RetrogeneDB ID: retro_ocun_1277

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 6:19259763..19260658(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025910
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCND2
• Ensembl ID: ENSOCUG00000015589
• Aliases: None
• Description: cyclin D2 [Source:HGNC Symbol;Acc:1583]

Sequence

>retro_ocun_1277
AGTCCGGAGAAGGCAGGGGAACGAAGGGTCACCCGGCTGGCATGGAGCTGCTGTGCTGCGAGGTGGACCCCGTCCGCAGG
GCCGTGCAACCTGCTGGACGACCAGGCCCTGCAGAACTTGCTCACCATCGAGGAACGCTACCTTCCCCAGTGCTGCTACT
TCAAGTGTGTGCAGAAGGACATCCAGCCCTACATGCACAGGATGGTGGCCACCTGGACGCTGGAGGTCTGTAAGGAACAG
AAGTGTGAGGAGGAGGTCTTCCCGCTGGCCATGAACTACCTGGACCCTTCCTGGCCGGGGTGCCGACTCCCAAGACCCAT
CTGCAGCTGCTGGGGACCGTGTGCATGTTTCTGGCCTCCAAGCTGAAAGAGACCATCCTGCTGACGGCCGAGAAGCTGTG
CATCTACACGGGCAACTCCATCAAGCCCCAGGAGCTGCTGGAGTGGGAGCTGGTGGTGCTGGGGAAGCTGAAGTGGAACC
TGGCTGCCGTCTCCCCTCAAAACTGCAGGAGCATATCCTGCGCAAGCTTCCGCAGCAGAGGGAGAAGCTGTCTCTGATCC
GCAAGCACGCGCAGACCTTCATTGCTCTCTGCGCCACCGACTTCAAGTTCGCCATGTACCCGCCGTCCATGATCGCGACT
GGAAGCGTGGGGGCAGCCATCCGCGGGCTCCAGCAGGACGAAGAAGTGAGCTCGCTCACTTGCGATGCCCTGAGCGAGCT
GCTAGCCAAGATCACCAACACGGATGTGGATTGTCTCAGAGCCTGCCAGGAGCAGATTGCGGCCGTGCTTCTCAACAGCC
TGCAGCAGTTCCGTCAGGAGCAGCGCGACGGATCCAAGTCGGAGGATGAACTGGACCAAGCCAGCACCCCTACAGACGTG
CAGGACATCGACCTG

Alignment

ORF - retro_ocun_1277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.17 %
• Parental protein coverage: 70.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NPEKAGERRVARLAMELLCCEVDPVRRAVPDRNLLDDRVLQNLLTIEERYLPQCSYFKCVQKDIQPYMRR
          .PEKAGERRV.RLA....CC.......A.P..NLLDD..LQNLLTIEERYLPQC.YFKCVQKDIQPYM.R
Retrocopy SPEKAGERRVTRLAWS--CCAARWTPSAGPC-NLLDDQALQNLLTIEERYLPQCCYFKCVQKDIQPYMHR

Parental  MVATWMLEVCEEQKCEEEVFPLAMNYLDR-FLAGVPTPKTHLQLLGAVCMFLASKLKETIPLTAEKLCIY
          MVATW.LEVC.EQKCEEEVFPLAMNYLD..FLAGVPTPKTHLQLLG.VCMFLASKLKETI.LTAEKLCIY
Retrocopy MVATWTLEVCKEQKCEEEVFPLAMNYLDP<FLAGVPTPKTHLQLLGTVCMFLASKLKETILLTAEKLCIY

Parental  TDNSIKPQELLEWELVVLGKLKWNLAAVTPHD-FIEHILRKLPQQREKLSLIRKHPQTFIALCATDFKFA
          T.NSIKPQELLEWELVVLGKLKWNLAAV.P.....EHILRKLPQQREKLSLIRKH.QTFIALCATDFKFA
Retrocopy TGNSIKPQELLEWELVVLGKLKWNLAAVSPQN<LQEHILRKLPQQREKLSLIRKHAQTFIALCATDFKFA

Parental  MYPPSMIATGSVGAAICGLQQDEEVSSLTCDALTELLAKITNTDVDCLKACQEQIEAVLLNSLQQFRQEQ
          MYPPSMIATGSVGAAI.GLQQDEEVSSLTCDAL.ELLAKITNTDVDCL.ACQEQI.AVLLNSLQQFRQEQ
Retrocopy MYPPSMIATGSVGAAIRGLQQDEEVSSLTCDALSELLAKITNTDVDCLRACQEQIAAVLLNSLQQFRQEQ

Parental  RDGSKSEDELDQASTPTDVRDIDL
          RDGSKSEDELDQASTPTDV.DIDL
Retrocopy RDGSKSEDELDQASTPTDVQDIDL

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	0.33 RPM	77.21 RPM
SRP017611_kidney	0.00 RPM	16.72 RPM
SRP017611_liver	0.15 RPM	9.33 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1277 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1277 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1277 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001593	1 retrocopy	retro_cjac_3884,
Felis catus	ENSFCAG00000000138	1 retrocopy	retro_fcat_809,
Oryctolagus cuniculus	ENSOCUG00000009143	1 retrocopy	retro_ocun_676,
Oryctolagus cuniculus	ENSOCUG00000015589	1 retrocopy	retro_ocun_1277 ,
Oryctolagus cuniculus	ENSOCUG00000028042	1 retrocopy	retro_ocun_169,
Otolemur garnettii	ENSOGAG00000005208	1 retrocopy	retro_ogar_977,