RetrogeneDB ID:

retro_mmus_356

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:1:118249862..118250702(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Rbbp4
Ensembl ID:ENSMUSG00000057236
Aliases:Rbbp4, mRbAp48
Description:retinoblastoma binding protein 4 [Source:MGI Symbol;Acc:MGI:1194912]


Retrocopy-Parental alignment summary:






>retro_mmus_356
CTGGCTGACAAGGAAGCAGCCTTTGATGACACGGTAAAAGAATATGTGATCAACAAGGAGTAAAAACTATGGAAGAAGAA
CACCCCTTTTCTTTATGATTTGGTGATGACCCAGTCTCTGGAGTGGCCAAACTTAACTGGCCAGTGGCTTCCAGATGTGA
CTAGTCCTGAAGGGAAAGATTTCAGCATTCATCAGCTTGTCCAGAGAACACACACATCAGATGAACAAAACGACCTAGTG
ATAGCCAGTGTTCAGCTCCCTAATGATGATGTTCAGTTGTATGCATTCCCTTATGACAGCAAAAAAGGCAAATTAAGAGG
TTTTAGTTCTGTCAGTGGAAAAACTGACATAGAAATCAAGATTAACCATGAAAGAGAAGTAAACAGGGCCTGGTAAATGC
CTCAGAATCCTTGCATCATTGCAACAAAGACTCCATCCAGTGATATTTTTGTTTTTGACTACACAAAGTACCCTTCTAAA
CCAGACCCTTCCAGAGAATGCAACTCAAATTTGTATCTCCTTGAACATCAGAAGAAAGGTTATGGGCTTTCTTGGAATCC
AAATCTCACCGGGCACTTACTTAGTGCTTCAGATGACCATACCATCTGCCTGTGGGACATCAGTGCAGTTCCAAGAGAAG
GAAAAATGGTGGATGCAAAGATCATCTTTACAGGGCATACAGCAGTACTAGAGGATGTTTCCTGCCATCTGCTCCACAGG
TCTCTGTTTGGGACAGTTGCTTATGATCAGAAACTTATGATTTGAGATACTTGTTCAAACAATACTTCCAAGCTAAGCCA
CTCAGTTGATGCTCACACAGCTGAAGTGAATTGCTTATCT

ORF - retro_mmus_356 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.07 %
Parental protein coverage: 65.88 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGT
.ADKEAAFDD.V.E.VIN.E.K.WKKNTPFLYDLVMT..LEWP.LT.QWLPDVT.PEGKDFSIH.LV..T
RetrocopyLADKEAAFDDTVKEYVINKE*KLWKKNTPFLYDLVMTQSLEWPNLTGQWLPDVTSPEGKDFSIHQLVQRT
ParentalHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCII
HTSDEQN.LVIASVQLPNDD.Q..A..YDS.KG...GF.SVSGK..IEIKINHE.EVNRA..MPQNPCII
RetrocopyHTSDEQNDLVIASVQLPNDDVQLYAFPYDSKKGKLRGFSSVSGKTDIEIKINHEREVNRAW*MPQNPCII
ParentalATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAV
ATKTPSSD..VFDYTK.PSKPDPS.ECN..L.L..HQK.GYGLSWNPNL.GHLLSASDDHTICLWDISAV
RetrocopyATKTPSSDIFVFDYTKYPSKPDPSRECNSNLYLLEHQKKGYGLSWNPNLTGHLLSASDDHTICLWDISAV
ParentalPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLS
P.EGK.VDAK.IFTGHTAV.EDVS.HLLH.SLFG.VA.DQKLMI.DT.SNNTSK.SHSVDAHTAEVNCLS
RetrocopyPREGKMVDAKIIFTGHTAVLEDVSCHLLHRSLFGTVAYDQKLMI*DTCSNNTSKLSHSVDAHTAEVNCLS

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
SRP007412_brain 0 .00 RPM 104 .76 RPM
SRP007412_cerebellum 0 .00 RPM 108 .90 RPM
SRP007412_heart 0 .00 RPM 71 .47 RPM
SRP007412_kidney 0 .00 RPM 121 .39 RPM
SRP007412_liver 0 .00 RPM 99 .24 RPM
SRP007412_testis 0 .05 RPM 138 .91 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_356 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_356 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_356 retrocopy 5' end.

Lab - click to see more details

retro_mmus_356 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_356 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 23 parental genes, and 57 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000059042 retrocopies
retro_btau_1610, retro_btau_630,
Canis familiaris ENSCAFG000000105271 retrocopy
retro_cfam_1550,
Choloepus hoffmanni ENSCHOG000000040666 retrocopies
retro_chof_1382, retro_chof_1649, retro_chof_1867, retro_chof_2116, retro_chof_2327, retro_chof_908,
Callithrix jacchus ENSCJAG000000010217 retrocopies
retro_cjac_1157, retro_cjac_1787, retro_cjac_1873, retro_cjac_244, retro_cjac_2557, retro_cjac_2719, retro_cjac_2939,
Cavia porcellus ENSCPOG000000153523 retrocopies
retro_cpor_154, retro_cpor_27, retro_cpor_899,
Equus caballus ENSECAG000000227841 retrocopy
retro_ecab_767,
Echinops telfairi ENSETEG000000200084 retrocopies
retro_etel_1088, retro_etel_1462, retro_etel_1877, retro_etel_676,
Felis catus ENSFCAG000000270171 retrocopy
retro_fcat_1507,
Homo sapiens ENSG000001625216 retrocopies
retro_hsap_1305, retro_hsap_2675, retro_hsap_2814, retro_hsap_3292, retro_hsap_3600, retro_hsap_3601,
Macropus eugenii ENSMEUG000000143791 retrocopy
retro_meug_1032,
Myotis lucifugus ENSMLUG000000007492 retrocopies
retro_mluc_2275, retro_mluc_892,
Macaca mulatta ENSMMUG000000099401 retrocopy
retro_mmul_75,
Mustela putorius furoENSMPUG000000152141 retrocopy
retro_mputfur_104,
Mus musculus ENSMUSG000000313531 retrocopy
retro_mmus_3529,
Mus musculus ENSMUSG000000407821 retrocopy
retro_mmus_3678,
Mus musculus ENSMUSG00000057236 1 retrocopy
retro_mmus_356 ,
Nomascus leucogenys ENSNLEG000000028056 retrocopies
retro_nleu_1061, retro_nleu_1179, retro_nleu_1194, retro_nleu_1356, retro_nleu_1379, retro_nleu_2982,
Petromyzon marinus ENSPMAG000000071891 retrocopy
retro_pmar_26,
Pongo abelii ENSPPYG000000015886 retrocopies
retro_pabe_1093, retro_pabe_2210, retro_pabe_2720, retro_pabe_2958, retro_pabe_3529, retro_pabe_3611,
Pteropus vampyrus ENSPVAG000000109812 retrocopies
retro_pvam_1094, retro_pvam_902,
Rattus norvegicus ENSRNOG000000214921 retrocopy
retro_rnor_1270,
Sarcophilus harrisii ENSSHAG000000109231 retrocopy
retro_shar_399,
Ictidomys tridecemlineatus ENSSTOG000000120111 retrocopy
retro_itri_1168,


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