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ALMS1P Gene

pseudogene   GIFtS: 27
GCID: GC02P073872

Alstrom Syndrome 1 Pseudogene

(Previous name: Alstrom syndrome 1-like)
(Previous symbol: ALMS1L)
  See ALMS1P-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Alstrom Syndrome 1 Pseudogene1 2
ALMS1L1 2 3
Alstrom Syndrome 1-Like1

External Ids:    HGNC: 295861   Entrez Gene: 2004202   Ensembl: ENSG000001630167   UniProtKB: Q96L163   

Export aliases for ALMS1P gene to outside databases

Previous GC identifers: GC02P073721 GC02P073868 GC02P073607


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for ALMS1P Gene:
ALMS1P (Alstrom syndrome 1 pseudogene) is a pseudogene. Diseases associated with ALMS1P include alstrom syndrome.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the ALMS1P gene promoter:
         p53   NRSF form 1   Cart-1   Nkx2-5   NRSF form 2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for ALMS1P

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ALMS1P


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2p13.1   Ensembl cytogenetic band:  2p13.1   HGNC cytogenetic band: 2p13.2

ALMS1P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ALMS1P gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P073872:  view genomic region     (about GC identifiers)

Start:
73,872,046 bp from pter      End:
73,912,703 bp from pter
Size:
40,658 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: ALM1L_HUMAN, Q96L16 (See protein sequence)
Recommended Name: Putative ALMS1-like protein  
Size: 210 amino acids; 24624 Da
Miscellaneous: The protein is highly similar to the C-terminus of ALMS1
Caution: Could be the product of a pseudogene

Explore the universe of human proteins at neXtProt for ALMS1P: NX_Q96L16


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Search eBioscience for ELISAs for ALMS1P 


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR028781 ALMS1

Graphical View of Domain Structure for InterPro Entry Q96L16

ProtoNet protein and cluster: Q96L16


Find genes that share domains with ALMS1P           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for ALMS1P
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for ALMS1P
Interactions:

    Search GeneGlobe Interaction Network for ALMS1P

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for ALMS1P (ALM1L)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for ALMS1P gene: 
NM_145300.1  

2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000450720(uc010yrl.2) ENST00000428767
miRNA
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  QuantiFast Probe-based Assays in human, mouse, rat ALMS1P

16 AceView cDNA sequences:

AA862557 BX108483 BC014492 AW083995 NM_145300 BG334072 BG745759 BG746272 
AA577579 BF435095 BV197163 AA972002 BG474872 BG475683 BG475985 BG475634 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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ALMS1P expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TAAAACAAAA
ALMS1P Expression
About this image

ALMS1P Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
    Custom PCR Arrays for ALMS1P
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QuantiFast Probe-based Assays in human, mouse, rat ALMS1P
In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ALMS1P

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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ENSEMBL Gene Tree for ALMS1P (if available)
TreeFam Gene Tree for ALMS1P (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for ALMS1P gene
1 SIMAP similar gene for ALMS1P using alignment to 1 protein entry:     ALM1L_HUMAN:
ALMS1

Find genes that share paralogs with ALMS1P           About GenesLikeMe



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for ALMS1P (see all 887)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 2 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs127137871,2
C--73871567(+) CCTTCC/TTCAGC 1 -- us2k16Minor allele frequency- T:0.10NA WA CSA 10
rs133847561,2
C,F--73871665(+) ACCTCT/CGAGGA 1 -- us2k14Minor allele frequency- C:0.33NA CSA 6
rs1133364531,2
C,F--73871666(+) CCTCCG/AAGGAA 1 -- us2k11Minor allele frequency- A:0.50WA 2
rs134102321,2
C,F,H--73871689(+) CATCAA/TGTCTG 1 -- us2k18Minor allele frequency- T:0.18NS EA WA NA CSA 426
rs1159014931,2
F--73871752(+) AAGCAG/AGAGTT 1 -- us2k11Minor allele frequency- A:0.03WA 118
rs1429676551,2
--73871850(+) CTGCCA/GGTCAC 1 -- us2k10--------
rs1511243761,2
C--73871880(+) TGCTCC/TGTCCC 1 -- us2k10--------
rs1867633201,2
--73871945(+) AGCGAC/TCTCAC 1 -- us2k10--------
rs1425088511,2
--73872039(+) CTTGTC/TGGACC 1 -- us2k10--------
rs1114504351,2
C,F--73872060(+) ATTTAT/GTCATT 1 -- nc-transcript-variant1Minor allele frequency- G:0.05NA 120

HapMap Linkage Disequilibrium report for ALMS1P (73872046 - 73912703 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for ALMS1P (see all 19):    About this table    
Variant IDTypeSubtypePubMed ID
esv2720207CNV Deletion23290073
dgv707e199CNV Deletion23128226
esv2497164CNV Deletion19546169
nsv436746CNV Insertion17901297
nsv874282CNV Loss21882294
nsv874276CNV Loss21882294
dgv4163n71CNV Loss21882294
esv34157CNV Loss18971310
nsv515605CNV Loss19592680
nsv818046CNV Loss17921354

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing ALMS1P
DNA2.0 Custom Variant and Variant Library Synthesis for ALMS1P

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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1 disease for ALMS1P:    
About MalaCards
alstrom syndrome


Find genes that share disorders with ALMS1P           About GenesLikeMe

Genetic Association Database (GAD): ALMS1P

Export disorders for ALMS1P gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for ALMS1P gene integrated from 10 sources:
(articles sorted by number of sources associating them with ALMS1P)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Genetic loci influencing kidney function and chronic kidney disease. (PubMed id 20383145)1, 4 Chambers J.C....Kooner J.S. (Nat. Genet. 2010)
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  3. Using multiple measures for quantitative trait association analyses: application to estimated glomerular filtration rate. (PubMed id 23535967)1 Tin A....Kao W.H. (J. Hum. Genet. 2013)
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  5. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W.... Wilson R.K. (Nature 2005)
  6. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 200420 HGNC: 29586 AceView: LOC200420 Ensembl:ENSG00000163016 euGenes: HUgn200420
ECgene: ALMS1P H-InvDB: ALMS1P

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for ALMS1P gene:
Search GeneIP for patents involving ALMS1P

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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