Human Gene PPFIBP1 (ENST00000228425.11_6) from GENCODE V47lift37
  Description: PPFIA binding protein 1, transcript variant 1 (from RefSeq NM_003622.4)
Gencode Transcript: ENST00000228425.11_6
Gencode Gene: ENSG00000110841.14_18
Transcript (Including UTRs)
   Position: hg19 chr12:27,677,139-27,848,497 Size: 171,359 Total Exon Count: 30 Strand: +
Coding Region
   Position: hg19 chr12:27,786,330-27,845,815 Size: 59,486 Coding Exon Count: 28 

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 (chr12:27,677,139-27,848,497)mRNA (may differ from genome)Protein (1005 aa)
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-  Comments and Description Text from UniProtKB
  ID: LIPB1_HUMAN
DESCRIPTION: RecName: Full=Liprin-beta-1; AltName: Full=Protein tyrosine phosphatase receptor type f polypeptide-interacting protein-binding protein 1; Short=PTPRF-interacting protein-binding protein 1; AltName: Full=hSGT2;
FUNCTION: May regulate the disassembly of focal adhesions. Did not bind receptor-like tyrosine phosphatases type 2A.
SUBUNIT: Forms homodimers and heterodimers. Interacts with S100A4 in a calcium-dependent mode.
TISSUE SPECIFICITY: Widely expressed. Absent in liver.
DOMAIN: The N-terminal coiled coil regions mediate homodimerization preferentially and heterodimerization type beta/beta. The C-terminal, non-coiled coil regions mediate heterodimerization type beta/alpha and interaction with S100A4.
SIMILARITY: Belongs to the liprin family. Liprin-beta subfamily.
SIMILARITY: Contains 3 SAM (sterile alpha motif) domains.
SEQUENCE CAUTION: Sequence=AAH46159.1; Type=Erroneous initiation; Sequence=BAA86544.2; 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: PPFIBP1
Diseases sorted by gene-association score: inflammatory myofibroblastic tumor (3)

-  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: 24.23 RPKM in Ovary
Total median expression: 410.19 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 -85.70283-0.303 Picture PostScript Text
3' UTR -731.602682-0.273 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
IPR001660 - SAM
IPR013761 - SAM/pointed
IPR011510 - SAM_2
IPR021129 - SAM_type1

Pfam Domains:
PF00536 - SAM domain (Sterile alpha motif)
PF07647 - SAM domain (Sterile alpha motif)

SCOP Domains:
140612 - EB1 dimerisation domain-like
47769 - SAM/Pointed domain
144266 - MPN010-like

ModBase Predicted Comparative 3D Structure on Q86W92
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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 Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0045296 cadherin binding

Biological Process:
GO:0007155 cell adhesion

Cellular Component:
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005925 focal adhesion


