RetrogeneDB ID:

retro_rnor_1287

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:17:16406657..16408290(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Wbp11
Ensembl ID:ENSRNOG00000005505
Aliases:None
Description:WW domain-binding protein 11 [Source:UniProtKB/Swiss-Prot;Acc:Q5PQQ2]


Retrocopy-Parental alignment summary:






>retro_rnor_1287
TCTGCTTTTTTGAAGGTTAAGGTCGCAAACAGATTATCCGGGACTTGGAGAAATTGAATGAAACAGAGTTTAACCCAGTG
CAACAGCCACAGTTGAATGAGAAAATATGAAAGACAAGCGGAAAAAGGTGCGGGAAAACTTTGAATGAATTCTACGACTT
TATGAAAAAGAAAACCCAGATATTTATGAAGAGTTGAGAAAGCTAGACGTAGCTTATGAACAGAAGAGAGCTCAACTGAG
CCAATGCTTTGATGCCATCAGCAATGCTCACCATGTGGACGTAGAGAGCATTCCTTGGCCAGACATGCCGCATGCTCCTT
CCAACATCTTGATCCAGGACATTCCTCTTCCTGGTGCCCTGCCACCCTCCATCTTGAAGAAAACCTCAGCATATGGGTCT
CCAACTCGAGCTGTTTTGATCCTTCCTCTACTGGGACATGGTGTTCCACATTTGCCCCCTGATAGAAAACTGCACAGCCC
TCTACATGGCCCACCTCCTCCTCTGCAGATGCATGGCCAAAGACCGGGCTTTGCTCTAGATCTCCCCTCGGAGGTGAGAG
GAAGACATGCTGTACAGTCCAGAGCTTGCTCAGCGGGTCATGACGATGACATGTCCAGTACCAGTGAGGACAATGGCTAT
CCTGAGGTCATGGATCAGGATAAGCGGGATGACAATACTGAGGACGGTGACACGGACAGATTGGCCACAGAGAGTGATGG
GGATGAGGTGGGCACCACGATGTCAGTGAGCCCGACAACTCTGAGGAGGAGAAGTCAGGTCTGAGCATCTGATTTACAGA
TGCCTGGGAAACCAAGGGAGAAGAACATGAAGGAGCTGACTCCTCTTCAAGTCATGATGCTGCGAATGGCAGGTCAGGAA
ATCCCTGAGGAAGGACGGGAAGTGGAGGAGTTTTCAGAGGAGGATGACGATGAAGACGGATGATTCTGAAGCAGAGAAGC
AATCACAAAGCAGCATAAAGATTCCCACTCTGGTGGCTCGTCTGCTCCCTCTTCACAGCAGCAGGCTCCTGCACAGTCCG
TCCTCCTCCTCACACACAAGCACCTCCCATGCCAGGACCACCACGTCTTGGACAACCACCTGTCCCACCCTTGTGGTCTC
CTGGACCACCTATGGGCCTTCCTCCTGGGCCACCCCAGAGGCTCCTCCATTCCTAGAACCATCTGGAATGCCAGGAATTG
GAGGGCCTTTACCACAACTTTTACCTCCACCAGGACCACCACCAGACCAAACTCCTGATCCTCCCCCAGGCCCACCTCCT
GGCCTGCCCCCTGGTTCCTCCTCAAGACCCCCGTCAAAGCTACTTCCTCCCACACCTCATCCTGGCATGATGCGCCCACC
CTTGCTGCCCCCTATTGCACCTAACCCACCTGGCCTTTTCTCACCAGCTCCCTTGCCCAACCCAGAAGTGTTGAGTTTCC
TGCCCGCCCTCACTCAAAAACAAAAGGCAGATGATGCAAGTGCAGCCACCATCGAGAAGAAGCCACAGCAACCATGAGTG
CCAAGTCCCAGATCACCAATCCCAAGGCAAAGGTCACACGGTTTGTGCCCACTGCACTGCGGGTGCCCCATGAGAATAAG
AGGGCTACTGTTGTTGACCCCAAAGAGGGTCAG

ORF - retro_rnor_1287 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.75 %
Parental protein coverage: 87.36 %
Number of stop codons detected: 3
Number of frameshifts detected: 10


Retrocopy - Parental Gene Alignment:

