RetrogeneDB ID:

retro_rnor_311

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:4:236961009..236962044(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000008125
Aliases:Igbp1b, RGD1560971
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Igbp1
Ensembl ID:ENSRNOG00000026267
Aliases:None
Description:Immunoglobulin-binding protein 1 [Source:UniProtKB/Swiss-Prot;Acc:O08836]


Retrocopy-Parental alignment summary:






>retro_rnor_311
ATGGCGGCGTTTATGGACGAGCAGCAGAAGCCGAAGCTCCGGGAGCTGTTGGAAACCGGCATAGAACTTCTGGAGGAGGT
GGAAGCTACGACCCAACCCACAGGCTCCAAGCAAATCCAGGAGAAGGTGAGGAAGGCCTTGAAACTCCTGGAGAAGGCCT
CGGAAATGTTATCGCAGCTCGATTTGTTCAGCAGGAACGAAGATTGGGAGGAGATTGCTTCCGCTGACCTCAAGTACCTG
ATGCTTCCGGCCCTGAAGGGCGCGCTGACCCTGAAGCTGGTGGGCACCAGCAATCGCCTCCACCTCCTGCAGGATGCTCG
AGAGCTCTTCATGAACTTCCTAACCCAGAGCCACAACTACCATGTGGCTGAGTTTCAGCTGCCCTGGGCCCAGAGCAGCT
CACAGGAAAGCAACCCCGCTGCTGCTACTTCTGACACCCTGGAGCACAACCTCGTTGCCATGGCATCCCAGAGGCAGGCC
AAAATCCAGAGGTACAAGCAAAAGAAGGCGGTGGAGCAGAGGCTGTCTTCTCTGAAATCGGCCGTGGAGAGCGGCGAGGC
AGACGACGAGCGTGTCAGGGAGTATTACCTCCTTCAACTTCGTAGGTGGATTAACATCAGCTTGGATGAGATCGACAGCA
TCGACCAGGAGATAGAGATCCTGAGGGAAAGAGACTCCTTCGGTGAGGCATCAGTTTCTCAAGGGTCTCCTCAGGAGAGA
CCTCCGCTGAAACCCTTTGTCCTCACTCGAAGTGTTGCCCAAGCACAAGTCTTTGGAGCTGGATACCCAAGTCTGGCAAC
TCTGACGGTGAATGACTGGTACGAGCAGCGCCAGAAAGGTGAGGTCTCATCTTCTGTTCGGGAAGCAGAAAAGCAGGCAC
CACCACTCGAGACTCTCTCTGTATCTGAGCCAGAAAAGCCGGACCTGGAACAAAAGGAAGAGGAAGATGAGAATGCCCTC
CACAGGATGCAGGAGTGGGATGACTGGAAGGACACCCATCCTAGGGGCTACGGCAACCGACAGAACATGGGCTAA

