RetrogeneDB ID:

retro_mmus_209

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:10:31248166..31250878(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000039684
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Psmd2
Ensembl ID:ENSMUSG00000006998
Aliases:Psmd2, 9430095H01Rik, AA407121, TEG-190, Tex190
Description:proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 [Source:MGI Symbol;Acc:MGI:1096584]


Retrocopy-Parental alignment summary:






>retro_mmus_209
ATGAGACAAGACACCCGTGTAGTCCCAACAGCCCTCCGCGACCACCCCCAGCTGCGTGGACGAGAAGTGGCAAGGAGCGA
AGGGATGCGGGGGCGGGGGGCAGGGGAAGAACAGGAGCTGTCTGAGGTGGACAAACAGCTTCAAGATGAACTGGAGATGC
TCCTGGAGCGACTCCGAGAGAAGGATACATCTCTATATCGACCAGCTCTGGAGGAACTGAGAAGACAAATTCATTCTTCT
ACAACTTCCATGACTTCAGTACCCAAGCCTCTCAAATTTCTGCGTCCACACTATGGCAAATTGAAGGAAATCTATGAGAA
CATGGCCCCTGGGGAGAATAAGTGTTTTGCAGCTGACATCATCTCTGTTTTGGCCATGACCATGAGTGGTGAGCGGGAGT
GCCTCAAGTATCGGCTCGTGGGCTCCCAGGAAGAATTGGCGTCATGGGGCCATGAATACGTCAGACATCTGGCAGGAGAA
GTGACTAAGGAGTGGCAGGAGCTGGATGATGCAGAGAAAGCACAGCGGGAACCACTGCTTACCTTGGTAAAGGAAATCGT
CCCCTACAACATGGCTCACAATGCAGAGCACGAGGCTTGTGACCTGCTCATGGAAATTGAGCAGGTCGATGTGCTAGAGA
AGGACATCGATGAGAATGCCTACGCCAAGGTCTGCCTCTATCTCACCAGTTGTGTGAATTATTTACCAGAACCTGAGAAC
TCTGCCCTCCTGCGCTGTGCCTTGCGCATGTTCCGAAAGTTTAGCCGTTTCCCTGAATCTCTGAGATTGGCACTGATGCT
CAATGACATGGAACTGGTAGAAGACATTTTCACTTCCTGCAAAGATGTGGTGGTCCAGAAGCAGATGGCATCCATGCTGG
CTCGGCGTGGAGTGTTCCTGGAGCTGAGTGAAGATGTAGAGGAATATGAAGACCTCACAGAAATCATGTCCAATGTCCAG
CTCAACAGCAACTTCTTGGCCTTAGCTCGGGAGCTGGACATCATGGAGCCCAAGGTACCCGATGACATCTACAAAACCCA
CCTAGAGAATAACAGGTTTGGTAGCAGTGGCTCTCAAGTGGATTCTGCACGAATGAACCTAGCCTCCTCTTTTGTGAATG
GCTTTGTGAATGCCGCCTTTGGTCAAGATAAACTACTGACTGATGATGGCAACAAATGGCTTTACAAAAACAAGGACCAT
GGGATGTTAAGTGCTGCTGCGTCTCTTGGCATGATTCTGTTGTGGGATGTGGATGGTGGCCTCACCCAGATTGACAAGTA
TCTGTACTCCTCTGAGGACTACATCAAGTCAGGAGCTCTCCTTGCCTGTGGTATCGTGAATTCTGGAGTCCAGAATGAGT
GTGATCCTGCCCTGGCACTGCTTTCAGACTATGTTCTCCATAACAGCAATACCATGAGACTTGGCTCCATCTTTGGGCTA
GGTTTGGCCTATGCTGGCTCTAATCGGGAAGATGTTCTAACACTGCTGCTACCTGTAATGGGAGACTCCAAGTCCAGTAT
GGAGGTAGCAGGTGTGACGGCTCTAGCTTGTGGAATGATAGCAGTGTGGTCTTGCAATGGAGATGTCACTTCCACCATTC
TTCAGACCATCATGGAGAATTATAAGACTGAGCTCAAGGATACCTGTGCTCGTTGGCTTCCTCTTGGCCTGGGCCTCAAT
CACTTGGGGAAAGGCGAAGCTATTGAGGCCATCCTGGCTGACTTGGAGGTGGTGTCAGAGCCATTCCGCAGTTTTGCCAA
CACCCTGGTGGATGTATGTGCCTATGCAGGCTCTGGGAATGTGCTGACGGTTCAGCAGCTCCTCCACATCTGTAGTGAGC
ACTTTGACTCCAAGGAAAAGGAAGAAGACAAAAACAAGAAGGTAAAGAAGGACAAGGGCAAGAAGGACGTCCCTGCTGCC
ATGGGAGCACATCAGGGAGCAGCTGTTCTGGGGATTGCACTTACTGCTCTGGGGGAAGAGATTGGTGCAGAGATGGCATT
GCGAACTTTTGGTCACTTGCTGAGATATGGGGAACCTACCCTCTGTCGGGCTGTACCTTTAGCACTGGCACTAACTTCTG
TTTCAAATCCACGACTCAACATCCTGGATACGCTAAGCAAATTCTCTCATGATGCTGATCCAGAAGTTTCCTATAACTCC
ATCTTTGCTATGAGCATGGTGGGCCGTGGTACCAATAATGCCCGTCTGGCTGCAATGTTGCGCCAGTTAGCTCAACATCA
TGCCAAGGACCCCAATAACCTCTTCATGGTGCGCTTGGCACAGGGCCTGACACATTTAGGGAAGGGCACACTTACCCTCT
GCCCCTATCACACTGATAGGCAGCTCATGAGTCAAGTAGCGGTGGCAGGGCTGCTCACGGTGCTTGTTTCTTTCCTGGAT
GTTCGAAACATCATCCTAGGCAAGTCTCACTACGTCCTGTATCGGCTGGTAGCCGCCATGCAGCCTCGGATGCTGGTTAC
ATTTGATGAGGAGCTGCGACCATTGCCAGTTTCTGTCCGTGTGGGTCAGGCAGTGGATGTGGTGGGACAGGCTGGGAAGC
CAAAAACAATCACAGGGTTCCAGACTCATACAATGTCAGTGTTGCTGGCCCAGGGGGAGCGGGCAGAGTTGGCCACTGAG
GAGTTTCTTCCTGTCACCTCCATTCTGGAAGGCTTTGTTATTCTTCGGAAGAACCCCAACTATGATCTTTGA

