Human Gene SPTBN1 (ENST00000356805.9_11) from GENCODE V47lift37
  Description: spectrin beta, non-erythrocytic 1, transcript variant 1 (from RefSeq NM_003128.3)
Gencode Transcript: ENST00000356805.9_11
Gencode Gene: ENSG00000115306.17_14
Transcript (Including UTRs)
   Position: hg19 chr2:54,683,464-54,898,583 Size: 215,120 Total Exon Count: 36 Strand: +
Coding Region
   Position: hg19 chr2:54,753,556-54,895,706 Size: 142,151 Coding Exon Count: 35 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:54,683,464-54,898,583)mRNA (may differ from genome)Protein (2364 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SPTB2_HUMAN
DESCRIPTION: RecName: Full=Spectrin beta chain, non-erythrocytic 1; AltName: Full=Beta-II spectrin; AltName: Full=Fodrin beta chain; AltName: Full=Spectrin, non-erythroid beta chain 1;
FUNCTION: Fodrin, which seems to be involved in secretion, interacts with calmodulin in a calcium-dependent manner and is thus candidate for the calcium-dependent movement of the cytoskeleton at the membrane.
SUBUNIT: Like erythrocyte spectrin, the spectrin-like proteins are capable to form dimers which can further associate to tetramers. The short form cannot bind to the axonal protein fodaxin. Interacts with ANK2.
INTERACTION: Q9NRI5:DISC1; NbExp=3; IntAct=EBI-351561, EBI-529989; P02549:SPTA1; NbExp=3; IntAct=EBI-351561, EBI-375617; Q13813:SPTAN1; NbExp=7; IntAct=EBI-351561, EBI-351450;
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton (By similarity). Cytoplasm, myofibril, sarcomere, M line (By similarity). Note=Colocalizes with ANK2 in a distinct intracellular compartment of neonatal cardiomyocytes (By similarity).
SUBCELLULAR LOCATION: Isoform 2: Cell membrane; Peripheral membrane protein; Cytoplasmic side (By similarity).
TISSUE SPECIFICITY: Isoform 2 is present in brain, lung and kidney (at protein level).
PTM: Isoform 2 is phosphorylated on Ser-8 and Ser-10 (By similarity).
SIMILARITY: Belongs to the spectrin family.
SIMILARITY: Contains 2 CH (calponin-homology) domains.
SIMILARITY: Contains 1 PH domain.
SIMILARITY: Contains 17 spectrin repeats.
SEQUENCE CAUTION: Sequence=BAD92985.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SPTBN1
Diseases sorted by gene-association score: beckwith-wiedemann syndrome (2)

-  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: 137.87 RPKM in Nerve - Tibial
Total median expression: 2739.37 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 -110.20239-0.461 Picture PostScript Text
3' UTR -784.702877-0.273 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
IPR001589 - Actinin_actin-bd_CS
IPR001715 - CH-domain
IPR001605 - PH_dom-spectrin-type
IPR011993 - PH_like_dom
IPR001849 - Pleckstrin_homology
IPR018159 - Spectrin/alpha-actinin
IPR016343 - Spectrin_bsu
IPR002017 - Spectrin_repeat

Pfam Domains:
PF00169 - PH domain
PF00307 - Calponin homology (CH) domain
PF00435 - Spectrin repeat
PF11971 - CAMSAP CH domain
PF15410 - Pleckstrin homology domain

SCOP Domains:
103657 - BAR/IMD domain-like
47576 - Calponin-homology domain, CH-domain
116907 - Hook domain
46966 - Spectrin repeat
50729 - PH domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1AA2 - X-ray MuPIT 1BKR - X-ray MuPIT 3EDV - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q01082
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0003779 actin binding
GO:0005088 Ras guanyl-nucleotide exchange factor activity
GO:0005200 structural constituent of cytoskeleton
GO:0005515 protein binding
GO:0005516 calmodulin binding
GO:0005543 phospholipid binding
GO:0030506 ankyrin binding
GO:0044877 macromolecular complex binding
GO:0045296 cadherin binding
GO:0051020 GTPase binding

