Sem1 (SEM1, 26S proteasome complex subunit) - Rat Genome Database

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Gene: Sem1 (SEM1, 26S proteasome complex subunit) Mus musculus
Analyze
Symbol: Sem1
Name: SEM1, 26S proteasome complex subunit
RGD ID: 1616831
MGI Page MGI
Description: Acts upstream of or within double-strand break repair via homologous recombination. Predicted to be located in nucleus. Predicted to be part of integrator complex and proteasome complex. Is expressed in several structures, including alimentary system; brain; genitourinary system; respiratory system; and sensory organ. Orthologous to human SEM1 (SEM1 26S proteasome subunit).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 26S proteasome complex subunit DSS1; 26S proteasome complex subunit SEM1; deleted in split hand/split foot protein 1 homolog; DS; DSS1; Shf; Shfdg; Shfdg1; Shfg; Shfm; Shfm1; split hand/foot deleted gene 1; split hand/foot deleted protein 1 homolog; split hand/foot malformation (ectrodactyly) type 1; split hand/foot malformation type 1 protein homolog
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3966,558,275 - 6,578,658 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl66,557,294 - 6,578,663 (-)EnsemblGRCm39 Ensembl
GRCm3866,558,275 - 6,578,658 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl66,557,294 - 6,578,663 (-)EnsemblGRCm38mm10GRCm38
MGSCv3766,508,275 - 6,528,658 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3666,508,288 - 6,528,592 (-)NCBIMGSCv36mm8
Celera66,710,797 - 6,731,239 (-)NCBICelera
Cytogenetic Map6A1NCBI
cM Map62.59NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
2. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8733122   PMID:9060422   PMID:9271682   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11578870   PMID:12112878   PMID:12228710   PMID:12419822   PMID:12466851  
PMID:12477932   PMID:12520002   PMID:12702772   PMID:12904583   PMID:14610273   PMID:14681479   PMID:15226823   PMID:15359272   PMID:15489334   PMID:16141072   PMID:16141073   PMID:16341224  
PMID:16679559   PMID:18775730   PMID:18799693   PMID:21267068   PMID:21873635   PMID:22914741   PMID:24165879  


Genomics

Comparative Map Data
Sem1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3966,558,275 - 6,578,658 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl66,557,294 - 6,578,663 (-)EnsemblGRCm39 Ensembl
GRCm3866,558,275 - 6,578,658 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl66,557,294 - 6,578,663 (-)EnsemblGRCm38mm10GRCm38
MGSCv3766,508,275 - 6,528,658 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3666,508,288 - 6,528,592 (-)NCBIMGSCv36mm8
Celera66,710,797 - 6,731,239 (-)NCBICelera
Cytogenetic Map6A1NCBI
cM Map62.59NCBI
SEM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38796,481,626 - 96,709,846 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl796,481,626 - 96,709,880 (-)EnsemblGRCh38hg38GRCh38
GRCh37796,110,938 - 96,339,158 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36796,156,015 - 96,177,139 (-)NCBINCBI36Build 36hg18NCBI36
Build 34795,962,730 - 95,983,854NCBI
Celera791,018,094 - 91,039,215 (-)NCBICelera
Cytogenetic Map7q21.3NCBI
HuRef790,925,925 - 90,947,056 (-)NCBIHuRef
CHM1_1796,248,097 - 96,269,218 (-)NCBICHM1_1
T2T-CHM13v2.0797,717,281 - 97,945,489 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2795,646,961 - 95,668,081 (-)NCBI
Sem1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8435,638,306 - 35,658,462 (-)NCBIGRCr8
mRatBN7.2434,671,848 - 34,692,005 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl434,671,848 - 34,692,005 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx439,630,761 - 39,650,917 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0435,556,939 - 35,577,095 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0433,967,809 - 33,986,207 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0432,067,444 - 32,087,600 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl432,067,444 - 32,087,600 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0431,935,396 - 31,955,552 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4431,316,084 - 31,336,240 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera430,194,687 - 30,214,799 (-)NCBICelera
Cytogenetic Map4q21NCBI
Sem1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543213,134,359 - 13,156,397 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543213,134,359 - 13,156,402 (-)NCBIChiLan1.0ChiLan1.0
SEM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26114,464,761 - 114,553,287 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17162,722,956 - 162,817,908 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0788,647,366 - 88,668,476 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.17102,216,150 - 102,253,046 (-)NCBIpanpan1.1PanPan1.1panPan2
SEM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11421,767,105 - 21,790,229 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1421,327,804 - 21,350,913 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01421,589,103 - 21,612,213 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1421,549,709 - 21,612,216 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11421,734,731 - 21,757,840 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01421,470,387 - 21,493,501 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01421,729,292 - 21,752,408 (-)NCBIUU_Cfam_GSD_1.0
Sem1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511835,115,413 - 35,136,091 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365853,727,126 - 3,750,473 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365853,727,199 - 3,747,873 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1976,324,550 - 76,349,261 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2983,962,666 - 83,987,375 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SEM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12152,342,382 - 52,364,110 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2152,342,397 - 52,364,103 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604251,986,099 - 52,022,116 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Sem1
647 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:270
Count of miRNA genes:204
Interacting mature miRNAs:232
Transcripts:ENSMUST00000041111
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
14746985Manh59_mmandible shape 59 (mouse)6120847193Mouse
1301178Lith10_mlithogenic gene 10 (mouse)Not determined6121465015Mouse
10043884Bhr8_mbronchial hyperresponsiveness 8 (mouse)Not determined6121465015Mouse
10044000Mobq9_mmultigenetic obesity QTL 9 (mouse)Not determined6121465015Mouse
1357503Nhdlq5_mnon-HDL QTL 5 (mouse)Not determined6121465015Mouse
12904934Edlmmq4_mextensor digitorum longus muscle mass QTL 4 (mouse)6125514064Mouse
12904942Tammq3_mtibialis anterior muscle mass QTL 3 (mouse)6125514064Mouse
12904955Gmmq3_mgastrocnemius muscle mass QTL 3 (mouse)6125514064Mouse
1301131Chol2_mcholesterol 2 (mouse)Not determined6132144495Mouse
5491191Mobq2_mmultigenic obesity QTL 2 (mouse)Not determined6132144495Mouse
1302024Skull7_mskull morphology 7 (mouse)Not determined6132144495Mouse
15039372Nmrs22_mNAFLD-associated magnetic resonance shift 22 (mouse)6147633435476334Mouse
25440480Moaq2_mmodifier of alien QTL 2 (mouse)63050001117476961Mouse
26884414Bzwq12_mbi-zygomatic width QTL 12, 16 week (mouse)63400000139076998Mouse
1300731Smdq3_msegregation of mitochondrial DNA QTL 3 (mouse)Not determined6424920638249325Mouse
1300556Cia6_mcollagen induced arthritis QTL 6 (mouse)Not determined6446488487403016Mouse
11353836Bmiq1_mbody mass index QTL 1 (mouse)6450382329751333Mouse
11353840Bmiq2_mbody mass index QTL 2 (mouse)6450382345291115Mouse
1357520Axtq2_manxiety QTL 2 (mouse)Not determined6450382348703611Mouse
1357481Aaj2_manxiety in A/J 2 (mouse)Not determined6450382348703611Mouse
11353841Bmiq3_mbody mass index QTL 3 (mouse)6450382348703611Mouse
4142271Egq8_mearly growth QTL 8 (mouse)Not determined450382396633110Mouse
4142232W6q4_mweight 6 weeks QTL 4 (mouse)Not determined450382396633110Mouse
4142126W3q3_mweight 3 weeks QTL 3 (mouse)Not determined450382396633110Mouse
4142361W10q11_mweight 10 weeks QTL 11 (mouse)Not determined450382396633110Mouse