ParentalAAVLKMK-DPKQIIRDMEKLDEMEFNPVQQPQLNEKV-LKDKRKKLRETFERILRLYEKENPDIYKELRK
.A.LK.K...KQIIRD.EKL.E.EFNPVQQPQLNEK...KDKRKK.RE.FE.ILRLYEKENPDIY.ELRK
RetrocopySAFLKVK<GRKQIIRDLEKLNETEFNPVQQPQLNEKI<MKDKRKKVRENFE*ILRLYEKENPDIYEELRK
ParentalLEVEYEQKRAQLSQYFDAVKNAQHVEVESIPLPDMPHAPSNILIQDIPLPGAQPPSILKKTSAYGPPTRA
L.V.YEQKRAQLSQ.FDA..NA.HV.VESIP.PDMPHAPSNILIQDIPLPGA.PPSILKKTSAYG.PTRA
RetrocopyLDVAYEQKRAQLSQCFDAISNAHHVDVESIPWPDMPHAPSNILIQDIPLPGALPPSILKKTSAYGSPTRA
ParentalVSILPLLGHGVPRLPPGRKPPGPPPGPPPPQVLQMYGR-KVGFALDLP-PRRRDEDMLYSPELAQR-GHD
V.ILPLLGHGVP.LPP.RK...P..GPPPP..LQM.G..K.G.....P.PRR..EDMLYSPELAQR.GHD
RetrocopyVLILPLLGHGVPHLPPDRKLHSPLHGPPPP--LQMHGQ<KTGLCSRSP<PRR*EEDMLYSPELAQR<GHD
ParentalDDMSSTSEDDGYPEDMDQDKHDDSTEDSDTDRSDAESDGDEFGHRDDSERDNTEEKKSGLSVRFADMPGK
DDMSSTSED.GYPE.MDQDK.DD.TED.DTDR...ESDGDE.G....S....T....S........MPGK
RetrocopyDDMSSTSEDNGYPEVMDQDKRDDNTEDGDTDRLATESDGDEVG-TTMSVSPTTLRRRSQV*ASDLQMPGK
ParentalSRKKKKNMKELTPLQAMMLRMAGQEIPEEGREVEEFSEEEDDDD-SEDSEAEKPSQ-KQHKEDSHADGSS
.R.K..NMKELTPLQ.MMLRMAGQEIPEEGREVEEFSEE.DDD....DSEAEK.SQ.KQHK.DSH..GSS
RetrocopyPREK--NMKELTPLQVMMLRMAGQEIPEEGREVEEFSEE-DDDE>TDDSEAEKQSQ<KQHK-DSHSGGSS
ParentalAASSQQQAPPQAV-PPSQIQAPPMPGPPPLGPPPAPPLRPPGPPTGLPPGPP-PGAPPFLRPPGMPGIRG
A.SSQQQAP.Q.V.PP...QAPPMPGPP.LG.PP.PPL..PGPP.GLPPGPP.P.APPFL.P.GMPGI.G
RetrocopyAPSSQQQAPAQSV<PPPHTQAPPMPGPPRLGQPPVPPLWSPGPPMGLPPGPP<PEAPPFLEPSGMPGIGG
ParentalPLPRLLPPGPPPGRPPGPPPGPPPGLPPGPPPRGPPPRLPPPAPPGIPPPRPGMMRPPLVPPLGPAPPGL
PLP.LL...PPPG.PP...P.PPPG.PPG.PP.G...R.P....P..P.P.PGMMRPPL.PP..P.PPGL
RetrocopyPLPQLL---PPPGPPPDQTPDPPPGPPPGLPP-GSSSRPPSKLLP--PTPHPGMMRPPLLPPIAPNPPGL
ParentalFPPAPLPNPGVLSAPPSLIQRPKADDASAATIEKK-ATATISAKPQITNPKAEVTRFVPTALRVRRENKG
F.PAPLPNP.VLS..P.L.Q..KADDASAATIEKK.ATAT.SAK.QITNPKA.VTRFVPTALRV..ENK.
RetrocopyFSPAPLPNPEVLSFLPALTQKQKADDASAATIEKK<ATATMSAKSQITNPKAKVTRFVPTALRVPHENKR
ParentalATAVPQRRSE
AT.V......
RetrocopyATVVDPKEGQ

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 0 .00 RPM 0 .00 RPM
SRP017611_kidney 0 .00 RPM 0 .07 RPM
SRP017611_liver 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_1287 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1287 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1287 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 22 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000147591 retrocopy
retro_btau_20,
Canis familiaris ENSCAFG000000129262 retrocopies
retro_cfam_1369, retro_cfam_1911,
Callithrix jacchus ENSCJAG000000216111 retrocopy
retro_cjac_1737,
Homo sapiens ENSG000000844632 retrocopies
retro_hsap_1878, retro_hsap_4719,
Gorilla gorilla ENSGGOG000000044483 retrocopies
retro_ggor_1375, retro_ggor_1711, retro_ggor_2932,
Macropus eugenii ENSMEUG000000139711 retrocopy
retro_meug_1952,
Myotis lucifugus ENSMLUG000000152161 retrocopy
retro_mluc_1074,
Macaca mulatta ENSMMUG000000192991 retrocopy
retro_mmul_1329,
Monodelphis domestica ENSMODG000000179491 retrocopy
retro_mdom_143,
Mustela putorius furoENSMPUG000000116191 retrocopy
retro_mputfur_280,
Mus musculus ENSMUSG000000302161 retrocopy
retro_mmus_2740,
Nomascus leucogenys ENSNLEG000000039261 retrocopy
retro_nleu_2651,
Oryctolagus cuniculus ENSOCUG000000171771 retrocopy
retro_ocun_974,
Otolemur garnettii ENSOGAG000000105181 retrocopy
retro_ogar_207,
Ochotona princeps ENSOPRG000000150083 retrocopies
retro_opri_107, retro_opri_1159, retro_opri_678,
Pongo abelii ENSPPYG000000043233 retrocopies
retro_pabe_1558, retro_pabe_2099, retro_pabe_3663,
Pan troglodytes ENSPTRG000000047243 retrocopies
retro_ptro_1260, retro_ptro_1637, retro_ptro_3136,
Rattus norvegicus ENSRNOG00000005505 3 retrocopies
retro_rnor_1287 , retro_rnor_2726, retro_rnor_741,
Rattus norvegicus ENSRNOG000000495931 retrocopy
retro_rnor_740,
Sorex araneus ENSSARG000000070851 retrocopy
retro_sara_753,
Sarcophilus harrisii ENSSHAG000000166491 retrocopy
retro_shar_81,
Tupaia belangeri ENSTBEG000000033941 retrocopy
retro_tbel_2213,


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