Human Gene SMAP1 (uc003pfr.3) Description and Page Index
  Description: Homo sapiens small ArfGAP 1 (SMAP1), transcript variant 1, mRNA.
RefSeq Summary (NM_001044305): The protein encoded by this gene is similar to the mouse stromal membrane-associated protein-1. This similarity suggests that this human gene product is also a type II membrane glycoprotein involved in the erythropoietic stimulatory activity of stromal cells. Alternate splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr6:71,377,479-71,571,716 Size: 194,238 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr6:71,377,727-71,570,037 Size: 192,311 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:71,377,479-71,571,716)mRNA (may differ from genome)Protein (467 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: SMAP1_HUMAN
DESCRIPTION: RecName: Full=Stromal membrane-associated protein 1;
FUNCTION: GTPase activating protein that acts on ARF6. Plays a role in clathrin-dependent endocytosis. May play a role in erythropoiesis (By similarity).
SUBUNIT: Interacts with ARF6. Interacts with clathrin heavy chains via the clathrin box-like motif (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Peripheral membrane protein; Cytoplasmic side (By similarity).
TISSUE SPECIFICITY: Detected in bone marrow, adrenal gland, trachea, lymph node, spinal cord, peripheral blood leukocytes, thyroid and stomach.
SIMILARITY: Contains 1 Arf-GAP domain.
SEQUENCE CAUTION: Sequence=AAH08672.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/SMAP1ID42974ch6q13.html";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SMAP1
CDC HuGE Published Literature: SMAP1
Positive Disease Associations: CD40 Ligand
Related Studies:
  1. CD40 Ligand
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
  2. CD40 Ligand
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
  3. CD40 Ligand
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SMAP1
Diseases sorted by gene-association score: retinitis pigmentosa (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 10.06 RPKM in Testis
Total median expression: 167.30 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -109.92248-0.443 Picture PostScript Text
3' UTR -399.911679-0.238 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001164 - ArfGAP

Pfam Domains:
PF01412 - Putative GTPase activating protein for Arf
PF12868 - Domain of unknwon function (DUF3824)

SCOP Domains:
57863 - Pyk2-associated protein beta ARF-GAP domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2CRR
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q8IYB5
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
  Ensembl  SGD
  Protein Sequence  Protein Sequence
  Alignment  Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005096 GTPase activator activity
GO:0030276 clathrin binding
GO:0046872 metal ion binding

Biological Process:
GO:0043547 positive regulation of GTPase activity
GO:0045648 positive regulation of erythrocyte differentiation
GO:2000369 regulation of clathrin-dependent endocytosis

Cellular Component:
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AF442495 - Homo sapiens putative protein mRNA, complete cds.
AK315579 - Homo sapiens cDNA, FLJ96655, highly similar to Homo sapiens stromal membrane-associated protein 1 (SMAP1), mRNA.
BC028074 - Homo sapiens small ArfGAP 1, mRNA (cDNA clone MGC:39901 IMAGE:5215869), complete cds.
BC008672 - Homo sapiens small ArfGAP 1, mRNA (cDNA clone IMAGE:3856134), partial cds.
AK303387 - Homo sapiens cDNA FLJ53002 complete cds, highly similar to Stromal membrane-associated protein 1.
BC036123 - Homo sapiens small ArfGAP 1, mRNA (cDNA clone MGC:33992 IMAGE:5313112), complete cds.
AK023221 - Homo sapiens cDNA FLJ13159 fis, clone NT2RP3003555, weakly similar to HYPOTHETICAL 32.6 KD PROTEIN IN MET30-PIG2 INTERGENIC REGION.
AY055003 - Homo sapiens stromal membrane-associated protein SMAP1A (SMAP1) mRNA, complete cds, alternatively spliced.
AY055004 - Homo sapiens stromal membrane-associated protein SMAP1B (SMAP1) mRNA, complete cds, alternatively spliced.
AK222711 - Homo sapiens mRNA for stromal membrane-associated protein variant, clone: COL04552.
AK290448 - Homo sapiens cDNA FLJ75639 complete cds, highly similar to Homo sapiens stromal membrane-associated protein 1, mRNA.
KJ894504 - Synthetic construct Homo sapiens clone ccsbBroadEn_03898 SMAP1 gene, encodes complete protein.
CU688386 - Synthetic construct Homo sapiens gateway clone IMAGE:100019407 5' read SMAP1 mRNA.
AK307807 - Homo sapiens cDNA, FLJ97755.
AK124239 - Homo sapiens cDNA FLJ42245 fis, clone TKIDN2006525.
AL833906 - Homo sapiens mRNA; cDNA DKFZp434G2419 (from clone DKFZp434G2419).
JD517074 - Sequence 498098 from Patent EP1572962.
JD406068 - Sequence 387092 from Patent EP1572962.
JD157276 - Sequence 138300 from Patent EP1572962.
AK074340 - Homo sapiens cDNA FLJ23760 fis, clone HEP18223.
DQ593981 - Homo sapiens piRNA piR-60093, complete sequence.
DQ573770 - Homo sapiens piRNA piR-41882, complete sequence.
JD097092 - Sequence 78116 from Patent EP1572962.
JD488407 - Sequence 469431 from Patent EP1572962.
JD553300 - Sequence 534324 from Patent EP1572962.
JD412532 - Sequence 393556 from Patent EP1572962.
JD302961 - Sequence 283985 from Patent EP1572962.
JD521160 - Sequence 502184 from Patent EP1572962.
JD269492 - Sequence 250516 from Patent EP1572962.
JD410238 - Sequence 391262 from Patent EP1572962.
JD148649 - Sequence 129673 from Patent EP1572962.
JD148650 - Sequence 129674 from Patent EP1572962.
JD161338 - Sequence 142362 from Patent EP1572962.
JD547323 - Sequence 528347 from Patent EP1572962.
JD183734 - Sequence 164758 from Patent EP1572962.
JD206819 - Sequence 187843 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04144 - Endocytosis

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001044305, NP_001037770, Q53H70, Q5SYQ2, Q6PK24, Q8IYB5, Q8NDH4, Q96L38, Q96L39, Q9H8X4, SMAP1_HUMAN
UCSC ID: uc003pfr.3
RefSeq Accession: NM_001044305
Protein: Q8IYB5 (aka SMAP1_HUMAN)
CCDS: CCDS43478.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001044305.1
exon count: 11CDS single in 3' UTR: no RNA size: 3344
ORF size: 1404CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2393.00frame shift in genome: no % Coverage: 99.61
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.