Biological Process:
GO:0000165 MAPK cascade
GO:0000281 mitotic cytokinesis
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0007009 plasma membrane organization
GO:0007010 cytoskeleton organization
GO:0007182 common-partner SMAD protein phosphorylation
GO:0007411 axon guidance
GO:0043001 Golgi to plasma membrane protein transport
GO:0051693 actin filament capping
GO:0060390 regulation of SMAD protein import into nucleus
GO:0071709 membrane assembly
GO:0072659 protein localization to plasma membrane
GO:1900042 positive regulation of interleukin-2 secretion
GO:1903076 regulation of protein localization to plasma membrane
GO:1903078 positive regulation of protein localization to plasma membrane

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0008091 spectrin
GO:0014069 postsynaptic density
GO:0014731 spectrin-associated cytoskeleton
GO:0016020 membrane
GO:0030673 axolemma
GO:0030863 cortical cytoskeleton
GO:0031430 M band
GO:0032437 cuticular plate
GO:0032991 macromolecular complex
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF209017 - JP 2014500723-A/16520: Polycomb-Associated Non-Coding RNAs.
EU794662 - Homo sapiens epididymis luminal protein 102 (HEL102) mRNA, complete cds.
AB371586 - Homo sapiens SPTBN1 mRNA for spectrin beta non-erythrocytic 1, complete cds, clone: HP07744-ARiS088A21.
AB209748 - Homo sapiens mRNA for spectrin, beta, non-erythrocytic 1 isoform 1 variant protein.
BC032061 - Homo sapiens spectrin, beta, non-erythrocytic 1, mRNA (cDNA clone IMAGE:5173539).
M96803 - Human general beta-spectrin (SPTBN1) mRNA, complete cds.
JQ599728 - Homo sapiens beta-spectrin non-erythrocytic 1 (SPTBN1) mRNA, complete cds.
AF327441 - Homo sapiens beta-spectrin 2 isoform 2 mRNA, complete cds.
BC137282 - Homo sapiens spectrin, beta, non-erythrocytic 1, mRNA (cDNA clone MGC:168902 IMAGE:9021279), complete cds.
BC137283 - Homo sapiens spectrin, beta, non-erythrocytic 1, mRNA (cDNA clone MGC:168903 IMAGE:9021280), complete cds.
MA444594 - JP 2018138019-A/16520: Polycomb-Associated Non-Coding RNAs.
BC018925 - Homo sapiens mRNA similar to major histocompatibility complex, class I, F (cDNA clone IMAGE:4298543).
AB209551 - Homo sapiens mRNA for spectrin, beta, non-erythrocytic 1 isoform 1 variant protein.
JD178204 - Sequence 159228 from Patent EP1572962.
LF325210 - JP 2014500723-A/132713: Polycomb-Associated Non-Coding RNAs.
LF325209 - JP 2014500723-A/132712: Polycomb-Associated Non-Coding RNAs.
LF325208 - JP 2014500723-A/132711: Polycomb-Associated Non-Coding RNAs.
S65762 - SPTBN1=beta-fodrin [human, mRNA, 3756 nt].
LF325207 - JP 2014500723-A/132710: Polycomb-Associated Non-Coding RNAs.
LF325206 - JP 2014500723-A/132709: Polycomb-Associated Non-Coding RNAs.
LF325204 - JP 2014500723-A/132707: Polycomb-Associated Non-Coding RNAs.
LF325203 - JP 2014500723-A/132706: Polycomb-Associated Non-Coding RNAs.
LF325202 - JP 2014500723-A/132705: Polycomb-Associated Non-Coding RNAs.
LF325197 - JP 2014500723-A/132700: Polycomb-Associated Non-Coding RNAs.
LF325196 - JP 2014500723-A/132699: Polycomb-Associated Non-Coding RNAs.
