RetrogeneDB ID:

retro_mmus_3570

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:8662245..8663840(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000082458
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Cdc6
Ensembl ID:ENSMUSG00000017499
Aliases:Cdc6, CDC18L
Description:cell division cycle 6 [Source:MGI Symbol;Acc:MGI:1345150]


Retrocopy-Parental alignment summary:






>retro_mmus_3570
TGTGTGGCCATCATGCCTCAAACCAGATCCCAGACACAAGCTACCATCGGTTTTTCGAAAAAGAAGTTATCCAATCCCTG
GAAGAAAACCAACTCCTGGGACTGTGAAGTAAAATTTAGAAACGTCCAGCCTGTACCCACCACTCCGTGTGCTGATGTAA
AACTTCTGCCTCTCAGTCCCCGAAAAAGTTTGGGTGATGACAACTTGTGCAACACTCCCCGGTTATCTCCCTGTTCTCCA
CCAAAGCTGGGCAAGAAAGAAAACAGACCCCCCCCCCTCGCTCACATACGTGGAAGGGGTGCAGATTAGTATTTGATGAT
GAGCCGACAGTTAAGGCTTCCCCCCAAAAGAACAAAACAGAGTTCACAAACACCAGATATGTTCCTCCTCTGCTCACAGA
AGTCCAGAGAGCAAAACAGATCCTAAGCAGAAATGTCTGCCTGAGAAGGAGTCTGTGTGTATAAGACTGTTCAAGCAAGA
AGGCACTTGCTATCAGCAAGCAAAGCTCGTTCTGAATACAGCTGTCCAGGATCGGCTGCCTGCCAGAGAGCAGGAGATGG
GTGTCATCAGGAATTTTCTGAAGGAGTACATCTGTGGGAAGAAAGCTGGCAGTCTCTACCTTTCTGGCGCTCCTGGAACT
GGAAAAACTGCCTTTTTAAGCCGGATTCTGCAAGACTTCAAGAAGGAAGTAAAAGGCTTTAAATCTATCCTGCTGAATTG
CCTGTCCCTGAGGAGTGCCCAGGCTGTGTTCCCAGCTATTGCTCAGGAGATTGGTCGGGAGGAGCTGTGCAGACCAACTG
GGAAGGACTTGATGAGAAAACTGGAAAAGCACTTGACGGCGGAGAAAGGCCCCATGATCGTGTTGGTGTTGGACGAGATG
GATCAGCTGGACAGCAAAGGGCAGGATGTATTATACACACTGTTTGAGTGGCCGTGGCTAAGCAACTCCTGATTGGTGCT
CATTGGTATTGCTAATACCCTAGATCTCACAGACAGAATTCTGCCGAGACTTGAAGCTAGAGAAAACTGTAAGCCGCAGT
TATTGAACTTCCCACCTTATACCAGGAATCAGATAGCTGCCATCTTGCAGGATAGACTTAATCAGGTGTCAAAAGACCAG
GTTCCGGACAGTGCTGAAATCCAGTTCTGTGCCCGCAAAGTGTCTTCTGTTTCAGGAGACATCCGTAAAGCGCTGGATGT
TTGCAGGCGAGCTATAGAAATTGTGGAGTCGCGTGTCAGGAGCCAGACAGTCCTCAAACCACTCTCCGAAAGTAAATCAC
CCAGTGAGTCGCCGGTTCCCAAACAGGTTGGTCTTGCTCACATATCCCAAGTCATTTTGGAAGTTGATGGGAACAGGGTG
ACTTTGAGCCAAGAAAACACACAGGATTCCCTTCCTCTCCAGCAGAAGATTCTGGTTTGCTCTTTGCTGCTTTTGACCCG
TGGGCTGAAAATCAAAGAGGTCATCTGGGGAAGTTATATGAAGCCTACAGTAGCATCTGTCCCAAACAGCAGGTGACAGC
CATAGACCAGTCTCAGTTTTGTCCCTTTCAGGACTCCTGGAGTCCAGGGGCCTTGTGGGATTAAAGAAAAATAAG

