RetrogeneDB ID: retro_ocun_425

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 10:32162199..32162798(+)
• Located in intron of: ENSOCUG00000015296

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNJ
• Ensembl ID: ENSOCUG00000011114
• Aliases: None
• Description: cyclin J [Source:HGNC Symbol;Acc:23434]

Sequence

>retro_ocun_425
ATGGAGCTGGAGGGGCAGTGGTGGCAGCAGCAGCTGGTTGCAGATAGTCACCACGCACTTTGGTACAAGGTGCTCAAGTC
GCCCTGCTACAAGGGCCGGTCCCCTCCAGCGAGTCTCAGACGGTATTCTGGTGACTCAACCGCCACTGTGAGCAACCGCT
TCCCACTCTGCCCCTCTGCCCAACACCCTGCTGTCTACTTGCTGGACCTGTTTATGGATCGCCAGGACATCTCCACCCAG
CAGCTGCATCTACCTGCTCTTTCCTGTCTGCGTCCAGCAAGCAAATGCGAAGGAAGAGAGAGAGTGTGCCCAGGCTGGAG
CAGCTCAGCAGCCTGGCTTGTGTGACTGACATGAATCTAGTTTCAACAAAGCAGAACCTGCTACATATGAACTGTTACTA
TGAGACACCTCTCAGCAGAACCTCTGCCTTCCGACAGCTGCTCATTTCATGGGTATTATCTTTCTGAAGCTGTACGCGAA
ACACATCTTCATGATGCTGGCCGATGCTTTGCTTGGAAAAAACAACTTACCTGGCCAAATGTGCAGATGACTTCCTAGAA
GTATCTCTGTGAGATTATGCCTTTCCAAATTATGCACCT

Alignment

ORF - retro_ocun_425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.82 %
• Parental protein coverage: 52.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MELEGQWWRGQLAADIHQALRYKELKLPSYKGQSPQLSLRRYFADLIAIVSNRFTLCPSARHLAVYLLDL
          MELEGQWW..QL.AD.H.AL.YK.LK.P.YKG.SP..SLRRY..D..A.VSNRF.LCPSA.H.AVYLLDL
Retrocopy MELEGQWWQQQLVADSHHALWYKVLKSPCYKGRSPPASLRRYSGDSTATVSNRFPLCPSAQHPAVYLLDL

Parental  FMDRYDISIQQLHLVALSCLLLASKFE-EKEDSVPKLEQLNSLGCMTNMNLVLTKQNLLHM-ELLLLETF
          FMDR.DIS.QQLHL.ALSCL..ASK.E..K..SVP.LEQL.SL.C.T.MNLV.TKQNLLHM.ELLL..T.
Retrocopy FMDRQDISTQQLHLPALSCLRPASKCE<RKRESVPRLEQLSSLACVTDMNLVSTKQNLLHM<ELLL*DTS

Parental  QWNLCLPTAAHFI-EYYLSEAVHETDLHDG-WPMICLEKTKLYMAKYADYFLEVSLQDYAFLNYAP
          Q.NLCLPTAAHF...YYLSEAV.ET.LHD..WPM.CLEKT..Y.AK.AD.FLEVSL.DYAF.NYAP
Retrocopy QQNLCLPTAAHFM<GYYLSEAVRETHLHDA<WPMLCLEKT-TYLAKCADDFLEVSL*DYAFPNYAP

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	8.94 RPM
SRP017611_kidney	0.00 RPM	5.78 RPM
SRP017611_liver	0.00 RPM	4.55 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_425 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_425 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_425 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016259	1 retrocopy	retro_cjac_3274,
Erinaceus europaeus	ENSEEUG00000002270	2 retrocopies	retro_eeur_535, retro_eeur_577,
Homo sapiens	ENSG00000107443	1 retrocopy	retro_hsap_3850,
Gorilla gorilla	ENSGGOG00000006034	1 retrocopy	retro_ggor_2595,
Oryctolagus cuniculus	ENSOCUG00000011114	1 retrocopy	retro_ocun_425 ,
Tarsius syrichta	ENSTSYG00000009466	1 retrocopy	retro_tsyr_741,