RetrogeneDB ID:

retro_mmus_238

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:94636256..94638155(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000071723
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Gspt1
Ensembl ID:ENSMUSG00000062203
Aliases:None
Description:G1 to S phase transition 1 [Source:MGI Symbol;Acc:MGI:1316728]


Retrocopy-Parental alignment summary:






>retro_mmus_238
ATGGATCTCGGCAGCAGCAGCGACTCGGCTCCCGACTGCTGGGATCAGGTGGACATGGAAGCCCCGGGTTCGGCTCCGAG
CGGGGATGGAATCGCCCCCGCAGCCATGGCAGCGGCTGAGGCCGCGGAAGCCGAGGCCCAGCGCAAGCATCTCAGCTTGG
CCTTCAGCAGTCAGCTCAACATCCACGCCAAACCTTTCGTGCCTAGCGTAAGCGCAGCGGAGTTCGTGCCGTCCTTCCTG
CCTGGATCGGCCCAGCCGCCCGCCCCCACAGCCTCCAGCTGCGACGAAACCTGCATCGGTGGCGCCGGGGAGCCTGAAGG
TAAACGGATGGAATGGGGAGCACCTGTAGAACCTTCCAAAGATGGCCCTTTAGTGTCGTGGGAGGGTTCCAGTTCAGTTG
TTACCATGGAACTTTCAGAACCTGTTGTAGAAAATGGAGAGGTGGAGATGGCCCTAGAAGAATCTTGGGAGCTTAAAGAA
GTGAGTGAAGCAAAGCCTGAGGCTTCTTTGGGAGATGCAGGGCCCCCAGAAGAAAGTGTCAAGGAAGTGATGGAGGAGAA
AGAGGAAGTAAGGAAATCAAAATCTGTGTCCATACCATCAGGTGCACCTAAGAAAGAACACGTAAATGTGGTCTTCATTG
GGCATGTGGATGCTGGCAAGTCAACCATTGGAGGACAAATAATGTTTTTGACAGGAATGGTTGACAGAAGGACACTTGAG
AAATACGAACGAGAAGCTAAGGAGAAGAATAGAGAGACCTGGTACTTGTCCTGGGCCTTAGATACAAACCAGGAAGAACG
AGACAAGGGTAAAACAGTGGAAGTGGGCCGTGCGTATTTTGAAACGGAAAAGAAGCATTTCACAATCCTAGATGCCCCTG
GCCACAAGAGTTTTGTCCCAAATATGATTGGCGGTGCCTCTCAAGCCGATTTAGCTGTGCTGGTGATCTCTGCCAGGAAA
GGGGAATTTGAGACTGGATTTGAAAAAGGTGGACAGACAAGAGAACATGCAATGCTGGCCAAAACAGCAGGGGTAAAATA
CTTAATAGTGCTTATTAATAAGATGGATGACCCCACAGTAGATTGGAGCAGTGAGCGATATGAAGAATGTAAAGAAAAAC
TGGTGCCCTTTTTGAAAAAAGTTGGTTTCAGTCCAAAAAAGGACATTCACTTTATGCCCTGCTCAGGACTGACTGGAGCA
AATATTAAAGAGCAATCTGATTTCTGTCCTTGGTACACCGGATTACCATTTATTCCGTATTTGGATAGTTTGCCAAACTT
CAACAGATCAATTGATGGGCCAATTAGGTTGCCAATTGTGGATAAGTACAAGGATATGGGCACTGTGGTCCTGGGTAAGC
TGGAATCAGGATCCATTTTTAAAGGCCAGCAGCTTGTGATGATGCCAAACAAGCACAGTGTGGAAGTTCTAGGAATCGTT
TCTGATGATGCCGAGACTGATTTTGTAGCTCCAGGTGAAAACCTCAAAATCAGACTGAAAGGGATTGAAGAGGAAGAGAT
TCTTCCAGGCTTCATACTTTGTGAACCCAGTAATCTTTGCCATTCCGGACGCACATTTGATGTTCAGATAGTGATCATTG
AGCACAAGTCTATCATCTGCCCAGGTTATAATGCGGTGCTTCACATTCATACTTGTATTGAGGAGGTTGAAATAACAGCC
TTGATCTCCTTAGTAGACAAAAAGTCAGGAGAAAAAAGCAAGACACGGCCCCGCTTTGTGAAGCAAGACCAAGTGTGCAT
TGCCCGGTTAAGGACAGCAGGAACTATCTGCCTGGAGACATTTAAAGATTTTCCTCAGATGGGTCGTTTTACTTTAAGAG
ATGAGGGTAAAACAATCGCCATTGGAAAAGTTCTGAAGCTGGTCCCAGAGAAGGACTAA