ORF - retro_mmus_3570 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.69 %
Parental protein coverage: 90.15 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalCVAIMPQTRSQTQATIGFPKKKLSNTLKKPNSRDCEVKLRNVQPVPTTPCVDVKLLPLSPRKRLGDDNLC
CVAIMPQTRSQTQATIGF.KKKLSN..KK.NS.DCEVK.RNVQPVPTTPC.DVKLLPLSPRK.LGDDNLC
RetrocopyCVAIMPQTRSQTQATIGFSKKKLSNPWKKTNSWDCEVKFRNVQPVPTTPCADVKLLPLSPRKSLGDDNLC
ParentalNTPRLSPCSPP-KLG--KKENGPPRSHTWKGCRLVFDDEPTFKASP-PKEQDRVRQHQIRSSSAQRSPES
NTPRLSPCSPP.K.G...K.....RSHTWKGCRLVFDDEPT.KASP.PKEQ.RV..HQI.SSSA.RSPES
RetrocopyNTPRLSPCSPP<KAGQERKQXXXXRSHTWKGCRLVFDDEPTVKASP<PKEQNRVHKHQICSSSAHRSPES
ParentalKADPEQKCPPEKESVCIRLFKQEGTCYQQAKLVLNTAVPDRLPAREQEMGVIRNFLKEHICGKKAGSLYL
K.DP.QKC.PEKESVCIRLFKQEGTCYQQAKLVLNTAV.DRLPAREQEMGVIRNFLKE.ICGKKAGSLYL
RetrocopyKTDPKQKCLPEKESVCIRLFKQEGTCYQQAKLVLNTAVQDRLPAREQEMGVIRNFLKEYICGKKAGSLYL
ParentalSGAPGTGKTACLSRILQDFKKEVKGFKSILLNCMSLRSAQAVFPAIAQEIGREELCRPAGKDLMRKLEKH
SGAPGTGKTA.LSRILQDFKKEVKGFKSILLNC.SLRSAQAVFPAIAQEIGREELCRP.GKDLMRKLEKH
RetrocopySGAPGTGKTAFLSRILQDFKKEVKGFKSILLNCLSLRSAQAVFPAIAQEIGREELCRPTGKDLMRKLEKH
ParentalLTAEKGPMIVLVLDEMDQLDSKGQDVLYTLFEWPWLSNSRLVLIGIANTLDLTDRILPRLEARENCKPQL
LTAEKGPMIVLVLDEMDQLDSKGQDVLYTLFEWPWLSNS.LVLIGIANTLDLTDRILPRLEARENCKPQL
RetrocopyLTAEKGPMIVLVLDEMDQLDSKGQDVLYTLFEWPWLSNS*LVLIGIANTLDLTDRILPRLEARENCKPQL
ParentalLNFPPYTRNQIAAILQDRLSQVSKDQVLDSAAIQFCARKVSAVSGDIRKALDVCRRAIEIVESDVRSQTV
LNFPPYTRNQIAAILQDRL.QVSKDQV.DSA.IQFCARKVS.VSGDIRKALDVCRRAIEIVES.VRSQTV
RetrocopyLNFPPYTRNQIAAILQDRLNQVSKDQVPDSAEIQFCARKVSSVSGDIRKALDVCRRAIEIVESRVRSQTV
ParentalLKPLSECKSPSESPVPKRVGLAHISQVISEVDGNRVTLSQENTQDSLPLQQKILVCSLLLLTRRLKIKEV
LKPLSE.KSPSESPVPK.VGLAHISQVI.EVDGNRVTLSQENTQDSLPLQQKILVCSLLLLTR.LKIKEV
RetrocopyLKPLSESKSPSESPVPKQVGLAHISQVILEVDGNRVTLSQENTQDSLPLQQKILVCSLLLLTRGLKIKEV
ParentalT-LGKLYEAYSSICRKQQVTAVDQSE-CLSLSGLLESRGLVGLKKNK
..LGKLYEAYSSIC.KQQVTA.DQS...LSLSGLLESRGLVGLKKNK
RetrocopyI<LGKLYEAYSSICPKQQVTAIDQSQ<VLSLSGLLESRGLVGLKKNK

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 0 .37 RPM
SRP007412_cerebellum 0 .00 RPM 0 .74 RPM
SRP007412_heart 0 .00 RPM 0 .47 RPM
SRP007412_kidney 0 .00 RPM 0 .85 RPM
SRP007412_liver 0 .00 RPM 0 .36 RPM
SRP007412_testis 0 .05 RPM 8 .69 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_3570 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_3570 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_3570 retrocopy 5' end.

Lab - click to see more details

retro_mmus_3570 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3570 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
Dasypus novemcinctus ENSDNOG000000115901 retrocopy
retro_dnov_2365,
Mus musculus ENSMUSG00000017499 1 retrocopy
retro_mmus_3570 ,


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