RetrogeneDB ID:

retro_mmus_1841

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:19:60080077..60081586(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Csf3r
Ensembl ID:ENSMUSG00000028859
Aliases:Csf3r, Cd114, Csfgr, G-CSF-R, G-CSFR
Description:colony stimulating factor 3 receptor (granulocyte) [Source:MGI Symbol;Acc:MGI:1339755]


Retrocopy-Parental alignment summary:






>retro_mmus_1841
GCCCCCACCATCAGACTGGACACGTGATGTCAGAAGAAGCAACTGGATCCAGGGATAGTGAGTGTGCAGCTGTTCTGGAA
GCCAACGCCCCTGCAGGAAGACAGTGGACAGATCCAGGGCTACCTGCTGTCCTGGAGTTCCTCAGATCACCAAGGGCAGG
ACATACACCTTTGCAACACCACACAGCTCAGCTGTATCTTCCTCCTGCCCTCAGAGGCCCAGAACGTGACCCTTGTGGCC
TACAACAAAGCAGGGACCTCTTCACCTACTACAGTGGTTTTCCTGGAGAACAAAGGTCCAGCTGTGACCGGACTCCATGC
CATGGCCCAAGACCTTAACACCATCTGGGTAGACTGAGCCCCCAGCCTTCTGCCTCAGGGCTATCTCATTGAGTGGGAAA
TGAGTTCTCCCAGCTACAATAACAGCTATAAGTCCTGGATGATAGAACCTAATGGGAACATCACTGGAATTCTGTTAAAG
GACAACATAAATCCCTTTCAGCTCTACAGAATCACAGTGGCTCCCCTATACCCAGGCATCGTGGGACCCCCTATAAATGT
CTACACCTACACTGGAGAGAGAGCTCTTCCTCATGCTCCAGCGCTACATCTAAAGCATGTTGGCACAACCTGGGGACAGC
TGGAGTGGGTACCTGAGGCCCCTAGGCTAGGGATGATACCCCTCACCCACTACACCATCTTCTGGGCCTATGCTGGGGAC
CACTCCTTCTCCTTCACCCTGAACATCTCCCTCCATGACTTTGTCCTGAAGCACCTGGAGCCTGCCAGTTTGTATCATGT
CTACCTCATGGCCACCAGTCGAGCAGGGTCCACCAACAGTACAGGCCTTACCCTGAGGACCCTAGATCCATCTGACATAA
ACATTTTCCTGGGCATACTTTGCTTAGTATTCTTGTCCATTACCCGTGTAATCACCTGGCTCTGCTACAAGCACAGAGGA
AAGATTTTCTTCTGGTCAGATGTGCCAGACCCAGCCCACAGTAGTCTGAGCTCCTGGTTGCCCACCATCATGACAGAGGA
AACCTTCCAGTTACCCACCTTCTGGGACTCCAGCTTGCCATCAATCACCAAGATCACTGAACTGGAGGAAGACAAGAAAC
CGACCCACTGGGATTCTGAAAGTTCTGGGAATGGTAGCCTTCCAGCCCTGGTTCAGGCCTATGTGCTCCAAGGAGATCCA
ACAGAAATTTCCAACCAGTCCCAGCCTCCCTCTCGCACTGGTGACCAGGTCCTCTATGGTCAGGTGCTTGAGAGCCCCAC
CAGCCCAGGAGTAATGCAGTACATTCACTCTAACTCCACTCAGCCCCTCTTGGGAGGCCTCACCCCTAGCCCTACATCTT
ATGAAAACATCTGGTTCCATTCAAGACCCCAGGAGACCTTTGTGCCCCAACCTCCAAGCCAGGAAGATGACTGTGTCTTT
GGGCCTCCATTTGATTTTTCCCTCTTTCAGGGGCTCCAGGTCCATGGAGTTGAAGAACAAGGGGGTTTC

