RetrogeneDB ID:

retro_mmus_1473

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:16:62716989..62718450(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000085783
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Gps1
Ensembl ID:ENSMUSG00000025156
Aliases:Gps1, Cops1, Csn1, R75577, Sgn1
Description:G protein pathway suppressor 1 [Source:MGI Symbol;Acc:MGI:2384801]


Retrocopy-Parental alignment summary:






>retro_mmus_1473
ATGCCGCTGCCGGTTCAGGTGTTTAACTTGCAGGGGGCCGTGGAACCCATGCAGATTGATGTCGATCCGCAGGAAGAACC
GCAGAACGCACCTGATGTCAACTATGTGGTGGAGAATCCCACCCTGGATCTGGAGCAGTATGCAGCCAGCTACAGTGGCC
TGATGCGAATTGAGCGACTACAGTTTATTGCTGACCGTTGCCCTCCACTGAGGGTAGAGGCCTTGAAAATGGCTCTATCC
TTCGTGCAGAGGACCTTCAATGTGGACATGTATGAAGAGATACACCGGAAGCTCTCCGAGGCTACCAGGGAGCTGCAGAA
TGCACCTGATGCCATCCCTGAGAGTGGAGTGGAGCCCCCGCCCCTGGACACAGCCTGGGTGGAGGCCACTCGGAAGAAGG
CTCTGTTGAAACTGGAGAAGCTGGACACGGACTTGAAGAACTATAAGGGCAATTCTATCAAAGAGAGCATCAGGCGCGGC
CACGATGACCTGGGTGATCACTACCTGGACTGTGGGGACCTCAGCAATGCCCTCAAATGTTACTCACGAGCCCGAGACTA
CTGCACCAGTGCTAAGCATGTCATCAACATGTGCCTCAACGTCATCAAGGTCAGTGTCTACTTGCAAAATTGGTCTCATG
TGTTAAGCTATGTCAGCAAGGCCGAGTCTACTCCAGAGATTGCTGAGCAGCGGGGAGAGCGGGACAGCCAGACGCAAGCC
ATCCTCACCAAGCTCAAGTGTGCTGCAGGCTTGGCTGAGCTGGCCGCACGGAAGTATAAGCAAGCAGCCAAGTGCTTCCT
TCTGGCTTCCTTTGATCACTGTGACTTCCCAGAGCTGCTGTCCCCCAGCAATGTGGCTGTCTATGGTGGCCTGTGTGCCT
TAGCCACCTCTGACCGGCAGGAGCTGCAACGAAATGTCATCTCCAGCAGTTCCTTCAAGCTGTTCCTGGAGCTGGAGCCA
CAGGTCAGAGACATCATCTTCAAATTCTATGAATCCAAGTATGCCTCATGCTTGAAGATGCTGGACGAGATGAAGGATAA
CCTGCTCCTGGACATGTACCTGGCCCCTCACGTCAGGACACTGTACACCCAGATTCGTAACCGGGCTCTTATCCAATACT
TCAGCCCCTATGTGTCAGCTGATATGCACAAGATGGCTGCAGCCTTCAACACAACAGTTGCAGCTCTGGAAGATGAGCTG
ACACAACTCATTCTGGAGGGCCTTATTAATGCCCGCATCGACTCACACAGCAAGATACTGTATGCTCGAGATGTGGATCA
GCGTAGCACCACCTTTGAGAAGTCCCTGCTGATGGGCAAGGAATTCCAACGACGTGCCAAAGCTATGATTCTGAGAGCAG
CTGTGCTCCGCAACCAGATCCATGTCAAGTCTCCTCCTAGAGAAGGGAGCCAAGGGGAGCTGACTCCAGCCAACAGCCAG
TCACGCATGAGTACCAACATG

