCACAAAGCTGTCTGGATTTAAAATTTGTATTGACAAAGGGTCTTTTGATGCCATAAGCCT
TAATCTTGACAATGCAGTTGAGAAGAGGAAGCAATATGTGAAATCTCTCTCCAGGTGCTGAAACTAAAAGGCTTTTTTCT
AATAACCTCATGTAATTGGACCAAGGCAGAGTTCTGAAGGAATTCAGTGAAGGATAT

Alignment

ORF - retro_ocun_1889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.3 %
• Parental protein coverage: 65.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SGADDDGGGGGVAAAPSRGGSPAE-DGFVPSALGTLEHWDAVYERELQTFQEYGDTGEIWFGEESMMRLI
          S....D.....VA....R.G.P.E.D.F...ALG..EHW.AVYERELQT.QEYGDT.EIWFGEES...LI
Retrocopy SSSTEDSSPSSVALVSFREGNPTE<DDFISLALGKQEHWNAVYERELQTLQEYGDTKEIWFGEESVT*LI

Parental  R-WMQKQKIPLDAS-VLDIGTGNGVFLVELAKFGFSNITGIDYSPSAIQLSERILEKEGLSNIKLKVED-
          R..M.KQ.IPLDA..VL.IG.G..VFLVE.AKFGFSNI.GI.YSPSAIQ.S..ILEKEGLSN.KLKV.D.
Retrocopy R<MMKKQNIPLDAT>VLHIGIGYSVFLVEPAKFGFSNIIGIEYSPSAIQISGSILEKEGLSNFKLKV*D<

Parental  FLNLSTKLSGFQICIDKGTFDAISLNPDNAIEKRKQYVKSLSR-VLKVKGFFLITSCNWTKEE-LLNEFS
          FLNLSTKLSGF.ICIDKG.FDAISLN.DNA.EKRKQYVKSLSR.VLK.KGFFLITSCNWTK.E..L.EFS
Retrocopy FLNLSTKLSGFKICIDKGSFDAISLNLDNAVEKRKQYVKSLSR<VLKLKGFFLITSCNWTKAE<VLKEFS

Parental  EGF
          EG.
Retrocopy EGY

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	4.30 RPM
SRP017611_kidney	0.10 RPM	9.12 RPM
SRP017611_liver	0.08 RPM	2.85 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1889 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1889 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1889 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000004774	1 retrocopy	retro_ocun_1889 ,
Ochotona princeps	ENSOPRG00000003353	1 retrocopy	retro_opri_608,