RetrogeneDB ID:

retro_mmus_2588

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:5:95974239..95975623(+)
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_2588
ATGAGCAACTTTACTAAGGACGAGTTTGACTGCCACATCCTTGATGAAGGCTTTACTGCTAAGGACATTCTGGAACAAAA
AAATCAATGAAGTCTCTTCCTCTGACGATAAGGATGCGTTCTATGTTGCGGACCTCGGAGACATTCTAAAGAAGCATCTG
AGGTGGCTAAAAGCTCTTCCCCGCGTTACTCCCGTTTACGCAGTCAAGTGTAACGATAGCAGAGCCATAGTGAGCACCCT
AGCTGCCTTTGGGATAGGATTTGACTGTGCAAGCAAGACTGAAATACAGTTGGTACAGGGGCCTGGGGTGCCTCCAGAGA
CGATTATCTATGCAAATCCTTGTAAACAAGTCTCTCAAATCAAGTATGCTGCCAGTAGCGGAGTCCAGATGATGACTTTT
GACAGTGAAATTGAACTGATGAAAGTCGCCAGAGCACATCCAAAGGCAAAGTTGGTTCTGCGGATTGCCACTGATGATTC
CAAAGCTGTCTGTCGCCTCAGTGTTAAGTTTGGTGCCACACTCAAAACCAGCAGGCTTCTCTTGGAACGGGCAAAAGAGC
TAAATATTGACGTCATTGGTGTGAGCTTCCATGTGGGCAGTGGATGTACTGATCCTGAGACCTTCGTGCAGGCAGTGTCG
GATGCCCGCTGTGTGTTTGACATGGCAACAGAAGTTGGTTTCAGCATGCATCTGCTTGATATTGGTGGTGGCTTTCCTGG
ATCTGAAGATACAAAGCTTAAATTTGAAGAGATCACCAGTGTAATCAAACCAGCTCTGGACAAGTACTTCCCATCAGACT
CTGGAGTGAGAATCATAGCCGAGCCAGGCAGCTTTCACGCTTGCAGTCAACATCATTGCCAAAAAAAAAAAAAAAAAAAA
AAAAACGTGTGAAAGGAGCAGCCGAGTTCTGACGATGATGATGAGTCAAATGAGCAAACCTTCATGTATTATGTGAATGA
TGGAGTGTACGGATCATTTAACTGCATTCTTTATGACCATGCCCATGTGAAGGCCCTGCTGCAGAAGAGACCCAAGCCAG
ATGAGAAGTATTACTCATCCAGCATCTGGGGACCAACATGTGATGGCCTTGATCGGATCCTGGAGCGCTGTAACCTGCCT
GAAATGCATGTGGGTGATTGGATGCTGTTTGAGAACATGGGTGCATACACCGTTGCTGCTGCTTCTACTTTCAATGGGTT
CCAGAGGCCAAACATCTACTATGTAATGTCACGGCCAATGTGGCAACTCATGAAACAGATCCAGAGCCATGGCTTCCCGC
CGGAGGTGGAGGAGCAGGATGATGGCACGCTGCCCATGTCTTGTGCCCAGGAGAGCGGGATGGACCGTCACCCTGCAGCC
TGTGCTTCTGCTAGGATCAATGTG

ORF - retro_mmus_2588 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.64 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSSFTKDEFDCHILDEGFTAKDILDQK-INEVSSSDDKDAFYVADLGDILKKHLRWLKALPRVTPFYAVK
MS.FTKDEFDCHILDEGFTAKDIL.QK.INEVSSSDDKDAFYVADLGDILKKHLRWLKALPRVTP.YAVK
RetrocopyMSNFTKDEFDCHILDEGFTAKDILEQK>INEVSSSDDKDAFYVADLGDILKKHLRWLKALPRVTPVYAVK
ParentalCNDSRAIVSTLAAIGTGFDCASKTEIQLVQGLGVPAERVIYANPCKQVSQIKYAASNGVQMMTFDSEIEL
CNDSRAIVSTLAA.G.GFDCASKTEIQLVQG.GVP.E..IYANPCKQVSQIKYAAS.GVQMMTFDSEIEL
RetrocopyCNDSRAIVSTLAAFGIGFDCASKTEIQLVQGPGVPPETIIYANPCKQVSQIKYAASSGVQMMTFDSEIEL
ParentalMKVARAHPKAKLVLRIATDDSKAVCRLSVKFGATLKTSRLLLERAKELNIDVIGVSFHVGSGCTDPETFV
MKVARAHPKAKLVLRIATDDSKAVCRLSVKFGATLKTSRLLLERAKELNIDVIGVSFHVGSGCTDPETFV
RetrocopyMKVARAHPKAKLVLRIATDDSKAVCRLSVKFGATLKTSRLLLERAKELNIDVIGVSFHVGSGCTDPETFV
ParentalQAVSDARCVFDMATEVGFSMHLLDIGGGFPGSEDTKLKFEEITSVINPALDKYFPSDSGVRIIAEPGRYY
QAVSDARCVFDMATEVGFSMHLLDIGGGFPGSEDTKLKFEEITSVI.PALDKYFPSDSGVRIIAEPG...
RetrocopyQAVSDARCVFDMATEVGFSMHLLDIGGGFPGSEDTKLKFEEITSVIKPALDKYFPSDSGVRIIAEPGSFH
ParentalVASAFTLAVNIIAKKTVWKEQPGSDDEDESNEQTFMYYVNDGVYGSFNCILYDHAHVKALLQKRPKPDEK
..S.............V.KEQP.SDD.DESNEQTFMYYVNDGVYGSFNCILYDHAHVKALLQKRPKPDEK
RetrocopyACSQHHCXXXXXXXXXV*KEQPSSDDDDESNEQTFMYYVNDGVYGSFNCILYDHAHVKALLQKRPKPDEK
ParentalYYSSSIWGPTCDGLDRIVERCNLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPNIYYVMSRPMWQLMKQ
YYSSSIWGPTCDGLDRI.ERCNLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPNIYYVMSRPMWQLMKQ
RetrocopyYYSSSIWGPTCDGLDRILERCNLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPNIYYVMSRPMWQLMKQ
ParentalIQSHGFPPEVEEQDDGTLPMSCAQESGMDRHPAACASARINV
IQSHGFPPEVEEQDDGTLPMSCAQESGMDRHPAACASARINV
RetrocopyIQSHGFPPEVEEQDDGTLPMSCAQESGMDRHPAACASARINV

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






(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 36 .54 RPM
SRP007412_cerebellum 0 .04 RPM 43 .94 RPM
SRP007412_heart 0 .12 RPM 40 .72 RPM
SRP007412_kidney 0 .42 RPM 253 .38 RPM
SRP007412_liver 0 .05 RPM 51 .94 RPM
SRP007412_testis 0 .50 RPM 221 .74 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_2588 was not detected
No EST(s) were mapped for retro_mmus_2588 retrocopy.


TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_116676560 libraries289 libraries195 libraries21 libraries7 libraries

The graphical summary, for retro_mmus_2588 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

retro_mmus_2588 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2588 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
Bos taurus ENSBTAG000000042561 retrocopy
Dasypus novemcinctus ENSDNOG0000001847431 retrocopies
Myotis lucifugus ENSMLUG000000104231 retrocopy
Macaca mulatta ENSMMUG000000204412 retrocopies
Monodelphis domestica ENSMODG000000147791 retrocopy
Mus musculus ENSMUSG00000011179 12 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000003862 retrocopies



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