ORF - retro_mmus_238 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.66 %
Parental protein coverage: 84.12 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGAAGGDHGAGSGAGGPSEPVESSQDQSCEGSNSTVSMELSEPVVENGETEMSPEESWEHKEEISEAEPGG
G.AG...G.....G.P.EP.......S.EGS.S.V.MELSEPVVENGE.EM..EESWE.KE..SEA.P..
RetrocopyGGAGEPEGKRMEWGAPVEPSKDGPLVSWEGSSSVVTMELSEPVVENGEVEMALEESWELKE-VSEAKPEA
ParentalGSSGDGRPPEESTQEMMEEEEEIPKPKSAVAPPGAPKKEHVNVVFIGHVDAGKSTIGGQIMYLTGMVDKR
.S.GD..PPEES..E.MEE.EE..K.KS...P.GAPKKEHVNVVFIGHVDAGKSTIGGQIM.LTGMVD.R
Retrocopy-SLGDAGPPEESVKEVMEEKEEVRKSKSVSIPSGAPKKEHVNVVFIGHVDAGKSTIGGQIMFLTGMVDRR
ParentalTLEKYEREAKEKNRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGAS
TLEKYEREAKEKNRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGAS
RetrocopyTLEKYEREAKEKNRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGAS
ParentalQADLAVLVISARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYEECKEKLVPF
QADLAVLVISARKGEFETGFEKGGQTREHAMLAKTAGVK.LIVLINKMDDPTV.WS.ERYEECKEKLVPF
RetrocopyQADLAVLVISARKGEFETGFEKGGQTREHAMLAKTAGVKYLIVLINKMDDPTVDWSSERYEECKEKLVPF
ParentalLKKVGFNPKKDIHFMPCSGLTGANLKEQSDFCPWYIGLPFIPYLDNLPNFNRSVDGPIRLPIVDKYKDMG
LKKVGF.PKKDIHFMPCSGLTGAN.KEQSDFCPWY.GLPFIPYLD.LPNFNRS.DGPIRLPIVDKYKDMG
RetrocopyLKKVGFSPKKDIHFMPCSGLTGANIKEQSDFCPWYTGLPFIPYLDSLPNFNRSIDGPIRLPIVDKYKDMG
ParentalTVVLGKLESGSICKGQQLVMMPNKHNVEVLGILSDDVETDSVAPGENLKIRLKGIEEEEILPGFILCDLN
TVVLGKLESGSI.KGQQLVMMPNKH.VEVLGI.SDD.ETD.VAPGENLKIRLKGIEEEEILPGFILC...
RetrocopyTVVLGKLESGSIFKGQQLVMMPNKHSVEVLGIVSDDAETDFVAPGENLKIRLKGIEEEEILPGFILCEPS
ParentalNLCHSGRTFDAQIVIIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCI
NLCHSGRTFD.QIVIIEHKSIICPGYNAVLHIHTCIEEVEITALI.LVDKKSGEKSKTRPRFVKQDQVCI
RetrocopyNLCHSGRTFDVQIVIIEHKSIICPGYNAVLHIHTCIEEVEITALISLVDKKSGEKSKTRPRFVKQDQVCI
ParentalARLRTAGTICLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
ARLRTAGTICLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD
RetrocopyARLRTAGTICLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVPEKD

