RetrogeneDB ID: retro_rnor_814

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:72645978..72647084(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ccnb1
• Ensembl ID: ENSRNOG00000018635
• Aliases: None
• Description: G2/mitotic-specific cyclin-B1 [Source:UniProtKB/Swiss-Prot;Acc:P30277]

Sequence

>retro_rnor_814
CCTCTGAGAGAGGAAGCAAAAACATTAGGTACTGGAAAAGTTACTGTTAAAGTCTGCCAAACCTGTGGAGAAGGTGCCTG
TGTGTGAACCAGAGGTAGAACTTGCTGAGCACGAGCCTGAACTTGAACCTGCTGTAGAGGAGAAGCCTTCTCCTGAGCCT
ATTTTGGTTGATAATCCCCCTCCCAGCCCAATGGAAACATCTGGATGTGCACCTGCAGAAGCATATCTGTGTCAGGCTTT
CTCTGACGTAATTCTTGCAGTGAGTGATGTAGATGCAGACGATGGAGCTGATCCAAACCTCTGTAGAGACTATGTGAATG
ATCTCCACGCTTATCTCAGACAACTGGAGGAAGAGCAGTCAGTCAGTCAGACCAAAATACTTCCTGGGTCAGGTCACTGG
AAACATGAGAGCCATCCTAATTGACTGGCTAATACAGGTTCAGATGAAATTCAGGCGCTGCAGGAGACTGCGTGCGTACA
GGGCTGTCTCCATTACTGATCGGTTCATACAGAACAATTGTGTGCCCAAGAAGATGCCGCAGCTGGTTGGTGTAACTGCT
GTGTTTACCGAAAGCAATGTGAGGAGATGTGCCCTCCAGAGATAGGTGGCTTTGCTTTTGTGACTAACAACACTTAGACT
AAGCACCAGATCAGGCAGATGGAGATAAAGACTCTGAGAGTTCTAAACTTCAGTCCGGGTCGCCCTCTGCCTCAGCACCT
CCTCTGTAGAGCATCTTAAATTGGAGCCGCTGTTGAGCCGCTTACTCTGGCCAAATACCTCCTGGAGCTCTCTATGCTAG
ACTCCGGACATGGTGTATCTTGCTCCTTCTCAAACTGCAGCCGGGGCTTTGTGCTTAGCACTAAAAACTCTTGACAGTGG
TGAATGGACGCCAACTCTGTGGCACTTCCTCTCCTACACCAAAGAATCTCGGCTTCCTGTCATGCAGCACCCGGCTGAGA
ACAGAGCCATGGTGAACGGTGGTGGCCTTACACAGCACACGACTACCGAGAACGCGTATGCACCATCTAAGCATGCTAAG
ATCAGCACTCGGGCACAGCTGAATTGTACACTAGATCAGAATCTGTCTAAGGCCATGACAACGGCA

Alignment

ORF - retro_rnor_814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.94 %
• Parental protein coverage: 86.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PLKKETKKLGSGTVTVK-ALP-KPVDKVPVCEPEVELDEPEPE--PVMEVKHSPEPILVDTPSPSPMETS
          PL..E.K.LG.G.VTVK..LP.KPV.KVPVCEPEVEL.E.EPE..P..E.K.SPEPILVD.P.PSPMETS
Retrocopy PLREEAKTLGTGKVTVK<SLP<KPVEKVPVCEPEVELAEHEPELEPAVEEKPSPEPILVDNPPPSPMETS

Parental  GCAPAEEYLCQAFSDVILAVSDVDADDGGDPNLCSEYVKDIYAYLRQL-EEE-QSVRPKYLLGREVTGNM
          GCAPAE.YLCQAFSDVILAVSDVDADDG.DPNLC..YV.D..AYLRQL.EE..QSVRPKY.LG..VTGNM
Retrocopy GCAPAEAYLCQAFSDVILAVSDVDADDGADPNLCRDYVNDLHAYLRQLEEEQ>QSVRPKYFLG-QVTGNM

Parental  RAILIDWLIQVQMKFRLLQE-TMYMTVSIIDRFMQDSCVPKKMLQLVGVTAMFIAS-KYEEMYPPEIGDF
          RAILIDWLIQVQMKFR.......Y..VSI.DRF.Q..CVPKKM.QLVGVTA.F..S...EEM.PPEIG.F
Retrocopy RAILIDWLIQVQMKFRRCRRLRAYRAVSITDRFIQNNCVPKKMPQLVGVTAVFTES<QCEEMCPPEIGGF

Parental  AFVTNNTYTKHQIRQMEMKILRVLNFSLGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELSMLDY-DMVH
          AFVTNNT.TKHQIRQME.K.LRVLNFS.GRPLP.H.L.RAS.IG...VE..TLAKYL.ELSMLD..DMV.
Retrocopy AFVTNNT*TKHQIRQMEIKTLRVLNFSPGRPLPQHLLCRAS*IGAA-VEPLTLAKYLLELSMLDS>DMVY

Parental  FAPSQIAAGAFCLALKILDNGEWTPTLQHYLSHTEESLLPVMQHLAKNIVMVN-RGLTKHMTIKNKYATS
          .APSQ.AAGA.CLALK.LD.GEWTPTL.H.LS.T.ES.LPVMQH.A.N..MVN..GLT.H.T..N.YA.S
Retrocopy LAPSQTAAGALCLALKTLDSGEWTPTLWHFLSYTKESRLPVMQHPAENRAMVNGGGLTQHTTTENAYAPS

Parental  KHAKISTLAQLNCTLVQNLSKAVTKA
          KHAKIST.AQLNCTL.QNLSKA.T.A
Retrocopy KHAKISTRAQLNCTLDQNLSKAMTTA

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	0.07 RPM	1.87 RPM
SRP017611_kidney	0.00 RPM	1.19 RPM
SRP017611_liver	0.00 RPM	0.20 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_814 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_814 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_814 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007705	1 retrocopy	retro_cfam_213,
Callithrix jacchus	ENSCJAG00000016075	1 retrocopy	retro_cjac_4137,
Cavia porcellus	ENSCPOG00000014629	1 retrocopy	retro_cpor_13,
Felis catus	ENSFCAG00000001572	1 retrocopy	retro_fcat_840,
Mustela putorius furo	ENSMPUG00000014648	1 retrocopy	retro_mputfur_58,
Mus musculus	ENSMUSG00000041431	5 retrocopies	retro_mmus_1170, retro_mmus_1550, retro_mmus_2508, retro_mmus_2615, retro_mmus_3023,
Procavia capensis	ENSPCAG00000002451	1 retrocopy	retro_pcap_176,
Rattus norvegicus	ENSRNOG00000018635	2 retrocopies	retro_rnor_568, retro_rnor_814 ,
Sarcophilus harrisii	ENSSHAG00000007685	1 retrocopy	retro_shar_290,
Tupaia belangeri	ENSTBEG00000011817	4 retrocopies	retro_tbel_1185, retro_tbel_3200, retro_tbel_4185, retro_tbel_4531,