RetrogeneDB ID:

retro_mmus_1811

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:19:12905334..12906684(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Rmnd1
Ensembl ID:ENSMUSG00000019763
Aliases:None
Description:required for meiotic nuclear division 1 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913334]


Retrocopy-Parental alignment summary:






>retro_mmus_1811
ATGCCATCCAGGCTTCTCCACACCCTGGCAAGTTTACACAGCATATCAGCAAAGGCTCATCAGTGCCAGAGACTTACTTG
GCTTACATTAAGACCACTTAGGAAATCTGAAAGTACAACATGCCACAATGGCCTGACAATACAGCAACATTTACACTCAT
TCTTTCCAAGTATAACAGCTGACAGTTTGAATAAGCCAGAGATCCTGGAAATGAGCCGGATAACATCAGACACAAGCAGA
CTCTTTCCGTTAAATGCTGTCCATTGGTTGGACGGCAAAGAACACTGGCCAAGCATGCACCCCTTTGGGACTCACAGGAG
CATGATCCACAAACCAAATCTCTTGTGTTCTAAGTGGTTTATAAAAGCAGTAAAGAGGCATCACTCATCTGTATCAAATG
AAGCACTTGTTCCCAAACAAGACCTTCCGCAGATCAAGAGGCCGCTGAGAGCATCCCGGACCCGGCAGCCATCCAGGACC
AACCTTCCAGATCTGTCTGTGAATGAGGACCTGATGCAGTGCACAGCATTTGCAACCGCAGATGAGTATCACCTGGGAAG
TCTGTCTCAAGAGCTGGTCTCCTGTGGCTATGTGGAAGTGACAAGCCTGCCTAGAGATGCAGCAAATATTTTGGTGATGG
GTGTGGAAAGTTCTGCAAAAGAAGGTGATCCCGGAACAATATTCTTGTTCAGGGAAGGAGCTGCTGTGTTCTGGAATGTA
AAAGAAAAAACTATGAAGCACGTGATGCAAGTTCTAGAGAGACACGAAACCCAGCCCTATGAAGTGGCTCTCGTTCACTG
GGAGAACGAAGAACTCAACTACATAAAGACAGAGGGACAATCAAAACTGCACAGAGGGGAAATCAAGCTAAACTCTGAGC
TGAACTTGGATGACGCCATTCTAGAGAAGTTTGCGTTCTCCAACGCTCTCTGCCTCTCAGTGAAGCTGGCTATTTGGGAA
GCAACCCTGGACAAATTTATTGAGTCTATTCAGTCCATTCCAGAGGCATTAAAAGCTGGGAAGAAAGTCAAACTGTCTCA
TAAAGAAGTTATGCAGAAAATGGGTGAGCTCTTTGCCCTCAGGCACCGAATAAACCTGAGCTCAGATTTCTTGATCACCC
CTGACTTCTACTGGGACAGAGCGAACCTGGAAGAGCTTTATGACAAGACCTGCCAGTTCCTTAGCATCACGTGAAGAGTT
AAGGTCATGAATGAAAAACTGCAGCACTGCATGGAACTAACAGACCTAATGCGGAATCACCTCAATGAGAAGCGAGCACT
CCGCTTGGAGTGGATGATCGTCATCCTCATCACCATTGAGGTAATGTTTGAGCTGGGGAGAGTCTTCTTC

