RetrogeneDB ID: retro_ocun_441

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:13703795..13704735(+)
• Located in intron of: ENSOCUG00000007299

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000014347
• Aliases: None
• Description: None

Sequence

>retro_ocun_441
CTAGTCACTGTGGTGTCTGATCCCCACACACAGCTCTTTGCCTGCCTCTTCAGGGTCAACCCTCAGTAGGTCGGCTCCCT
CCAGCTGCACACAGGGGCCAGCTGTGCAGTCAGAAACCACTATGAAGTGCTGGTGCTGGGTGGAGGCAGCGGAGGGATCC
CCATGGCTGCCCACATGAAGAGGAAAGTGGGCGCAGGGAATGTGGCCATTGTTGAGCCCAGCGAGAGACATTTCTACCAG
CCAATCTGGACTCTGGTAGGCACTGGTGCCAAACAGTTGTCCTCATTGGGTCATCTCACAACACGTATGATTACATCTGG
TGTAGAACAGATAAAAGCTAAAGTGGTTGAATTGAACCCAGATAAGAACTGCATCCAAACTGACAATGGCAAGGAGATCT
ACAAATATCTTATTATTGCTCTTGGAATCCACCTGGACTATGAGAAGATTAAAGGCCTGCCTGAAGGCTTTGCTCAACCC
AAAATAGGGTCTAACTATTCAGTGAAGATGGTAGAGAAGACATGGAGGCTCTACAGGACTTCAAGGAGGGCAACACCATC
TTTACCTCCCCAAACACTTCCATGAAGTGTACTGGAGCCCCCCTGAAGTTCATGCATTTATGAGATGCCTATTTCAGGAA
GACAGGGATGCAATCCAAGGCCAACACAGCTCTTAGAACAAGTTTTGGGGTTAAGAAGTATGCAAAAAGCCCTGCAGGAG
ATCATCCATGAGAGGAACCTTACCGTTAACTACAGGCAAAACCTCACTGAAGTCCAAGTCCATAACAAGAAGCTGTTTTT
GAGAATCAACAAACCTGGAGACACCCAAGCGTCTTCCTATGAAATGCTTTATGTCACATCACCAGTGAGCCCATCGGATG
TCCTCAAGACAAGTCCTGTGGCTGATGCTGCTTTTTTGGGTGGATGTGGATAAAGAAACT

Alignment

ORF - retro_ocun_441 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.71 %
• Parental protein coverage: 70.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LVTVMSGPHARLFACLLRLGPQQVGSLQLHTGASCAARSHYEVLVLGGGSGGITMAARMKRKVGAENVAI
          LVTV.S.PH..LFACL.R..PQ.VGSLQLHTGASCA.R.HYEVLVLGGGSGGI.MAA.MKRKVGA.NVAI
Retrocopy LVTVVSDPHTQLFACLFRVNPQ*VGSLQLHTGASCAVRNHYEVLVLGGGSGGIPMAAHMKRKVGAGNVAI

Parental  VEPSERHFYQPIWTLVGAGAKQLSSSGRPTASVIPSGVEWIKAKVAELNPDKNCIQTDNGKEISYKYLII
          VEPSERHFYQPIWTLVG.GAKQLSS.G..T...I.SGVE.IKAKV.ELNPDKNCIQTDNGKEI.YKYLII
Retrocopy VEPSERHFYQPIWTLVGTGAKQLSSLGHLTTRMITSGVEQIKAKVVELNPDKNCIQTDNGKEI-YKYLII

Parental  ALGIQLDYEKIKGLPEGFAHPKIGSNYSVKTVEKTWK-ALQDFKEGNAIFTFPNTPVKCAGAPQKIMYLS
          ALGI.LDYEKIKGLPEGFA.PKIGSNYSVK.VEKTW..ALQDFKEGN.IFT.PNT..KC.GAP.K.M.L.
Retrocopy ALGIHLDYEKIKGLPEGFAQPKIGSNYSVKMVEKTWR<ALQDFKEGNTIFTSPNTSMKCTGAPLKFMHL*

Parental  EAYFRKTGKRSKANIIFNTSLGTIFGVKKYAE-ALEEIIQERNLTVNYKQNLIEVRADKQEAVFENLDKP
          .AYFRKTG..SKA....NT.L.T.FGVKKYA..AL.EII.ERNLTVNY.QNL.EV........F....KP
Retrocopy DAYFRKTGMQSKA----NTALRTSFGVKKYAK>ALQEIIHERNLTVNYRQNLTEVQVHNKK-LFLRINKP

Parental  GETQVFSYEMLHVTPPMSPPDVLKTSPVADAA-GWVDVDKET
          G.TQ..SYEML.VT.P.SP.DVLKTSPVADAA..WVDVDKET
Retrocopy GDTQASSYEMLYVTSPVSPSDVLKTSPVADAA>FWVDVDKET

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	11.70 RPM
SRP017611_kidney	0.00 RPM	29.90 RPM
SRP017611_liver	0.00 RPM	41.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_441 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_441 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_441 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000005597	1 retrocopy	retro_mmur_174,
Oryctolagus cuniculus	ENSOCUG00000014347	1 retrocopy	retro_ocun_441 ,