ORF - retro_mmus_1473 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.59 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPLPVQVFNLQGAVEPMQIDVDPQEDPQNAPDVNYVVENPTLDLEQYAASYSGLMRIERLQFIADRCPPL
MPLPVQVFNLQGAVEPMQIDVDPQE.PQNAPDVNYVVENPTLDLEQYAASYSGLMRIERLQFIADRCPPL
RetrocopyMPLPVQVFNLQGAVEPMQIDVDPQEEPQNAPDVNYVVENPTLDLEQYAASYSGLMRIERLQFIADRCPPL
ParentalRVEALKMALSFVQRTFNVDMYEEIHRKLSEATRELQNAPDAIPESGVEPPPLDTAWVEATRKKALLKLEK
RVEALKMALSFVQRTFNVDMYEEIHRKLSEATRELQNAPDAIPESGVEPPPLDTAWVEATRKKALLKLEK
RetrocopyRVEALKMALSFVQRTFNVDMYEEIHRKLSEATRELQNAPDAIPESGVEPPPLDTAWVEATRKKALLKLEK
ParentalLDTDLKNYKGNSIKESIRRGHDDLGDHYLDCGDLSNALKCYSRARDYCTSAKHVINMCLNVIKVSVYLQN
LDTDLKNYKGNSIKESIRRGHDDLGDHYLDCGDLSNALKCYSRARDYCTSAKHVINMCLNVIKVSVYLQN
RetrocopyLDTDLKNYKGNSIKESIRRGHDDLGDHYLDCGDLSNALKCYSRARDYCTSAKHVINMCLNVIKVSVYLQN
ParentalWSHVLSYVSKAESTPEIAEQRGERDSQTQAILTKLKCAAGLAELAARKYKQAAKCFLLASFDHCDFPELL
WSHVLSYVSKAESTPEIAEQRGERDSQTQAILTKLKCAAGLAELAARKYKQAAKCFLLASFDHCDFPELL
RetrocopyWSHVLSYVSKAESTPEIAEQRGERDSQTQAILTKLKCAAGLAELAARKYKQAAKCFLLASFDHCDFPELL
ParentalSPSNVAVYGGLCALATFDRQELQRNVISSSSFKLFLELEPQVRDIIFKFYESKYASCLKMLDEMKDNLLL
SPSNVAVYGGLCALAT.DRQELQRNVISSSSFKLFLELEPQVRDIIFKFYESKYASCLKMLDEMKDNLLL
RetrocopySPSNVAVYGGLCALATSDRQELQRNVISSSSFKLFLELEPQVRDIIFKFYESKYASCLKMLDEMKDNLLL
ParentalDMYLAPHVRTLYTQIRNRALIQYFSPYVSADMHKMAAAFNTTVAALEDELTQLILEGLINARIDSHSKIL
DMYLAPHVRTLYTQIRNRALIQYFSPYVSADMHKMAAAFNTTVAALEDELTQLILEGLINARIDSHSKIL
RetrocopyDMYLAPHVRTLYTQIRNRALIQYFSPYVSADMHKMAAAFNTTVAALEDELTQLILEGLINARIDSHSKIL
ParentalYARDVDQRSTTFEKSLLMGKEFQRRAKAMILRAAVLRNQIHVKSPPREGSQGELTPANSQSRMSTNM
YARDVDQRSTTFEKSLLMGKEFQRRAKAMILRAAVLRNQIHVKSPPREGSQGELTPANSQSRMSTNM
RetrocopyYARDVDQRSTTFEKSLLMGKEFQRRAKAMILRAAVLRNQIHVKSPPREGSQGELTPANSQSRMSTNM

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 .37 RPM 57 .01 RPM
SRP007412_cerebellum 0 .09 RPM 43 .42 RPM
SRP007412_heart 0 .53 RPM 32 .10 RPM
SRP007412_kidney 0 .46 RPM 34 .23 RPM
SRP007412_liver 0 .05 RPM 26 .35 RPM
SRP007412_testis 0 .73 RPM 69 .71 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_1473 was not detected

EST - click to see more details

13 EST(s) were mapped to retro_mmus_1473 retrocopy
EST ID Start End Identity Match Mis-match Score
AA065408 62717289 62717535 98.4 242 3 237
AV477952 62717318 62717825 99.9 506 1 505
AV584159 62717216 62717713 100 497 0 497
AW491649 62717535 62717755 100 220 0 220
BB603883 62716960 62717194 97.1 227 7 220
BE381848 62716975 62717465 99.8 489 1 488
BE944569 62717535 62717755 100 220 0 220
BF468999 62717584 62717738 100 154 0 154
CA568085 62716983 62717466 99.8 482 1 481
CX732507 62717235 62717809 100 574 0 574
W09671 62717880 62718120 99.6 238 1 236
W65922 62717326 62717721 99.4 319 1 316
W89993 62717935 62718188 98.1 248 4 242

TSS - click to see more details

No TSS is located nearby retro_mmus_1473 retrocopy 5' end.

Lab - click to see more details

retro_mmus_1473 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1473 has 0 orthologous retrocopies within eutheria group .

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

Species Parental gene accession Retrocopies number
Macropus eugenii ENSMEUG000000046091 retrocopy
retro_meug_586,
Mus musculus ENSMUSG00000025156 1 retrocopy
retro_mmus_1473 ,


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