RetrogeneDB ID:

retro_mmus_604

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:10:118253258..118255043(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Cdc5l
Ensembl ID:ENSMUSG00000023932
Aliases:Cdc5l, 1200002I02Rik, AA408004, PCDC5RP
Description:cell division cycle 5-like (S. pombe) [Source:MGI Symbol;Acc:MGI:1918952]


Retrocopy-Parental alignment summary:






>retro_mmus_604
ATGCCCCGGATTATGATCAAAGGAGGAGTGTGGAGGAACACAGAGGATGAAATTCTGAAAGCAGCGGTAATGAAATATGG
GAAAAACCAGTGGTCTAGGATTGCCTCATTGCTGCATAGGAAATCGGCAAAGCAGTGCAAAGCCAGATGGTACGAATGGC
TGGATCCAAGTATTAAAAAAACTGAATGGTCCAGAGAAGAGGAAGAAAAACTCTTGCACCTGGCCAAGCTGATGCCAACG
CAGTGGAGGACCATTGCTCCAATCATAGGAAGAACAGCAGCCCAGTGCCTGGAACACTATGAATTCCTCCTGGACAGAAC
TGCTCAAAGGGACAATGAAGAGGAAACAACAGATGACCCCCGAAAGCTTAAGCCTGGAGAGATCGATCCAAACCCAGAGA
CCAAGCCAGCCCGGCCCGACCCGATTGACATGGATGAGGATGAACTTGAGATGCTCTCTGAGGCTCGAGCCCGTCTGGCC
AATACTCAAGGAAAGAAGGCTAAAAGGAAAGCAAGAGAAAAGCAGTTGGAAGAAGCCAGGCGCCTTGCTGCCCTCCAGAA
AAGACGAGAGCTTCGAGCAGCTGGCATAGAGATTCAGAAGAAAAGGAAAAGGAAGAGAGGCGTTGATTATAATGCTGAAA
TCCCATTTGAAAAAAAGCCAGCTCTTGGTTTTTATGATACTTCTGAGGAGAATTACCAGGCCCTTGATGCAGACTTCAGG
AAATTGCGACAGCAGGATCTTGATGGGGAGCTAAGATCTGAAAAAGAAGGAAGAGATAGAAAAAAAGACAAACAGCGTTT
AAAAAGGAAAAAGGAGTCTGATTTACCATCAGCTATCCTCCAAACCAGTGGTGTCTCCGAGTTGACTAAAAAGAGAAGCA
AACTTGTGTTGCCTGCGCCTCAGATTTCAGATGCTGAACTCCAGGAAGTTGTCAAGGTAGGCCAGGCCAGTGAAGTCGCA
CGGCAGACGGCGGAGGAGTCAGGAATAACAAACTCTGCTTCTAGCACTCTCCTGTCTGAGTACAATGTCACAAACAACAG
CATCGCTCTGAGAACACCACGGACGCCAGCCTCTCAAGACAGGATTCTACAGGAAGCTCAGAACCTCATGGCCTTGACCA
ATGTGGACACTCCATTGAAAGGTGGGCTTAATACCCCACTGCATGAGAGTGACTTCTCTGGTGTGACCCCACAGCAGCAA
GTTGTGCAGACTCCAAATACAGTTCTGTCTACCCCTCTCAGGACTCCTTTTAATGGAGCTGAAGGGCTGACTCCCCGAAG
TGGAACAACTCCTAAACCAGTCACTAATGCCACCCCAGGTAGAACACCACTTAGAGACAAGTTAAACATTAATCCAGAGG
ATGGAATGGCAGACTACAGTGACCCCTCTTACGTGAAGCAGATGGAAAGAGAATCTCGTGAACATCTCCGTCTCGGGTTC
TTAGGCCTCCCTGCACCTAAGAACGATTTTGAAATCGTTCTGCCTGAAAATGCCGAGAAGGAACTGGAAGAACGTGAAAT
AGATGATACCTACATTGAAGATGCTGCTGATGTGGATGCTCGAAAGCAGGCCACCCGAGATGCTGAGCGTGTAAAGGAAA
TGAAACGAATGCACAAAGCCGTTCAGAAGGATCTGCCCAGGCCGTCTGAAGTAAATGAAACTATTTTAAGACCTTTCAAT
GTAGAACCACCTCTAACAGATTTACAGAAGAGCAAAGAACTGATCAAAAAAGAAATGATTACGATGCTTCATTATGATCT
TCTACATCATCCCTACGAACCATCT