ORF - retro_mmus_209 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.22 %
Parental protein coverage: 97.14 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKSSGKERRDAGEKDKEQELSEEDKQLQDELEMLVERLGEKDTSLYRPALEELRRQIRSSTTSMTSVPKPL
.S.G...R.AGE...EQELSE.DKQLQDELEML.ERL.EKDTSLYRPALEELRRQI.SSTTSMTSVPKPL
RetrocopyRSEGMRGRGAGE---EQELSEVDKQLQDELEMLLERLREKDTSLYRPALEELRRQIHSSTTSMTSVPKPL
ParentalKFLRPHYGKLKEIYENMAPGENKCFAADIISVLAMTMSGERECLKYRLVGSQEELASWGHEYVRHLAGEV
KFLRPHYGKLKEIYENMAPGENKCFAADIISVLAMTMSGERECLKYRLVGSQEELASWGHEYVRHLAGEV
RetrocopyKFLRPHYGKLKEIYENMAPGENKCFAADIISVLAMTMSGERECLKYRLVGSQEELASWGHEYVRHLAGEV
ParentalAKEWQELDDAEKAQREPLLTLVKEIVPYNMAHNAEHEACDLLMEIEQVDMLEKDIDENAYAKVCLYLTSC
.KEWQELDDAEKAQREPLLTLVKEIVPYNMAHNAEHEACDLLMEIEQVD.LEKDIDENAYAKVCLYLTSC
RetrocopyTKEWQELDDAEKAQREPLLTLVKEIVPYNMAHNAEHEACDLLMEIEQVDVLEKDIDENAYAKVCLYLTSC
ParentalVNYVPEPENSALLRCALGVFRKFSRFPEALRLALMLNDMELVEDIFTSCKDVVVQKQMAFMLGRHGVFLE
VNY.PEPENSALLRCAL..FRKFSRFPE.LRLALMLNDMELVEDIFTSCKDVVVQKQMA.ML.R.GVFLE
RetrocopyVNYLPEPENSALLRCALRMFRKFSRFPESLRLALMLNDMELVEDIFTSCKDVVVQKQMASMLARRGVFLE
ParentalLSEDVEEYEDLTEIMSNVQLNSNFLALARELDIMEPKVPDDIYKTHLENNRFGGSGSQVDSARMNLASSF
LSEDVEEYEDLTEIMSNVQLNSNFLALARELDIMEPKVPDDIYKTHLENNRFG.SGSQVDSARMNLASSF
RetrocopyLSEDVEEYEDLTEIMSNVQLNSNFLALARELDIMEPKVPDDIYKTHLENNRFGSSGSQVDSARMNLASSF
ParentalVNGFVNAAFGQDKLLTDDGNKWLYKNKDHGMLSAAASLGMILLWDVDGGLTQIDKYLYSSEDYIKSGALL
VNGFVNAAFGQDKLLTDDGNKWLYKNKDHGMLSAAASLGMILLWDVDGGLTQIDKYLYSSEDYIKSGALL
RetrocopyVNGFVNAAFGQDKLLTDDGNKWLYKNKDHGMLSAAASLGMILLWDVDGGLTQIDKYLYSSEDYIKSGALL
ParentalACGIVNSGVRNECDPALALLSDYVLHNSNTMRLGSIFGLGLAYAGSNREDVLTLLLPVMGDSKSSMEVAG
ACGIVNSGV.NECDPALALLSDYVLHNSNTMRLGSIFGLGLAYAGSNREDVLTLLLPVMGDSKSSMEVAG
RetrocopyACGIVNSGVQNECDPALALLSDYVLHNSNTMRLGSIFGLGLAYAGSNREDVLTLLLPVMGDSKSSMEVAG
ParentalVTALACGMIAVGSCNGDVTSTILQTIMEKSETELKDTYARWLPLGLGLNHLGKGEAIEAILAALEVVSEP
VTALACGMIAV.SCNGDVTSTILQTIME...TELKDT.ARWLPLGLGLNHLGKGEAIEAILA.LEVVSEP
RetrocopyVTALACGMIAVWSCNGDVTSTILQTIMENYKTELKDTCARWLPLGLGLNHLGKGEAIEAILADLEVVSEP
ParentalFRSFANTLVDVCAYAGSGNVLKVQQLLHICSEHFDSKEKEEDKDKKEKKDKDKKEAPADMGAHQGVAVLG