LF325195 - JP 2014500723-A/132698: Polycomb-Associated Non-Coding RNAs.
LF325194 - JP 2014500723-A/132697: Polycomb-Associated Non-Coding RNAs.
LF325193 - JP 2014500723-A/132696: Polycomb-Associated Non-Coding RNAs.
LF325192 - JP 2014500723-A/132695: Polycomb-Associated Non-Coding RNAs.
LF325191 - JP 2014500723-A/132694: Polycomb-Associated Non-Coding RNAs.
LF325190 - JP 2014500723-A/132693: Polycomb-Associated Non-Coding RNAs.
LF325189 - JP 2014500723-A/132692: Polycomb-Associated Non-Coding RNAs.
LF325188 - JP 2014500723-A/132691: Polycomb-Associated Non-Coding RNAs.
LF325187 - JP 2014500723-A/132690: Polycomb-Associated Non-Coding RNAs.
LF325186 - JP 2014500723-A/132689: Polycomb-Associated Non-Coding RNAs.
LF325185 - JP 2014500723-A/132688: Polycomb-Associated Non-Coding RNAs.
LF325182 - JP 2014500723-A/132685: Polycomb-Associated Non-Coding RNAs.
LF325181 - JP 2014500723-A/132684: Polycomb-Associated Non-Coding RNAs.
LF325180 - JP 2014500723-A/132683: Polycomb-Associated Non-Coding RNAs.
LF325178 - JP 2014500723-A/132681: Polycomb-Associated Non-Coding RNAs.
LF325177 - JP 2014500723-A/132680: Polycomb-Associated Non-Coding RNAs.
LF325176 - JP 2014500723-A/132679: Polycomb-Associated Non-Coding RNAs.
LF325174 - JP 2014500723-A/132677: Polycomb-Associated Non-Coding RNAs.
LF325173 - JP 2014500723-A/132676: Polycomb-Associated Non-Coding RNAs.
AK093946 - Homo sapiens cDNA FLJ36627 fis, clone TRACH2017965, highly similar to SPECTRIN BETA CHAIN, BRAIN.
LF325171 - JP 2014500723-A/132674: Polycomb-Associated Non-Coding RNAs.
LF325170 - JP 2014500723-A/132673: Polycomb-Associated Non-Coding RNAs.
LF325169 - JP 2014500723-A/132672: Polycomb-Associated Non-Coding RNAs.
LF325168 - JP 2014500723-A/132671: Polycomb-Associated Non-Coding RNAs.
AK295570 - Homo sapiens cDNA FLJ55845 complete cds, highly similar to Spectrin beta chain, brain 1.
LF325167 - JP 2014500723-A/132670: Polycomb-Associated Non-Coding RNAs.
LF325166 - JP 2014500723-A/132669: Polycomb-Associated Non-Coding RNAs.
LF325164 - JP 2014500723-A/132667: Polycomb-Associated Non-Coding RNAs.
AJ005694 - Homo sapiens mRNA for short form of beta II spectrin, partial.
AF218848 - Homo sapiens beta II spectrin-short isoform mRNA, partial cds.
AK023762 - Homo sapiens cDNA FLJ13700 fis, clone PLACE2000216, highly similar to SPECTRIN BETA CHAIN, BRAIN.
JD019785 - Sequence 809 from Patent EP1572962.
LF325159 - JP 2014500723-A/132662: Polycomb-Associated Non-Coding RNAs.
LF325158 - JP 2014500723-A/132661: Polycomb-Associated Non-Coding RNAs.
LF325156 - JP 2014500723-A/132659: Polycomb-Associated Non-Coding RNAs.
LF325155 - JP 2014500723-A/132658: Polycomb-Associated Non-Coding RNAs.
JD048585 - Sequence 29609 from Patent EP1572962.
JD151548 - Sequence 132572 from Patent EP1572962.
LF325154 - JP 2014500723-A/132657: Polycomb-Associated Non-Coding RNAs.
BC009640 - Homo sapiens cDNA clone IMAGE:3897439, partial cds.
LF325153 - JP 2014500723-A/132656: Polycomb-Associated Non-Coding RNAs.
LF325152 - JP 2014500723-A/132655: Polycomb-Associated Non-Coding RNAs.
MA560787 - JP 2018138019-A/132713: Polycomb-Associated Non-Coding RNAs.
