Alms1 (ALMS1, centrosome and basal body associated) - Rat Genome Database
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Gene: Alms1 (ALMS1, centrosome and basal body associated) Mus musculus
Analyze
Symbol: Alms1
Name: ALMS1, centrosome and basal body associated
RGD ID: 1616534
MGI Page MGI
Description: Is expressed in several structures, including central nervous system; pharynx epithelium; and sensory organ. Used to study Alstrom syndrome and obesity. Human ortholog(s) of this gene implicated in Alstrom syndrome. Orthologous to human ALMS1 (ALMS1 centrosome and basal body associated protein); INTERACTS WITH 1,1-dichloroethene; 1,2-dichloroethane; 1,2-dimethylhydrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Alstrom syndrome 1; Alstrom syndrome 1 homolog; Alstrom syndrome protein 1 homolog; bbb
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Alms1-ps1   Alms1-ps2  
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39685,564,482 - 85,698,973 (+)NCBIGRCm39mm39
GRCm39 Ensembl685,564,513 - 85,679,735 (+)Ensembl
GRCm38685,587,498 - 85,726,611 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl685,587,531 - 85,702,753 (+)EnsemblGRCm38mm10GRCm38
MGSCv37685,537,525 - 85,652,745 (+)NCBIGRCm37mm9NCBIm37
MGSCv36685,553,189 - 85,668,300 (+)NCBImm8
Celera687,559,405 - 87,708,447 (+)NCBICelera
Cytogenetic Map6C3NCBI
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

Cellular Component
centriole  (IBA,ISO)
centrosome  (IBA,ISO)
ciliary basal body  (ISO)
cytosol  (IBA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal circulating cholesterol level  (IAGP)
abnormal eye electrophysiology  (IAGP)
abnormal eye physiology  (IAGP)
abnormal hepatocyte morphology  (IAGP)
abnormal locomotor behavior  (IEA)
abnormal proximal convoluted tubule morphology  (IAGP)
abnormal renal tubule epithelial cell primary cilium morphology  (IAGP)
abnormal retinal outer nuclear layer morphology  (IAGP)
abnormal seminiferous tubule morphology  (IAGP)
abnormal spermatogenesis  (IAGP)
albuminuria  (IAGP)
crystalluria  (IAGP)
decreased eosinophil cell number  (IEA)
degranulated pancreatic beta cells  (IAGP)
dilated proximal convoluted tubules  (IAGP)
dilated renal tubules  (IAGP)
enlarged kidney  (IAGP)
enlarged liver  (IAGP)
hepatic steatosis  (IAGP)
hyperglycemia  (IAGP)
impaired glucose tolerance  (IEA)
impaired hearing  (IEA)
increased body size  (IEA)
increased body weight  (IAGP)
increased circulating cholesterol level  (IAGP)
increased circulating HDL cholesterol level  (IAGP)
increased circulating insulin level  (IAGP)
increased circulating leptin level  (IAGP)
increased circulating triglyceride level  (IAGP)
increased fasting circulating glucose level  (IEA)
increased fat cell size  (IAGP)
increased food intake  (IAGP)
increased kidney apoptosis  (IAGP)
increased kidney cell proliferation  (IAGP)
increased kidney weight  (IAGP)
increased liver weight  (IAGP)
increased or absent threshold for auditory brainstem response  (IAGP)
increased susceptibility to weight gain  (IAGP)
increased total body fat amount  (IAGP)
increased urine protein level  (IAGP)
increased white adipose tissue amount  (IAGP)
insulin resistance  (IAGP)
liver fibrosis  (IAGP)
macrovesicular hepatic steatosis  (IAGP)
microvesicular hepatic steatosis  (IAGP)
obese  (IAGP)
pancreatic islet hyperplasia  (IAGP)
retinal degeneration  (IAGP)
retinal outer nuclear layer degeneration  (IAGP)
retinal photoreceptor degeneration  (IAGP)
retinal pigment epithelium atrophy  (IAGP)
seminiferous tubule degeneration  (IAGP)
small gonad  (IAGP)
tubulointerstitial nephritis  (IAGP)
References

Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12520002   PMID:12904583   PMID:14610273   PMID:15368895   PMID:16141072   PMID:16141073  
PMID:16516152   PMID:16602821   PMID:17015433   PMID:17206865   PMID:20381594   PMID:21071598   PMID:21267068   PMID:21873635   PMID:22581473   PMID:22693585   PMID:24595103   PMID:25299671  
