Human Gene RIMBP3 (ENST00000619918.1) from GENCODE V44
  Description: Homo sapiens RIMS binding protein 3 (RIMBP3), mRNA. (from RefSeq NM_015672)
Gencode Transcript: ENST00000619918.1
Gencode Gene: ENSG00000275793.1
Transcript (Including UTRs)
   Position: hg38 chr22:18,605,815-18,611,919 Size: 6,105 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg38 chr22:18,606,515-18,611,434 Size: 4,920 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Methods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:18,605,815-18,611,919)mRNA (may differ from genome)Protein (1639 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHGNC
HPRDLynxMalacardsMGIneXtProtOMIM
PubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RIM3A_HUMAN
DESCRIPTION: RecName: Full=RIMS-binding protein 3A; Short=RIM-BP3.A; AltName: Full=RIMS-binding protein 3.1; Short=RIM-BP3.1;
SIMILARITY: Belongs to the RIMBP family.
SIMILARITY: Contains 2 fibronectin type-III domains.
SIMILARITY: Contains 3 SH3 domains.
SEQUENCE CAUTION: Sequence=AAH35246.2; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB33336.1; Type=Frameshift; Positions=652; Sequence=CAB61362.2; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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 -222.50485-0.459 Picture PostScript Text
3' UTR -188.20700-0.269 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
IPR003961 - Fibronectin_type3
IPR011511 - SH3_2
IPR001452 - SH3_domain

Pfam Domains:
PF07653 - Variant SH3 domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2EGE - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9UFD9
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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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0007283 spermatogenesis
GO:0030154 cell differentiation

Cellular Component:
GO:0005737 cytoplasm
GO:0005856 cytoskeleton


-  Descriptions from all associated GenBank mRNAs
  AB051453 - Homo sapiens mRNA for KIAA1666 protein, partial cds.
JD566727 - Sequence 547751 from Patent EP1572962.
JD102723 - Sequence 83747 from Patent EP1572962.
JD196306 - Sequence 177330 from Patent EP1572962.
JD318832 - Sequence 299856 from Patent EP1572962.
JD241916 - Sequence 222940 from Patent EP1572962.
JD181289 - Sequence 162313 from Patent EP1572962.
BC035246 - Homo sapiens RIMS binding protein 3, mRNA (cDNA clone IMAGE:4827837), complete cds.
AL133030 - Homo sapiens mRNA; cDNA DKFZp434H177 (from clone DKFZp434H177).
AL117509 - Homo sapiens mRNA; cDNA DKFZp434H0735 (from clone DKFZp434H0735).
JD300305 - Sequence 281329 from Patent EP1572962.
JD260252 - Sequence 241276 from Patent EP1572962.
JD310384 - Sequence 291408 from Patent EP1572962.
JD439778 - Sequence 420802 from Patent EP1572962.
JD103263 - Sequence 84287 from Patent EP1572962.
JD477200 - Sequence 458224 from Patent EP1572962.
JD347011 - Sequence 328035 from Patent EP1572962.
KJ903518 - Synthetic construct Homo sapiens clone ccsbBroadEn_12912 RIMBP3 gene, encodes complete protein.
BC167855 - Synthetic construct Homo sapiens clone IMAGE:100068245, MGC:195862 RIMS binding protein 3 (RIMBP3) mRNA, encodes complete protein.
DQ574836 - Homo sapiens piRNA piR-42948, complete sequence.
CU690054 - Synthetic construct Homo sapiens gateway clone IMAGE:100020098 5' read KIAA1666 mRNA.
DQ594316 - Homo sapiens piRNA piR-60428, complete sequence.
DQ588106 - Homo sapiens piRNA piR-55218, complete sequence.
JD362756 - Sequence 343780 from Patent EP1572962.
JD125556 - Sequence 106580 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA1666, NM_015672, Q8IYP7, Q9BY94, Q9UFD9, Q9UFQ5, RIM3A_HUMAN, RIMBP3A, uc002zsd.1, uc002zsd.2, uc002zsd.3, uc002zsd.4, uc002zsd.5
UCSC ID: ENST00000619918.1
RefSeq Accession: NM_015672
Protein: Q9UFD9 (aka RIM3A_HUMAN)
CCDS: CCDS46665.1

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