RetrogeneDB ID:

retro_mmus_2745

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:6:70408698..70409825(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Odc1
Ensembl ID:ENSMUSG00000011179
Aliases:Odc1, ODC
Description:ornithine decarboxylase, structural 1 [Source:MGI Symbol;Acc:MGI:97402]


Retrocopy-Parental alignment summary:






>retro_mmus_2745
TCTGAACACCAAATAACAAATGAAGTCTCTTCTTTCTATGTTGCAGACCTCGGAGACATTCTAACGAAGCATCTGAAGTG
GCTAAAAGCTCTTCCCCTTGTTACTCCCTTTTATACACTCAAGTGAAAGGACAACAGAGCCATGGTGAACAGCCTAGCTG
CTATTGGGACAGGATTTGACTGTGCAAGCAAGACTGAAATACTGTTGGTGCAGGGGCTTAGGGTGCCTCCAGAGAGGATT
ACCTATGCACGGCTTTGTTGTAAACAAGTGTCTCAAATCAAGTATGCTGCCAGTAATGGAGACCATATGATGACTTTTGA
CAGTGAAATTGAATTCATGAAAGTCGTCAGAGCACATCAAAAGACAAAGTTGGTTTTGTGGACTGTCACTGATGATTGCA
AAGCAGTTTGTTGACTCGGTGTTAAGTCTGATGCCACACTCAAAACCAGCAGTCTCCTCCTGAAAAGGGCAAAAGAGCTA
AATATTGACGTCATTGGTGTCAGCTTCCATGTGTGCAGTAGAATTATTGACCCTGAGACCTTCATGCAGGCAGTATCAGA
TGCCCGCTGTGTATTTGACATAAGAACAGAAGTTGGTTTCAGCATGTATCTGCTTGATATTGGTGGTAGCTTTCGTGGAT
CTGAAGATACAAAGCTTAAATTTGAAGAGATCACCAGTGTGATCAACCCAACTCTGGACAAGTATTTCCCATCAGACTCT
GGAGTGAGAATCACAGCTGAGCCAGGCAGATACTATGCTCAGCTTTCATACTCGCAGTCAACATCATTGCCCCCCCACAA
AAAAAAATCGTAGAAGGAGCAGACCTGCTCTGACGATGAAGATGAGCAAACCTTCATGCATTATGTGAATGATGGAGTGT
ACTGATCATTTAACTGCATTCTTTATGATCATGCACATGTGAAGGCCCTGCTGCAGAAGAGACCCAAGTCAGATGAGAAG
TATTACTAATCCAGCATCTGGGAGCCAACATGCGATGGCCTTGATCCAATCGTTGAGCACTGTAACCAGCCTGAAATGCA
TGTGGGTGATTGGATGCTGTTTGAAACATGGGTGAATACACCATTGCTGTTGCTTCTACTTTCATTGGGTTCCAGAGGCC
CAACATC