PMID:25670793   PMID:26035863   PMID:27757953   PMID:27803297   PMID:28346477   PMID:28842428   PMID:28859131   PMID:29133593   PMID:29688375   PMID:30945293   PMID:31302159   PMID:32290105  
PMID:32325033  


Genomics

Comparative Map Data
Alms1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39685,564,482 - 85,698,973 (+)NCBIGRCm39mm39
GRCm39 Ensembl685,564,513 - 85,679,735 (+)Ensembl
GRCm38685,587,498 - 85,726,611 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl685,587,531 - 85,702,753 (+)EnsemblGRCm38mm10GRCm38
MGSCv37685,537,525 - 85,652,745 (+)NCBIGRCm37mm9NCBIm37
MGSCv36685,553,189 - 85,668,300 (+)NCBImm8
Celera687,559,405 - 87,708,447 (+)NCBICelera
Cytogenetic Map6C3NCBI
ALMS1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl273,385,758 - 73,625,166 (+)EnsemblGRCh38hg38GRCh38
GRCh38273,385,758 - 73,609,919 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37273,612,886 - 73,837,046 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36273,466,394 - 73,690,554 (+)NCBINCBI36hg18NCBI36
Build 34273,524,540 - 73,748,701NCBI
Celera273,463,729 - 73,687,908 (+)NCBI
Cytogenetic Map2p13.1NCBI
HuRef273,348,377 - 73,572,081 (+)NCBIHuRef
CHM1_1273,543,709 - 73,767,862 (+)NCBICHM1_1
Alms1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24118,125,581 - 118,226,005 (+)NCBI
Rnor_6.0 Ensembl4117,371,659 - 117,472,198 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04117,371,544 - 117,472,310 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04181,947,469 - 182,048,235 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44119,846,037 - 119,946,085 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14120,087,754 - 120,190,647 (+)NCBI
Celera4107,106,971 - 107,206,695 (+)NCBICelera
Cytogenetic Map4q34NCBI
Alms1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542412,130,607 - 12,258,522 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542412,130,496 - 12,258,684 (-)NCBIChiLan1.0ChiLan1.0
ALMS1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A74,926,650 - 75,158,734 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A74,926,650 - 75,152,139 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A73,438,657 - 73,671,313 (+)NCBIMhudiblu_PPA_v0panPan3
ALMS1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1749,301,606 - 49,513,625 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11749,301,397 - 49,513,729 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Alms1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493649117,152,759 - 17,342,648 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ALMS1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl369,253,748 - 69,417,397 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1369,253,742 - 69,417,043 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2372,455,187 - 72,619,961 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ALMS1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11433,571,894 - 33,795,404 (-)NCBI
ChlSab1.1 Ensembl1433,573,296 - 33,789,549 (-)Ensembl
Alms1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624762129,349 - 268,945 (-)NCBI

Position Markers
Alms1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
cM Map6 UniSTS
Alms1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map6C3UniSTS
cM Map6 UniSTS
Alms1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map6C3UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
25440480Moaq2_mmodifier of alien QTL 2 (mouse)61117500000Mouse
26884414Bzwq12_mbi-zygomatic width QTL 12, 16 week (mouse)63400000139100000Mouse
1300556Cia6_mcollagen induced arthritis QTL 6 (mouse)Not determined6446488487426034Mouse
4142126W3q3_mweight 3 weeks QTL 3 (mouse)Not determined450382396656149Mouse