FRSFANTLVDVCAYAGSGNVL.VQQLLHICSEHFDSKEKEEDK.KK.KKDK.KK..PA.MGAHQG.AVLG
RetrocopyFRSFANTLVDVCAYAGSGNVLTVQQLLHICSEHFDSKEKEEDKNKKVKKDKGKKDVPAAMGAHQGAAVLG
ParentalIALIAMGEEIGAEMALRTFGHLLRYGEPTLRRAVPLALALISVSNPRLNILDTLSKFSHDADPEVSYNSI
IAL.A.GEEIGAEMALRTFGHLLRYGEPTL.RAVPLALAL.SVSNPRLNILDTLSKFSHDADPEVSYNSI
RetrocopyIALTALGEEIGAEMALRTFGHLLRYGEPTLCRAVPLALALTSVSNPRLNILDTLSKFSHDADPEVSYNSI
ParentalFAMGMVGSGTNNARLAAMLRQLAQYHAKDPNNLFMVRLAQGLTHLGKGTLTLCPYHSDRQLMSQVAVAGL
FAM.MVG.GTNNARLAAMLRQLAQ.HAKDPNNLFMVRLAQGLTHLGKGTLTLCPYH.DRQLMSQVAVAGL
RetrocopyFAMSMVGRGTNNARLAAMLRQLAQHHAKDPNNLFMVRLAQGLTHLGKGTLTLCPYHTDRQLMSQVAVAGL
ParentalLTVLVSFLDVRNIILGKSHYVLYGLVAAMQPRMLVTFDEELRPLPVSVRVGQAVDVVGQAGKPKTITGFQ
LTVLVSFLDVRNIILGKSHYVLY.LVAAMQPRMLVTFDEELRPLPVSVRVGQAVDVVGQAGKPKTITGFQ
RetrocopyLTVLVSFLDVRNIILGKSHYVLYRLVAAMQPRMLVTFDEELRPLPVSVRVGQAVDVVGQAGKPKTITGFQ
ParentalTHTTPVLLAHGERAELATEEFLPVTPILEGFVILRKNPNYDL
THT..VLLA.GERAELATEEFLPVT.ILEGFVILRKNPNYDL
RetrocopyTHTMSVLLAQGERAELATEEFLPVTSILEGFVILRKNPNYDL

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 .58 RPM 180 .57 RPM
SRP007412_cerebellum 0 .52 RPM 190 .14 RPM
SRP007412_heart 0 .68 RPM 209 .23 RPM
SRP007412_kidney 0 .37 RPM 187 .70 RPM
SRP007412_liver 0 .25 RPM 167 .07 RPM
SRP007412_testis 0 .69 RPM 434 .38 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_209 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_209 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_209 retrocopy 5' end.

Lab - click to see more details

retro_mmus_209 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_209 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001751661 retrocopy
retro_hsap_531,
Gorilla gorilla ENSGGOG000000271361 retrocopy
retro_ggor_486,
Mus musculus ENSMUSG00000006998 2 retrocopies
retro_mmus_209 , retro_mmus_3247,
Nomascus leucogenys ENSNLEG000000063051 retrocopy
retro_nleu_1786,
Pongo abelii ENSPPYG000000143541 retrocopy
retro_pabe_218,
Pan troglodytes ENSPTRG000000156891 retrocopy
retro_ptro_397,


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