-  Descriptions from all associated GenBank mRNAs
  BC022873 - Homo sapiens PTPRF interacting protein, binding protein 1 (liprin beta 1), mRNA (cDNA clone IMAGE:4102924), partial cds.
BC001560 - Homo sapiens PTPRF interacting protein, binding protein 1 (liprin beta 1), mRNA (cDNA clone IMAGE:3453148), with apparent retained intron.
AK294267 - Homo sapiens cDNA FLJ54647 partial cds, highly similar to Liprin-beta-1.
AB033056 - Homo sapiens KIAA1230 mRNA for KIAA1230 protein.
BC050281 - Homo sapiens PTPRF interacting protein, binding protein 1 (liprin beta 1), mRNA (cDNA clone MGC:39493 IMAGE:5276255), complete cds.
AB049149 - Homo sapiens hSGT2 mRNA, complete cds.
AK314350 - Homo sapiens cDNA, FLJ95114.
AF034802 - Homo sapiens liprin-beta1 mRNA, complete cds.
BC046159 - Homo sapiens, Similar to PTPRF interacting protein, binding protein 1 (liprin beta 1), clone IMAGE:6065417, mRNA, partial cds.
AJ276680 - Homo sapiens partial mRNA for putative Liprin related protein (L2 gene).
AB384585 - Synthetic construct DNA, clone: pF1KA1230, Homo sapiens PPFIBP1 gene for liprin-beta-1, complete cds, without stop codon, in Flexi system.
KJ897852 - Synthetic construct Homo sapiens clone ccsbBroadEn_07246 PPFIBP1 gene, encodes complete protein.
JD223483 - Sequence 204507 from Patent EP1572962.
JD065662 - Sequence 46686 from Patent EP1572962.
LF207469 - JP 2014500723-A/14972: Polycomb-Associated Non-Coding RNAs.
LF366524 - JP 2014500723-A/174027: Polycomb-Associated Non-Coding RNAs.
AK000807 - Homo sapiens cDNA FLJ20800 fis, clone ADSU01576.
BX648761 - Homo sapiens mRNA; cDNA DKFZp686K23123 (from clone DKFZp686K23123).
JD184430 - Sequence 165454 from Patent EP1572962.
JD496384 - Sequence 477408 from Patent EP1572962.
JD334294 - Sequence 315318 from Patent EP1572962.
JD237225 - Sequence 218249 from Patent EP1572962.
JD404264 - Sequence 385288 from Patent EP1572962.
JD272024 - Sequence 253048 from Patent EP1572962.
JD198374 - Sequence 179398 from Patent EP1572962.
JD153088 - Sequence 134112 from Patent EP1572962.
JD160943 - Sequence 141967 from Patent EP1572962.
JD132198 - Sequence 113222 from Patent EP1572962.
JD526391 - Sequence 507415 from Patent EP1572962.
JD248741 - Sequence 229765 from Patent EP1572962.
JD344004 - Sequence 325028 from Patent EP1572962.
JD560535 - Sequence 541559 from Patent EP1572962.
JD480202 - Sequence 461226 from Patent EP1572962.
JD113661 - Sequence 94685 from Patent EP1572962.
JD358593 - Sequence 339617 from Patent EP1572962.
JD291308 - Sequence 272332 from Patent EP1572962.
JD428408 - Sequence 409432 from Patent EP1572962.
JD428410 - Sequence 409434 from Patent EP1572962.
JD293562 - Sequence 274586 from Patent EP1572962.
JD542284 - Sequence 523308 from Patent EP1572962.
JD084923 - Sequence 65947 from Patent EP1572962.
JD248823 - Sequence 229847 from Patent EP1572962.
JD110442 - Sequence 91466 from Patent EP1572962.
JD521094 - Sequence 502118 from Patent EP1572962.
JD478779 - Sequence 459803 from Patent EP1572962.
JD072919 - Sequence 53943 from Patent EP1572962.
JD146127 - Sequence 127151 from Patent EP1572962.
JD054323 - Sequence 35347 from Patent EP1572962.
JD565980 - Sequence 547004 from Patent EP1572962.
JD295398 - Sequence 276422 from Patent EP1572962.
JD328239 - Sequence 309263 from Patent EP1572962.
JD373722 - Sequence 354746 from Patent EP1572962.
JD077904 - Sequence 58928 from Patent EP1572962.
JD219722 - Sequence 200746 from Patent EP1572962.
JD106101 - Sequence 87125 from Patent EP1572962.
JD071216 - Sequence 52240 from Patent EP1572962.
JD256136 - Sequence 237160 from Patent EP1572962.
JD116199 - Sequence 97223 from Patent EP1572962.
JD356650 - Sequence 337674 from Patent EP1572962.
JD238894 - Sequence 219918 from Patent EP1572962.
JD374408 - Sequence 355432 from Patent EP1572962.
JD248051 - Sequence 229075 from Patent EP1572962.
JD322036 - Sequence 303060 from Patent EP1572962.
JD166353 - Sequence 147377 from Patent EP1572962.
JD348145 - Sequence 329169 from Patent EP1572962.
JD094504 - Sequence 75528 from Patent EP1572962.
JD072875 - Sequence 53899 from Patent EP1572962.
JD163481 - Sequence 144505 from Patent EP1572962.
JD072016 - Sequence 53040 from Patent EP1572962.
MA602101 - JP 2018138019-A/174027: Polycomb-Associated Non-Coding RNAs.
MA443046 - JP 2018138019-A/14972: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q86W92 (Reactome details) participates in the following event(s):

R-HSA-388824 PTPRF, PTPRS, PTPRD bind Liprins
R-HSA-388844 Receptor-type tyrosine-protein phosphatases
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000228425.1, ENST00000228425.10, ENST00000228425.2, ENST00000228425.3, ENST00000228425.4, ENST00000228425.5, ENST00000228425.6, ENST00000228425.7, ENST00000228425.8, ENST00000228425.9, KIAA1230, LIPB1_HUMAN, NM_003622, O75336, Q86W92, Q86X70, Q9NY03, Q9ULJ0, uc317dnv.1, uc317dnv.2
UCSC ID: ENST00000228425.11_6
RefSeq Accession: NM_003622.4
Protein: Q86W92 (aka LIPB1_HUMAN or LPB1_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.