MA560786 - JP 2018138019-A/132712: Polycomb-Associated Non-Coding RNAs.
MA560785 - JP 2018138019-A/132711: Polycomb-Associated Non-Coding RNAs.
MA560784 - JP 2018138019-A/132710: Polycomb-Associated Non-Coding RNAs.
MA560783 - JP 2018138019-A/132709: Polycomb-Associated Non-Coding RNAs.
MA560781 - JP 2018138019-A/132707: Polycomb-Associated Non-Coding RNAs.
MA560780 - JP 2018138019-A/132706: Polycomb-Associated Non-Coding RNAs.
MA560779 - JP 2018138019-A/132705: Polycomb-Associated Non-Coding RNAs.
MA560774 - JP 2018138019-A/132700: Polycomb-Associated Non-Coding RNAs.
MA560773 - JP 2018138019-A/132699: Polycomb-Associated Non-Coding RNAs.
MA560772 - JP 2018138019-A/132698: Polycomb-Associated Non-Coding RNAs.
MA560771 - JP 2018138019-A/132697: Polycomb-Associated Non-Coding RNAs.
MA560770 - JP 2018138019-A/132696: Polycomb-Associated Non-Coding RNAs.
MA560769 - JP 2018138019-A/132695: Polycomb-Associated Non-Coding RNAs.
MA560768 - JP 2018138019-A/132694: Polycomb-Associated Non-Coding RNAs.
MA560767 - JP 2018138019-A/132693: Polycomb-Associated Non-Coding RNAs.
MA560766 - JP 2018138019-A/132692: Polycomb-Associated Non-Coding RNAs.
MA560765 - JP 2018138019-A/132691: Polycomb-Associated Non-Coding RNAs.
MA560764 - JP 2018138019-A/132690: Polycomb-Associated Non-Coding RNAs.
MA560763 - JP 2018138019-A/132689: Polycomb-Associated Non-Coding RNAs.
MA560762 - JP 2018138019-A/132688: Polycomb-Associated Non-Coding RNAs.
MA560759 - JP 2018138019-A/132685: Polycomb-Associated Non-Coding RNAs.
MA560758 - JP 2018138019-A/132684: Polycomb-Associated Non-Coding RNAs.
MA560757 - JP 2018138019-A/132683: Polycomb-Associated Non-Coding RNAs.
MA560755 - JP 2018138019-A/132681: Polycomb-Associated Non-Coding RNAs.
MA560754 - JP 2018138019-A/132680: Polycomb-Associated Non-Coding RNAs.
MA560753 - JP 2018138019-A/132679: Polycomb-Associated Non-Coding RNAs.
MA560751 - JP 2018138019-A/132677: Polycomb-Associated Non-Coding RNAs.
MA560750 - JP 2018138019-A/132676: Polycomb-Associated Non-Coding RNAs.
MA560748 - JP 2018138019-A/132674: Polycomb-Associated Non-Coding RNAs.
MA560747 - JP 2018138019-A/132673: Polycomb-Associated Non-Coding RNAs.
MA560746 - JP 2018138019-A/132672: Polycomb-Associated Non-Coding RNAs.
MA560745 - JP 2018138019-A/132671: Polycomb-Associated Non-Coding RNAs.
MA560744 - JP 2018138019-A/132670: Polycomb-Associated Non-Coding RNAs.
MA560743 - JP 2018138019-A/132669: Polycomb-Associated Non-Coding RNAs.
MA560741 - JP 2018138019-A/132667: Polycomb-Associated Non-Coding RNAs.
MA560736 - JP 2018138019-A/132662: Polycomb-Associated Non-Coding RNAs.
MA560735 - JP 2018138019-A/132661: Polycomb-Associated Non-Coding RNAs.
MA560733 - JP 2018138019-A/132659: Polycomb-Associated Non-Coding RNAs.
MA560732 - JP 2018138019-A/132658: Polycomb-Associated Non-Coding RNAs.
MA560731 - JP 2018138019-A/132657: Polycomb-Associated Non-Coding RNAs.
MA560730 - JP 2018138019-A/132656: Polycomb-Associated Non-Coding RNAs.
MA560729 - JP 2018138019-A/132655: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_PDZsPathway - Synaptic Proteins at the Synaptic Junction

