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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

ALMS1P Gene

pseudogene   GIFtS: 31
GCID: GC02P073872

Alstrom Syndrome 1 Pseudogene

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

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

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Alstrom Syndrome 1 Pseudogene1 2
ALMS1L1 2 3
Alstrom Syndrome 1-Like1

External Ids:    HGNC: 295861   Entrez Gene: 2004202   Ensembl: ENSG000001630167   UniProtKB: Q96L163   
ORGUL members:         
NONCODE14:n406230      

Export aliases for ALMS1P gene to outside databases

Previous GC identifers: GC02P073721 GC02P073868 GC02P073607


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for ALMS1P Gene: 
ALMS1P (Alstrom syndrome 1 pseudogene) is a pseudogene, and is affiliated with the lncRNA class. Diseases associated with ALMS1P include alstrom syndrome, and kidney disease.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NC_018913.2  NT_022184.15  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for ALMS1P

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

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

ALMS1P Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

ProtoNet protein and cluster: Q96L16


(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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Animal Models:
   inGenious Targeting Laboratory - Custom generated mouse model solutions for ALMS1P 
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(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ALMS1P

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for ALMS1P (ALM1L)

Search CenterWatch for drugs/clinical trials and news about ALMS1P

(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,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for ALMS1P gene: 
NM_145300.1  

Unigene Cluster for ALMS1P:

Alstrom syndrome 1 pseudogene
Hs.745426  [show with all ESTs]
Unigene Representative Sequence: BC014492
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000450720(uc010yrl.2) ENST00000428767
miRNA
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Additional mRNA sequence: 

AK307160.1 BC014492.1 NR_003683.2 

3 DOTS entries:

DT.313705  DT.95132786  DT.408958 

16 AceView cDNA sequences:

BC014492 NM_145300 BX108483 AA577579 BF435095 AW083995 BG334072 BV197163 
BG745759 AA862557 BG746272 AA972002 BG475683 BG474872 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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

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


Genevestigator expression for ALMS1P

SOURCE GeneReport for Unigene cluster: Hs.745426
    SABiosciences Custom PCR Arrays for ALMS1P
Primer
Products:
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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)
About This Section
  --

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)
About This Section
Paralogs for ALMS1P gene
1 SIMAP similar gene for ALMS1P using alignment to 1 protein entry:     ALM1L_HUMAN:
ALMS1

ALMS1P for paralogs           About GeneDecksing



(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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/887 SNPs in ALMS1P are shown (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) 10/19 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

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


ALMS1P for disorders           About GeneDecksing

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)
About This Section

PubMed articles for ALMS1P gene integrated from 9 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. (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. (2002)
  3. Using multiple measures for quantitative trait associa tion analyses: application to estimated glomerular filtration rate. (PubMed id 23535967)1 Tin A....Kao W.H. (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. (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. (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. (2004)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 200420 HGNC: 29586 AceView: LOC200420 Ensembl:ENSG00000163016 euGenes: HUgn200420
ECgene: ALMS1P H-InvDB: ALMS1P

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
  --

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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About This Section

 
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