ORF - retro_mmus_2745 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.61 %
Parental protein coverage: 81.78 %
Number of stop codons detected: 5
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalNEVSSSDDKDAFYVADLGDILKKHLRWLKALPRVTPFYAVKCNDSRAIVSTLAAIGTGFDCASKTEIQLV
.E.........FYVADLGDIL.KHL.WLKALP.VTPFY..K..D.RA.V..LAAIGTGFDCASKTEI.LV
RetrocopySEHQITNEVSSFYVADLGDILTKHLKWLKALPLVTPFYTLK*KDNRAMVNSLAAIGTGFDCASKTEILLV
ParentalQGLGVPAERVIYANPC-KQVSQIKYAASNGVQMMTFDSEIELMKVARAHPKAKLVLRIATDDSKAVCRLS
QGL.VP.ER..YA..C.KQVSQIKYAASNG..MMTFDSEIE.MKV.RAH.K.KLVL...TDD.KAVC.L.
RetrocopyQGLRVPPERITYARLCCKQVSQIKYAASNGDHMMTFDSEIEFMKVVRAHQKTKLVLWTVTDDCKAVC*LG
ParentalVKFGATLKTSRLLLERAKELNIDVIGVSFHVGSGCTDPETFVQAVSDARCVFDMATEVGFSMHLLDIGGG
VK..ATLKTS.LLL.RAKELNIDVIGVSFHV.S...DPETF.QAVSDARCVFD..TEVGFSM.LLDIGG.
RetrocopyVKSDATLKTSSLLLKRAKELNIDVIGVSFHVCSRIIDPETFMQAVSDARCVFDIRTEVGFSMYLLDIGGS
ParentalFPGSEDTKLKFEEITSVINPALDKYFPSDSGVRIIAEPGRYYVASAFTLAVNIIAKKTVWKEQPGSDDED
F.GSEDTKLKFEEITSVINP.LDKYFPSDSGVRI.AEPGRYY.........................D..
RetrocopyFRGSEDTKLKFEEITSVINPTLDKYFPSDSGVRITAEPGRYYAQLSYSQSTSLPPHXXXS*KEQTCSDDE
ParentalESNEQTFMYYVNDGVYGSFNCILYDHAHVKALLQKRPKPDEKYYSSSIWGPTCDGLDRIVERCNLPEMHV
...EQTFM.YVNDGVY.SFNCILYDHAHVKALLQKRPK.DEKYY.SSIW.PTCDGLD.IVE.CN.PEMHV
RetrocopyD--EQTFMHYVNDGVY*SFNCILYDHAHVKALLQKRPKSDEKYY*SSIWEPTCDGLDPIVEHCNQPEMHV
ParentalGDWMLFE-NMGAYTVAAASTFNGFQRPNI
GDWMLFE.NMG.YT.A.ASTF.GFQRPNI
RetrocopyGDWMLFE<NMGEYTIAVASTFIGFQRPNI

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 .02 RPM 36 .54 RPM
SRP007412_cerebellum 0 .00 RPM 43 .94 RPM
SRP007412_heart 0 .00 RPM 40 .72 RPM
SRP007412_kidney 0 .00 RPM 253 .38 RPM
SRP007412_liver 0 .00 RPM 51 .94 RPM
SRP007412_testis 0 .00 RPM 221 .74 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_mmus_2745 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2745 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_2745 retrocopy 5' end.

Lab - click to see more details

retro_mmus_2745 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2745 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 8 parental genes, and 51 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000114151 retrocopy
retro_amel_414,
Bos taurus ENSBTAG000000042561 retrocopy
retro_btau_552,
Dasypus novemcinctus ENSDNOG0000001847431 retrocopies
retro_dnov_1032, retro_dnov_1128, retro_dnov_1129, retro_dnov_1137, retro_dnov_1212, retro_dnov_1235, retro_dnov_1418, retro_dnov_1434, retro_dnov_1493, retro_dnov_1594, retro_dnov_1595, retro_dnov_1677, retro_dnov_1778, retro_dnov_1810, retro_dnov_1813, retro_dnov_2016, retro_dnov_2027, retro_dnov_2108, retro_dnov_2147, retro_dnov_2180, retro_dnov_2212, retro_dnov_2461, retro_dnov_2551, retro_dnov_2564, retro_dnov_392, retro_dnov_740, retro_dnov_766, retro_dnov_781, retro_dnov_923, retro_dnov_943, retro_dnov_958,
Myotis lucifugus ENSMLUG000000104231 retrocopy
retro_mluc_281,
Macaca mulatta ENSMMUG000000204412 retrocopies
retro_mmul_157, retro_mmul_1645,
Monodelphis domestica ENSMODG000000147791 retrocopy
retro_mdom_262,
Mus musculus ENSMUSG00000011179 12 retrocopies
retro_mmus_2588, retro_mmus_2744, retro_mmus_2745 , retro_mmus_2746, retro_mmus_2747, retro_mmus_2834, retro_mmus_2922, retro_mmus_3237, retro_mmus_3677, retro_mmus_503, retro_mmus_912, retro_mmus_984,
Ictidomys tridecemlineatus ENSSTOG000000003862 retrocopies
retro_itri_1751, retro_itri_801,


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