4142361W10q11_mweight 10 weeks QTL 11 (mouse)Not determined450382396656149Mouse
4142271Egq8_mearly growth QTL 8 (mouse)Not determined450382396656149Mouse
4142232W6q4_mweight 6 weeks QTL 4 (mouse)Not determined450382396656149Mouse
1558984Cplaq9_mcircadian period of locomotor activity 9 (mouse)Not determined63866962592607450Mouse
1300618Pgia19_mproteoglycan induced arthritis 19 (mouse)Not determined64531405987426034Mouse
10412157Fl1n_mfatty liver 1 in NSY (mouse)Not determined645314059128835032Mouse
4142259Tabw2_mtally ho associated body weight 2 (mouse)Not determined46935985136423692Mouse
25314319Histh6_mhistamine hypersensitivity 6 (mouse)648720000125360000Mouse
25314320Histh5_mhistamine hypersensitivity 5 (mouse)648720000148450000Mouse
1301962Eila2_methanol induced locomotor activity 2 (mouse)Not determined648726556125356785Mouse
1357683Igf1sl1_mIGF-1 serum levels 1 (mouse)Not determined652161713116155267Mouse
4141028Mclr_mmethylcholanthrene lymphoma resistance (mouse)Not determined5437342788379171Mouse
15039373Adip28_madiposity 28 (mouse)65630821190308211Mouse
15039375Bw41_mbody weight QTL 41 (mouse)65630821190308211Mouse
1558977Skmw10_mskeletal muscle weight 10 (mouse)Not determined65844758392447710Mouse
10043972Obq28_mobesity QTL 28 (mouse)Not determined65854043392540433Mouse
1301740Bwq2_mbody weight QTL 2 (mouse)Not determined66005768094057799Mouse
1301369Im4_mimmunoregulatory 4 (mouse)Not determined66348473897484905Mouse
1300650Bw18_mbody weight QTL 18 (mouse)Not determined666713869100714031Mouse
1301876Bits2_mbitterness sensitivity 2 (mouse)Not determined670425898104426034Mouse
1301813Skl3_mskeletal size (tail length) 3 (mouse)Not determined670425898104426034Mouse
1301034Egrm2_mearly growth rate (mouse)Not determined670425898104426034Mouse
4141990Etax6_methanol induced ataxia 6 (mouse)Not determined7132262186275719Mouse
1302020Bbaa20_mB.burgdorferi-associated arthritis 20 (mouse)Not determined67132262193464093Mouse
1300869Stheal5_msoft tissue heal 5 (mouse)Not determined671575060105575178Mouse
1300954Fcsa1_mfemoral cross-sectional area 1 (mouse)Not determined671981024105981170Mouse
1301521Pas1c_mpulmonary adenoma susceptibility 1c (mouse)Not determined671981024105981170Mouse
13506930Recrq9_mrecombination rate in male meiosis QTL 9 (mouse)673500000134700000Mouse
1301320Ots1_movarian teratoma susceptibility 1 (mouse)Not determined675447583104503555Mouse
1301571Arrd1_mage-related retinal degeneration 1 (mouse)Not determined67554435692607450Mouse
1300674Nidd3n_mnon-insulin-dependent diabetes mellitus 3 in NSY (mouse)Not determined67554435694225955Mouse
10412195Efw_mepididymal fat weight (mouse)Not determined67554435694225955Mouse
10043901Pfat5_mpredicted fat percentage 5 (mouse)Not determined675607306109607450Mouse
10412208Cypr4_mcytokine production 4 (mouse)Not determined675716503109716697Mouse
1357875Pfat2_mpredicted fat percentage 2 (mouse)Not determined676463949110464093Mouse
14697704Stsl4_mSalmonella typhimurium susceptibility locus 4 (mouse)67710000090000000Mouse
13824985Alh1_mamplitude of lateral head displacement 1 (mouse)67800000097000000Mouse
4141376Dbm1_mdiabetes modifier 1 (mouse)Not determined678629504121115387Mouse
14696731Pairq1_mP. aeruginosa infection resistance QTL 1 (mouse)681500000102200000Mouse
10043864T2dm4sa_mtype 2 diabetes mellitus 4 in SMXA RI mice (mouse)Not determined683713869147052561Mouse
11251720Ewc4_methanol withdrawal and consumption 4 (mouse)684122513118122513Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:41
Interacting mature miRNAs:41
Transcripts:ENSMUST00000072018
Prediction methods:Miranda, Rnahybrid
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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000072018   ⟹   ENSMUSP00000071904
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl685,587,531 - 85,702,753 (+)Ensembl
RefSeq Acc Id: ENSMUST00000201221