ORF - retro_mmus_1841 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.85 %
Parental protein coverage: 60.22 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAPTIRLDTWCQKKQLDPGTVSVQLFWKPTPLQEDSGQIQGYLLSWSSPDHQGQDIHLCNTTQLSCIFLLP
APTIRLDT.CQKKQLDPG.VSVQLFWKPTPLQEDSGQIQGYLLSWSS.DHQGQDIHLCNTTQLSCIFLLP
RetrocopyAPTIRLDT*CQKKQLDPGIVSVQLFWKPTPLQEDSGQIQGYLLSWSSSDHQGQDIHLCNTTQLSCIFLLP
ParentalSEAQNVTLVAYNKAGTSSPTTVVFLENEGPAVTGLHAMAQDLNTIWVDWEAPSLLPQGYLIEWEMSSPSY
SEAQNVTLVAYNKAGTSSPTTVVFLEN.GPAVTGLHAMAQDLNTIWVD..APSLLPQGYLIEWEMSSPSY
RetrocopySEAQNVTLVAYNKAGTSSPTTVVFLENKGPAVTGLHAMAQDLNTIWVD*-APSLLPQGYLIEWEMSSPSY
ParentalNNSYKSWMIEPNGNITGILLKDNINPFQLYRITVAPLYPGIVGPPVNVYTFAGERAPPHAPALHLKHVGT
NNSYKSWMIEPNGNITGILLKDNINPFQLYRITVAPLYPGIVGPP.NVYT..GERA.PHAPALHLKHVGT
RetrocopyNNSYKSWMIEPNGNITGILLKDNINPFQLYRITVAPLYPGIVGPPINVYTYTGERALPHAPALHLKHVGT
ParentalTWAQLEWVPEAPRLGMIPLTHYTIFWADAGDHSFSVTLNISLHDFVLKHLEPASLYHVYLMATSRAGSTN
TW.QLEWVPEAPRLGMIPLTHYTIFWA.AGDHSFS.TLNISLHDFVLKHLEPASLYHVYLMATSRAGSTN
RetrocopyTWGQLEWVPEAPRLGMIPLTHYTIFWAYAGDHSFSFTLNISLHDFVLKHLEPASLYHVYLMATSRAGSTN
ParentalSTGLTLRTLDPSDLNIFLGILCLVLLSTTCVVTWLCCKRRGKTSFWSDVPDPAHSSLSSWLPTIMTEETF
STGLTLRTLDPSD.NIFLGILCLV.LS.T.V.TWLC.K.RGK..FWSDVPDPAHSSLSSWLPTIMTEETF
RetrocopySTGLTLRTLDPSDINIFLGILCLVFLSITRVITWLCYKHRGKIFFWSDVPDPAHSSLSSWLPTIMTEETF
ParentalQLPSFWDSSVPSITKITELEEDKKPTHWDSESSGNGSLPALVQAYVLQGDPREISNQSQPPSRTGDQVLY
QLP.FWDSS.PSITKITELEEDKKPTHWDSESSGNGSLPALVQAYVLQGDP.EISNQSQPPSRTGDQVLY
RetrocopyQLPTFWDSSLPSITKITELEEDKKPTHWDSESSGNGSLPALVQAYVLQGDPTEISNQSQPPSRTGDQVLY
ParentalGQVLESPTSPGVMQYIRSDSTQPLLGGPTPSPKSYENIWFHSRPQETFVPQPPNQEDDCVFGPPFDFPLF
GQVLESPTSPGVMQYI.S.STQPLLGG.TPSP.SYENIWFHSRPQETFVPQPP.QEDDCVFGPPFDF.LF
RetrocopyGQVLESPTSPGVMQYIHSNSTQPLLGGLTPSPTSYENIWFHSRPQETFVPQPPSQEDDCVFGPPFDFSLF
ParentalQGLQVHGVEEQGGF
QGLQVHGVEEQGGF
RetrocopyQGLQVHGVEEQGGF

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 5 .89 RPM
SRP007412_cerebellum 0 .09 RPM 3 .82 RPM
SRP007412_heart 0 .00 RPM 1 .34 RPM
SRP007412_kidney 0 .00 RPM 4 .47 RPM
SRP007412_liver 0 .00 RPM 2 .81 RPM
SRP007412_testis 0 .00 RPM 0 .87 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_1841 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1841 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_1841 retrocopy 5' end.

Lab - click to see more details

retro_mmus_1841 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1841 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 ENSMUSG00000028859 1 retrocopy
retro_mmus_1841 ,


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