Reactome (by CSHL, EBI, and GO)

Protein Q01082 (Reactome details) participates in the following event(s):

R-HSA-451403 Interaction of nephrin with adherens junction-associated proteins
R-HSA-391868 Dephosphorylation of NCAM1 bound pFyn
R-NUL-420388 Dephosphorylation of NCAM1 bound pFyn
R-HSA-391865 Recruitment of FAK to NCAM1:Fyn in lipid rafts
R-HSA-391871 Autophosphorylation of NCAM1 bound Fyn
R-HSA-392751 L1 linked to actin cytoskeleton by ankyrin
R-HSA-6807875 ARFGAP, cargo, v-SNAREs and p24 proteins bind nascent COPI complex
R-NUL-420398 Autophosphorylation of NCAM1 bound Fyn
R-HSA-391866 Phosphorylation of FAK by Src kinase
R-HSA-392051 Recruitment of Grb2 to pFAK:NCAM1
R-HSA-392053 SOS binds Grb2 bound to pFAK:NCAM1
R-HSA-373739 Ankyrins link voltage-gated sodium and potassium channels to spectrin and L1
R-HSA-6807877 ARFGAPs stimulate ARF GTPase activity
R-HSA-6809003 ERGIC-to-Golgi vesicles bind dynein:dynactin
R-HSA-392054 NCAM1:pFAK:Grb2:Sos-mediated nucleotide exchange of Ras
R-HSA-6809006 Vesicle is tethered through binding GOLGA2:GORASP1, GOLGB1 and the COG complex
R-HSA-6809011 cis-Golgi t-SNAREs bind YKT6 on tethered vesicle
R-HSA-5672965 RAS GEFs promote RAS nucleotide exchange
R-HSA-373753 Nephrin family interactions
R-HSA-375165 NCAM signaling for neurite out-growth
R-HSA-1500931 Cell-Cell communication
R-HSA-445095 Interaction between L1 and Ankyrins
R-HSA-6807878 COPI-mediated anterograde transport
R-HSA-422475 Axon guidance
R-HSA-373760 L1CAM interactions
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-1266738 Developmental Biology
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-5673001 RAF/MAP kinase cascade
R-HSA-5653656 Vesicle-mediated transport
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-5684996 MAPK1/MAPK3 signaling
R-HSA-597592 Post-translational protein modification
R-HSA-5683057 MAPK family signaling cascades
R-HSA-392499 Metabolism of proteins
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B2RP63, ENST00000356805.1, ENST00000356805.2, ENST00000356805.3, ENST00000356805.4, ENST00000356805.5, ENST00000356805.6, ENST00000356805.7, ENST00000356805.8, NM_003128, O60837, Q01082, Q16057, Q53R99, Q59ER3, Q8IX99, SPTB2, SPTB2_HUMAN, uc317zsv.1, uc317zsv.2
UCSC ID: ENST00000356805.9_11
RefSeq Accession: NM_003128.3
Protein: Q01082 (aka SPTB2_HUMAN or SPCO_HUMAN)

-  Gene Model Information
  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.