ORF - retro_mmus_1811 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.11 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPSRLLHTLASLHSISAKAHQCQRLTWLTLRPLRKSESTTCHNGLTIQQHLHSFFPSITADSLNKPEILE
MPSRLLHTLASLHSISAKAHQCQRLTWLTLRPLRKSESTTCHNGLTIQQHLHSFFPSITADSLNKPEILE
RetrocopyMPSRLLHTLASLHSISAKAHQCQRLTWLTLRPLRKSESTTCHNGLTIQQHLHSFFPSITADSLNKPEILE
ParentalMSRITSDTSRLFPLNAVHWLDGKEHWPSMHPFGTHRSMTHKPNLLCSKWFIKAVKRHHSSVSNEALVPKQ
MSRITSDTSRLFPLNAVHWLDGKEHWPSMHPFGTHRSM.HKPNLLCSKWFIKAVKRHHSSVSNEALVPKQ
RetrocopyMSRITSDTSRLFPLNAVHWLDGKEHWPSMHPFGTHRSMIHKPNLLCSKWFIKAVKRHHSSVSNEALVPKQ
ParentalDLPQIKRPLKASRTRQPSRTNLPDLSVNEDLMQCTAFATADEYHLGSLSQELVSCGYVEVTSLPRDAANI
DLPQIKRPL.ASRTRQPSRTNLPDLSVNEDLMQCTAFATADEYHLGSLSQELVSCGYVEVTSLPRDAANI
RetrocopyDLPQIKRPLRASRTRQPSRTNLPDLSVNEDLMQCTAFATADEYHLGSLSQELVSCGYVEVTSLPRDAANI
ParentalLVMGVESSAKEGDPGTIFLFREGAAVFWNVKEKTMKHVMQVLERHETQPYEVALVHWENEELNYIKTEGQ
LVMGVESSAKEGDPGTIFLFREGAAVFWNVKEKTMKHVMQVLERHETQPYEVALVHWENEELNYIKTEGQ
RetrocopyLVMGVESSAKEGDPGTIFLFREGAAVFWNVKEKTMKHVMQVLERHETQPYEVALVHWENEELNYIKTEGQ
ParentalSKLHRGEIKLNSELDLDDAILEKFAFSNALCLSVKLAIWEATLDKFIESIQSIPEALKAGKKVKLSHKEV
SKLHRGEIKLNSEL.LDDAILEKFAFSNALCLSVKLAIWEATLDKFIESIQSIPEALKAGKKVKLSHKEV
RetrocopySKLHRGEIKLNSELNLDDAILEKFAFSNALCLSVKLAIWEATLDKFIESIQSIPEALKAGKKVKLSHKEV
ParentalMQKMGELFALRHRINLSSDFLITPDFYWDRANLEELYDKTCQFLSITRRVKVMNEKLQHCMELTDLMRNH
MQKMGELFALRHRINLSSDFLITPDFYWDRANLEELYDKTCQFLSIT.RVKVMNEKLQHCMELTDLMRNH
RetrocopyMQKMGELFALRHRINLSSDFLITPDFYWDRANLEELYDKTCQFLSIT*RVKVMNEKLQHCMELTDLMRNH
ParentalLNEKRALRLEWMIVILITIEVMFELGRVFF
LNEKRALRLEWMIVILITIEVMFELGRVFF
RetrocopyLNEKRALRLEWMIVILITIEVMFELGRVFF

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 .19 RPM 15 .07 RPM
SRP007412_cerebellum 0 .87 RPM 21 .28 RPM
SRP007412_heart 0 .12 RPM 22 .10 RPM
SRP007412_kidney 0 .48 RPM 21 .00 RPM
SRP007412_liver 0 .36 RPM 15 .87 RPM
SRP007412_testis 1 .37 RPM 45 .14 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_1811 was not detected

EST - click to see more details

4 EST(s) were mapped to retro_mmus_1811 retrocopy
EST ID Start End Identity Match Mis-match Score
AA118434 12905787 12906174 100 387 0 387
AA124398 12906006 12906372 96.9 307 6 299
AV048209 12906233 12906390 98.4 119 1 115
CK334097 12905367 12905468 97.1 101 0 100

TSS - click to see more details

No TSS is located nearby retro_mmus_1811 retrocopy 5' end.

Lab - click to see more details

retro_mmus_1811 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1811 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Mus musculus ENSMUSG00000019763 1 retrocopy
retro_mmus_1811 ,


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