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 20 .79 RPM 63 .34 RPM
SRP007412_cerebellum 16 .02 RPM 55 .41 RPM
SRP007412_heart 0 .62 RPM 60 .61 RPM
SRP007412_kidney 1 .44 RPM 92 .32 RPM
SRP007412_liver 0 .25 RPM 82 .72 RPM
SRP007412_testis 4 .94 RPM 83 .66 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_mmus_238 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001XVA POLR2A X:94636002..94636310

EST - click to see more details

7 EST(s) were mapped to retro_mmus_238 retrocopy
EST ID Start End Identity Match Mis-match Score
AV512414 94636801 94637281 99.8 479 1 478
BB180433 94636568 94636829 95.8 253 8 244
CA752205 94636990 94637623 99.9 630 1 629
CB196124 94636112 94636945 98.5 828 1 819
CF536599 94636740 94637362 100 622 0 622
CO808645 94636436 94637117 100 670 0 661
CX240774 94636110 94636916 99.4 800 5 794

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_158566595 libraries386 libraries89 libraries2 libraries0 libraries
TSS #2 TSS_158567214 libraries210 libraries432 libraries112 libraries104 libraries
TSS #3 TSS_158568686 libraries307 libraries76 libraries3 libraries0 libraries

The graphical summary, for retro_mmus_238 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_238 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_238 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 26 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000095891 retrocopy
retro_amel_4,
Bos taurus ENSBTAG000000035772 retrocopies
retro_btau_1793, retro_btau_1840,
Canis familiaris ENSCAFG000000188561 retrocopy
retro_cfam_2072,
Callithrix jacchus ENSCJAG000000181911 retrocopy
retro_cjac_618,
Cavia porcellus ENSCPOG000000093811 retrocopy
retro_cpor_73,
Equus caballus ENSECAG000000211951 retrocopy
retro_ecab_739,
Echinops telfairi ENSETEG000000182491 retrocopy
retro_etel_1626,
Felis catus ENSFCAG000000222811 retrocopy
retro_fcat_1913,
Gorilla gorilla ENSGGOG000000040711 retrocopy
retro_ggor_2906,
Microcebus murinus ENSMICG000000141371 retrocopy
retro_mmur_28,
Myotis lucifugus ENSMLUG000000007921 retrocopy
retro_mluc_98,
Macaca mulatta ENSMMUG000000231781 retrocopy
retro_mmul_118,
Monodelphis domestica ENSMODG000000047281 retrocopy
retro_mdom_1420,
Mustela putorius furoENSMPUG000000145041 retrocopy
retro_mputfur_147,
Mus musculus ENSMUSG000000199771 retrocopy
retro_mmus_24,
Mus musculus ENSMUSG00000062203 1 retrocopy
retro_mmus_238 ,
Nomascus leucogenys ENSNLEG000000101991 retrocopy
retro_nleu_2705,
Oryctolagus cuniculus ENSOCUG000000047591 retrocopy
retro_ocun_1664,
Otolemur garnettii ENSOGAG000000070831 retrocopy
retro_ogar_100,
Pteropus vampyrus ENSPVAG000000050091 retrocopy
retro_pvam_1426,
Rattus norvegicus ENSRNOG000000023351 retrocopy
retro_rnor_2931,
Sarcophilus harrisii ENSSHAG000000059081 retrocopy
retro_shar_14,
Ictidomys tridecemlineatus ENSSTOG000000154061 retrocopy
retro_itri_109,
Tupaia belangeri ENSTBEG000000088732 retrocopies
retro_tbel_3810, retro_tbel_4659,
Tarsius syrichta ENSTSYG000000138122 retrocopies
retro_tsyr_1169, retro_tsyr_148,
Tursiops truncatus ENSTTRG000000116301 retrocopy
retro_ttru_12,


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