Markers in Region
Shfm1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map6A2UniSTS
Shfdg1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map6A2UniSTS
cM Map6 UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000041111   ⟹   ENSMUSP00000040741
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl66,557,294 - 6,578,658 (-)Ensembl
GRCm38.p6 Ensembl66,557,294 - 6,578,658 (-)Ensembl
RefSeq Acc Id: ENSMUST00000205180
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl66,576,414 - 6,578,663 (-)Ensembl
GRCm38.p6 Ensembl66,576,414 - 6,578,663 (-)Ensembl
RefSeq Acc Id: NM_009169   ⟹   NP_033195
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3966,558,275 - 6,578,658 (-)NCBI
GRCm3866,558,275 - 6,578,658 (-)ENTREZGENE
MGSCv3766,508,275 - 6,528,658 (-)RGD
Celera66,710,797 - 6,731,239 (-)RGD
cM Map6 ENTREZGENE
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_033195   ⟸   NM_009169
- UniProtKB: P60897 (UniProtKB/Swiss-Prot),   Q3TV35 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000040741   ⟸   ENSMUST00000041111

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P60897-F1-model_v2 AlphaFold P60897 1-70 view protein structure

Promoters
RGD ID:6839984
Promoter ID:MM_KWN:45114
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6
Transcripts:NM_009169
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv3666,528,391 - 6,528,891 (-)MPROMDB
RGD ID:6888962
Promoter ID:EPDNEW_M7932
Type:initiation region
Name:Sem1_1
Description:Mus musculus SEM1, 26S proteasome complex subunit , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3866,578,636 - 6,578,696EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:109238 AgrOrtholog
Ensembl Genes ENSMUSG00000042541 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000041111 ENTREZGENE
  ENSMUST00000041111.10 UniProtKB/Swiss-Prot
InterPro DSS1_SEM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:20422 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:109238 ENTREZGENE
NCBI Gene 20422 ENTREZGENE
PANTHER 26S PROTEASOME COMPLEX SUBUNIT SEM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR16771 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DSS1_SEM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sem1 PhenoGen
SMART DSS1_SEM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt P60897 ENTREZGENE
  Q3TV35 ENTREZGENE, UniProtKB/TrEMBL
  SEM1_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary Q13437 UniProtKB/Swiss-Prot
  Q61067 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-01-24 Sem1  SEM1, 26S proteasome complex subunit  Shfm1  split hand/foot malformation (ectrodactyly) type 1  Symbol and/or name change 5135510 APPROVED