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl685,666,683 - 85,669,723 (+)Ensembl
RefSeq Acc Id: ENSMUST00000201244
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl685,639,463 - 85,642,191 (+)Ensembl
RefSeq Acc Id: ENSMUST00000202809
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl685,646,730 - 85,651,547 (+)Ensembl
RefSeq Acc Id: ENSMUST00000213058   ⟹   ENSMUSP00000148796
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl685,587,646 - 85,702,638 (+)Ensembl
RefSeq Acc Id: NM_145223   ⟹   NP_660258
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39685,564,513 - 85,679,733 (+)NCBI
GRCm38685,587,531 - 85,702,751 (+)NCBI
MGSCv37685,537,525 - 85,652,745 (+)RGD
Celera687,559,405 - 87,708,447 (+)RGD
cM Map6 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006506050   ⟹   XP_006506113
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39685,564,496 - 85,679,737 (+)NCBI
GRCm38685,587,512 - 85,702,755 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006506053   ⟹   XP_006506116
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39685,564,496 - 85,698,973 (+)NCBI
GRCm38685,587,512 - 85,721,995 (+)NCBI
Sequence:
RefSeq Acc Id: XR_001785126
RefSeq Status:
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39685,564,482 - 85,654,889 (+)NCBI
GRCm38685,587,498 - 85,677,907 (+)NCBI
Sequence:
RefSeq Acc Id: XR_377445
RefSeq Status:
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39685,564,482 - 85,628,359 (+)NCBI
GRCm38685,587,498 - 85,651,377 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_660258   ⟸   NM_145223
- UniProtKB: Q8K4E0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006506116   ⟸   XM_006506053
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006506113   ⟸   XM_006506050
- Peptide Label: isoform X1
- UniProtKB: A0A1D5RMI8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000071904   ⟸   ENSMUST00000072018
RefSeq Acc Id: ENSMUSP00000148796   ⟸   ENSMUST00000213058
Protein Domains
ALMS_motif

Promoters
RGD ID:6838926
Promoter ID:MM_KWN:46688
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_2Hour,   Brain,   ES_Cell,   Kidney,   Lung,   MEF_B4,   MEF_B6
Transcripts:OTTMUST00000059068
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36685,537,459 - 85,537,959 (+)MPROMDB
RGD ID:6890238
Promoter ID:EPDNEW_M8570
Type:multiple initiation site
Name:Alms1_1
Description:Mus musculus ALMS1, centrosome and basal body associated , 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
GRCm38685,587,613 - 85,587,673EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1934606 AgrOrtholog
Ensembl Genes ENSMUSG00000063810 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000071904 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000148796 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000072018 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000213058 UniProtKB/TrEMBL
InterPro ALMS1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ALMS_motif UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ALMS_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:236266 UniProtKB/Swiss-Prot
MGD MGI:1934606 ENTREZGENE
NCBI Gene 236266 ENTREZGENE
PANTHER PTHR21553:SF22 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam ALMS_motif UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ALMS_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Alms1 PhenoGen
UniProt A0A1D5RMI8 ENTREZGENE, UniProtKB/TrEMBL
  ALMS1_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary E9QKT8 UniProtKB/Swiss-Prot
  Q6A084 UniProtKB/Swiss-Prot
  Q8C9N9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-21 Alms1  ALMS1, centrosome and basal body associated    Alstrom syndrome 1  Symbol and/or name change 5135510 APPROVED
2012-07-10 Alms1  Alstrom syndrome 1  Alms1  Alstrom syndrome 1 homolog (human)  Symbol and/or name change 5135510 APPROVED