ORF - retro_mmus_604 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.3 %
Parental protein coverage: 74.19 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPRIMIKGGVWRNTEDEILKAAVMKYGKNQWSRIASLLHRKSAKQCKARWYEWLDPSIKKTEWSREEEEK
MPRIMIKGGVWRNTEDEILKAAVMKYGKNQWSRIASLLHRKSAKQCKARWYEWLDPSIKKTEWSREEEEK
RetrocopyMPRIMIKGGVWRNTEDEILKAAVMKYGKNQWSRIASLLHRKSAKQCKARWYEWLDPSIKKTEWSREEEEK
ParentalLLHLAKLMPTQWRTIAPIIGRTAAQCLEHYEFLLDKTAQRDNEEETTDDPRKLKPGEIDPNPETKPARPD
LLHLAKLMPTQWRTIAPIIGRTAAQCLEHYEFLLD.TAQRDNEEETTDDPRKLKPGEIDPNPETKPARPD
RetrocopyLLHLAKLMPTQWRTIAPIIGRTAAQCLEHYEFLLDRTAQRDNEEETTDDPRKLKPGEIDPNPETKPARPD
ParentalPIDMDEDELEMLSEARARLANTQGKKAKRKAREKQLEEARRLAALQKRRELRAAGIEIQKKRKKKRGVDY
PIDMDEDELEMLSEARARLANTQGKKAKRKAREKQLEEARRLAALQKRRELRAAGIEIQKKRK.KRGVDY
RetrocopyPIDMDEDELEMLSEARARLANTQGKKAKRKAREKQLEEARRLAALQKRRELRAAGIEIQKKRKRKRGVDY
ParentalNAEIPFEKKPALGFYDTSEENYQALDADFRKLRQQDLDGELRSEKEGRDRKKDKQHLKRKKESDLPSAIL
NAEIPFEKKPALGFYDTSEENYQALDADFRKLRQQDLDGELRSEKEGRD............ESDLPSAIL
RetrocopyNAEIPFEKKPALGFYDTSEENYQALDADFRKLRQQDLDGELRSEKEGRDXXXXXXXXXXXXESDLPSAIL
ParentalQTSGVSEFTKKRSKLVLPAPQISDAELQEVVKVGQASEVARQTAEESGITNSASSTLLSEYNVTNNSIAL
QTSGVSE.TKKRSKLVLPAPQISDAELQEVVKVGQASEVARQTAEESGITNSASSTLLSEYNVTNNSIAL
RetrocopyQTSGVSELTKKRSKLVLPAPQISDAELQEVVKVGQASEVARQTAEESGITNSASSTLLSEYNVTNNSIAL
ParentalRTPRTPASQDRILQEAQNLMALTNVDTPLKGGLNTPLHESDFSGVTPQRQVVQTPNTVLSTPFRTPSNGA
RTPRTPASQDRILQEAQNLMALTNVDTPLKGGLNTPLHESDFSGVTPQ.QVVQTPNTVLSTP.RTP.NGA
RetrocopyRTPRTPASQDRILQEAQNLMALTNVDTPLKGGLNTPLHESDFSGVTPQQQVVQTPNTVLSTPLRTPFNGA
ParentalEGLTPRSGTTPKPVTNATPGRTPLRDKLNINPEDGMADYSDPSYVKQMERESREHLRLGLLGLPAPKNDF
EGLTPRSGTTPKPVTNATPGRTPLRDKLNINPEDGMADYSDPSYVKQMERESREHLRLG.LGLPAPKNDF
RetrocopyEGLTPRSGTTPKPVTNATPGRTPLRDKLNINPEDGMADYSDPSYVKQMERESREHLRLGFLGLPAPKNDF
ParentalEIVLPENAEKELEEREIDDTYIEDAADVDARKQAIRDAERVKEMKRMHKAVQKDLPRPSEVNETILRPLN
EIVLPENAEKELEEREIDDTYIEDAADVDARKQA.RDAERVKEMKRMHKAVQKDLPRPSEVNETILRP.N
RetrocopyEIVLPENAEKELEEREIDDTYIEDAADVDARKQATRDAERVKEMKRMHKAVQKDLPRPSEVNETILRPFN
ParentalVEPPLTDLQKSEELIKKEMITMLHYDLLHHPYEPS
VEPPLTDLQKS.ELIKKEMITMLHYDLLHHPYEPS
RetrocopyVEPPLTDLQKSKELIKKEMITMLHYDLLHHPYEPS

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 33 .13 RPM
SRP007412_cerebellum 0 .00 RPM 33 .39 RPM
SRP007412_heart 0 .00 RPM 22 .51 RPM
SRP007412_kidney 0 .00 RPM 27 .07 RPM
SRP007412_liver 0 .00 RPM 13 .85 RPM
SRP007412_testis 0 .00 RPM 25 .43 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_604 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_mmus_604 retrocopy
EST ID Start End Identity Match Mis-match Score
AA636547 118254081 118254542 99.8 459 1 457

TSS - click to see more details



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_785507 libraries72 libraries437 libraries46 libraries10 libraries

The graphical summary, for retro_mmus_604 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)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_604 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_604 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 2 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Myotis lucifugus ENSMLUG000000128031 retrocopy
retro_mluc_2063,
Mus musculus ENSMUSG00000023932 10 retrocopies
retro_mmus_604 , retro_mmus_605, retro_mmus_675, retro_mmus_676, retro_mmus_677, retro_mmus_678, retro_mmus_679, retro_mmus_680, retro_mmus_681, retro_mmus_682,




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