ORF - retro_rnor_311 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.66 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMAASEEELLLPRLPELFETSKKLLEELEVATEPTGSRTIQDKVSKGLELLEKAAGMLSQLDLFSRNEDLE
MAA...E...P.L.EL.ET...LLEE.E..T.PTGS..IQ.KV.K.L.LLEKA..MLSQLDLFSRNED.E
RetrocopyMAAFMDEQQKPKLRELLETGIELLEEVEATTQPTGSKQIQEKVRKALKLLEKASEMLSQLDLFSRNEDWE
ParentalEIASIDLKYLMVPALQGALTMKQVNPSKRLDHLQRAREHFIHFLTQCHCYHVAEFQLPQTKNNSAENN--
EIAS.DLKYLM.PAL.GALT.K.V..S.RL..LQ.ARE.F..FLTQ.H.YHVAEFQLP.....S.E.N..
RetrocopyEIASADLKYLMLPALKGALTLKLVGTSNRLHLLQDARELFMNFLTQSHNYHVAEFQLPWAQSSSQESNPA
ParentalTARSSMAYPNLVAMASQRQAKIERYKQKKEVEHRLSALKSAVESGQADDERVREYYLLHLRRWIGISLEE
.A.S.....NLVAMASQRQAKI.RYKQKK.VE.RLS.LKSAVESG.ADDERVREYYLL.LRRWI.ISL.E
RetrocopyAATSDTLEHNLVAMASQRQAKIQRYKQKKAVEQRLSSLKSAVESGEADDERVREYYLLQLRRWINISLDE
ParentalIESIDQEIKILKDKDSPREESACQSSLPEKPPMKPFILTRNKAQAKVFGTGYPSLATMTVSDWYEQHQKY
I.SIDQEI.IL...DS..E.S..Q.S..E.PP.KPF.LTR..AQA.VFG.GYPSLAT.TV.DWYEQ.QK.
RetrocopyIDSIDQEIEILRERDSFGEASVSQGSPQERPPLKPFVLTRSVAQAQVFGAGYPSLATLTVNDWYEQRQKG
ParentalGALPDRGIAKPPSADFQRAAQQQEDQEQKDEENE--EKALHRMREWDDWKDTHPRGYGNRQNMG
........A........................E..E.ALHRM.EWDDWKDTHPRGYGNRQNMG
RetrocopyEVSSSVREAEKQAPPLETLSVSEPEKPDLEQKEEEDENALHRMQEWDDWKDTHPRGYGNRQNMG

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 1 .22 RPM 20 .49 RPM
SRP017611_kidney 0 .00 RPM 32 .80 RPM
SRP017611_liver 0 .00 RPM 16 .94 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_311 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_311 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_311 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Mus musculus retro_mmus_169
Parental genes homology:
Parental genes homology involve 19 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000077971 retrocopy
retro_btau_215,
Choloepus hoffmanni ENSCHOG000000136543 retrocopies
retro_chof_1523, retro_chof_2206, retro_chof_438,
Callithrix jacchus ENSCJAG000000125256 retrocopies
retro_cjac_111, retro_cjac_1225, retro_cjac_2278, retro_cjac_2968, retro_cjac_3417, retro_cjac_47,
Cavia porcellus ENSCPOG000000107971 retrocopy
retro_cpor_44,
Dasypus novemcinctus ENSDNOG000000147315 retrocopies
retro_dnov_1160, retro_dnov_2029, retro_dnov_2340, retro_dnov_2380, retro_dnov_678,
Echinops telfairi ENSETEG000000033971 retrocopy
retro_etel_1637,
Felis catus ENSFCAG000000296881 retrocopy
retro_fcat_23,
Homo sapiens ENSG000000892895 retrocopies
retro_hsap_1317, retro_hsap_1848, retro_hsap_2766, retro_hsap_2919, retro_hsap_3059,
Gorilla gorilla ENSGGOG000000277952 retrocopies
retro_ggor_112, retro_ggor_2020,
Myotis lucifugus ENSMLUG000000041791 retrocopy
retro_mluc_316,
Macaca mulatta ENSMMUG000000139292 retrocopies
retro_mmul_1545, retro_mmul_31,
Mus musculus ENSMUSG000000312211 retrocopy
retro_mmus_169,
Nomascus leucogenys ENSNLEG000000007475 retrocopies
retro_nleu_1399, retro_nleu_1653, retro_nleu_2334, retro_nleu_671, retro_nleu_828,
Otolemur garnettii ENSOGAG000000117971 retrocopy
retro_ogar_110,
Pongo abelii ENSPPYG000000204354 retrocopies
retro_pabe_1099, retro_pabe_1451, retro_pabe_2245, retro_pabe_2533,
Pan troglodytes ENSPTRG000000219905 retrocopies
retro_ptro_1233, retro_ptro_1873, retro_ptro_1973, retro_ptro_1982, retro_ptro_901,
Pteropus vampyrus ENSPVAG000000054831 retrocopy
retro_pvam_1462,
Rattus norvegicus ENSRNOG00000026267 1 retrocopy
retro_rnor_311 ,
Tarsius syrichta ENSTSYG000000062142 retrocopies
retro_tsyr_1537, retro_tsyr_2131,


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