RetrogeneDB ID:

retro_cjac_3584

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01186199.1:2769..4578(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000022354
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PRMT5
Ensembl ID:ENSCJAG00000008409
Aliases:None
Description:protein arginine methyltransferase 5 [Source:HGNC Symbol;Acc:10894]


Retrocopy-Parental alignment summary:






>retro_cjac_3584
AAGCAGGGGTTTGATTTCCTCTGAATGCCTGTCTTCCATCCACGTTTCAAGAGGGAATTCATTCAGGAACCTGCTAAGAA
TCAACCGGGCCCCCAGACACGATCAGACCTACTGCTGTCAGGAAGGGACTGGAATACACTAATTGTGGGAAAGCTTTCTC
CATGGATTTTTCCAGACTCAAAAGTGGAGAAGATTTGCAGAAACTCCGAGGCACCCATGTTACAGGAGCTGAATTTTGGT
GCATATTTGGGTCTTCCAGCTTTCCTGCTGCCCCTTAATCAGGAAGATAACACCAATCTGGCCAGAGTTTTGACCAACCA
CATCCACACTGGCCCCCACTCTTCCATGTTCTGGATGCGGGTACCATTGGTGGCACCAGAAGACCTGAGAGATGATATAA
TTGAGAATGCACCAATTACACACACACAGGAGTACAGTGGGGAGGAGAAGACATGGATGTGGTGGCACAACTTCCAGACT
TTGTGTGACTACAGCAAGAGGATTGCAGTGGCTCTTGAAATTGGGGCTGACCTCCCATCTAATCATGTCATTGATCGCTG
GCTTGGGGAGCCCATCAAAGCAGCCATTCTCCCCACCAGCATTTTCCTGACCAATAAGAAGGGATTTCCTATTCTTTCTA
AGATGCACCAGAGGCTCATCTTCCGGCTCCTTAAGTTGGAGGTGCAGTTCATTATCACAGGCACCAACCACCACTCAGAG
AAGGAGTTCTGCTCCTACCTCCAATACTTGGAATACTTAAGCCAAAACCGTCCTCCACCTACTGCCTATGAACTCTTTGC
TAAGGGCTATGAAGACTATCTGCAGTCTCTGCTTCAGCCACTGATGGGCAATCTGGAATCTCAGACATGTGAAGTGTTTG
AAAAGGACCCCATCAAATACTCTCAGTACCGGAAGGCCATCTATAAATGTCTGCTAGACCAAGTACCAGAAGAGGAGAAG
GATACCAATGTCCAGGTATTGATGGTGCTGGGAGCAGGACAGGGTCCCCTGGTGAACGCTTCCCTGTGGGCAGCCAAGCA
GGCTGACCAGCGGATAAAGCTGTATGCCGTGGAGAAAAACCCAAATGCTGTGGTGACGCTAGAGAACTGGCAGTTTGAAG
AATGGGGAAGCCAGGTGACTGTAGTCTCATCAGACATGAGGGAATGGGTGGCTCCAGAAAAAGCAGACATCATTGTCAGT
GAACTTCTGGGCTCATTTGCTGACAGTGAGTTGTCACCTGAATGCCTGGATGGAGCCCAGCACTTCCTAAAAGATGACGG
TGTGAGCATCCCTGGGGAGTATACTTCCTTCCTGGCTCCCATCTCCTCCTCCAAACTGTACAATGAGGTCCGAGCCTATA
GGGAGAAGGATCATGACCCTGAGGCACAGTTTGAGATGCCTTATGTGGTATGGCTGCACAACTTTCACCAGCTATCTGCA
CCCCAGCCCTGTTTCACCTTCAGCCATCCCAACAGAGATCCTATGATTGACAACAACCGCTATTGTACCTTGGAGTTTCC
TGTGGAAGTGAACACAGTACTGCATGGCTTTGCTGGCTACTTTGAAACTGTGCTTTATCAGGACATCACTCTGAGTATCC
ATCCAGAGACTCACTCTCCTGGAATGTTCTCATGGTTTCCCATTCTCTTCCCTATTAAGCAGCCCATAACGGTGCATGAA
GGCCAGCCCATCTGTGTGCGTTTCTGGCAATGCACCAATTCCAAGAAGGTGTGGTATGAGTGGGCTGTGACAACACCCAT
TTGTTCTGCTATTCACAACCCCACAGGCTGCTCATATACCATTGGCCTC

ORF - retro_cjac_3584 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.69 %
Parental protein coverage: 97.26 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSE
KQGFDFL.MPVFHPRFKREFIQEPAKN.PGPQTRSDLLLSGRDWNTLIVGKLSPWI.PDSKVEKI.RNSE
RetrocopyKQGFDFL*MPVFHPRFKREFIQEPAKNQPGPQTRSDLLLSGRDWNTLIVGKLSPWIFPDSKVEKICRNSE
ParentalVAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPIT
..MLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTG.HSSMFWMRVPLVAPEDLRDDIIENAPIT
RetrocopyAPMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGPHSSMFWMRVPLVAPEDLRDDIIENAPIT
ParentalHTQEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFP
HTQEYSGEEKTWMWWHNF.TLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFP
RetrocopyHTQEYSGEEKTWMWWHNFQTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFP
ParentalVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQP
.LSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPP.AYELFAKGYEDYLQS.LQP
RetrocopyILSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPTAYELFAKGYEDYLQSLLQP
ParentalLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADR
LM.NLESQT.EVFEKDPIKYSQY..AIYKCLLD.VPEEEKDTNVQVLMVLGAG.GPLVNASL.AAKQAD.
RetrocopyLMGNLESQTCEVFEKDPIKYSQYRKAIYKCLLDQVPEEEKDTNVQVLMVLGAGQGPLVNASLWAAKQADQ
ParentalRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQ
RIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFAD.ELSPECLDGAQ
RetrocopyRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADSELSPECLDGAQ
ParentalHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHP
HFLKDDGVSIPGEYTSFLAPISSSKLYNEVRA.REKD.DPEAQFEMPYVV.LHNFHQLSAPQPCFTFSHP
RetrocopyHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRAYREKDHDPEAQFEMPYVVWLHNFHQLSAPQPCFTFSHP
ParentalNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVRE
NRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSI.PETHSPGMFSWFPILFPIKQPITV.E
RetrocopyNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIHPETHSPGMFSWFPILFPIKQPITVHE
ParentalGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPPGRSYTIGL
GQ.ICVRFW.C.NSKKVWYEWAVT.P.CSAIHNP.G.SYTIGL
RetrocopyGQPICVRFWQCTNSKKVWYEWAVTTPICSAIHNPTGCSYTIGL

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
SRP051959_colon 0 .07 RPM 12 .60 RPM
SRP051959_heart 0 .04 RPM 15 .51 RPM
SRP051959_kidney 0 .11 RPM 24 .38 RPM
SRP051959_liver 0 .02 RPM 17 .03 RPM
SRP051959_lung 0 .10 RPM 16 .45 RPM
SRP051959_lymph_node 0 .11 RPM 16 .46 RPM
SRP051959_skeletal_muscle 0 .02 RPM 22 .91 RPM
SRP051959_spleen 0 .04 RPM 17 .71 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_3584 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3584 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3584 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
Callithrix jacchus ENSCJAG00000008409 1 retrocopy
retro_cjac_3584 ,


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