Human Gene ABLIM3 (ENST00000309868.12_4) from GENCODE V47lift37
  Description: actin binding LIM protein family member 3, transcript variant 2 (from RefSeq NM_014945.5)
Gencode Transcript: ENST00000309868.12_4
Gencode Gene: ENSG00000173210.21_8
Transcript (Including UTRs)
   Position: hg19 chr5:148,521,056-148,640,105 Size: 119,050 Total Exon Count: 24 Strand: +
Coding Region
   Position: hg19 chr5:148,521,659-148,637,967 Size: 116,309 Coding Exon Count: 23 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:148,521,056-148,640,105)mRNA (may differ from genome)Protein (683 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ABLM3_HUMAN
DESCRIPTION: RecName: Full=Actin-binding LIM protein 3; Short=abLIM-3; AltName: Full=Actin-binding LIM protein family member 3;
FUNCTION: May act as scaffold protein. May stimulate ABRA activity and ABRA-dependent SRF transcriptional activity.
SUBUNIT: Directly interacts with F-actin and ABRA.
SUBCELLULAR LOCATION: Cytoplasm (By similarity).
TISSUE SPECIFICITY: Expressed predominantly in heart and brain.
SIMILARITY: Contains 1 HP (headpiece) domain.
SIMILARITY: Contains 4 LIM zinc-binding domains.
SEQUENCE CAUTION: Sequence=BAA74866.2; 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


-  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: 36.21 RPKM in Adipose - Visceral (Omentum)
Total median expression: 561.91 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 -78.70249-0.316 Picture PostScript Text
3' UTR -683.942138-0.320 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
IPR003128 - Villin_headpiece
IPR001781 - Znf_LIM

Pfam Domains:
PF00412 - LIM domain
PF02209 - Villin headpiece domain
PF16182 - Putative adherens-junction anchoring region of AbLIM

SCOP Domains:
47050 - VHP, Villin headpiece domain
57716 - Glucocorticoid receptor-like (DNA-binding domain)

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1UJS - NMR MuPIT 2DJ7 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O94929
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003779 actin binding
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0007010 cytoskeleton organization
GO:0030032 lamellipodium assembly
GO:0030036 actin cytoskeleton organization
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0060271 cilium assembly
GO:1903955 positive regulation of protein targeting to mitochondrion

Cellular Component:
GO:0001725 stress fiber
GO:0005737 cytoplasm
GO:0030027 lamellipodium


-  Descriptions from all associated GenBank mRNAs
  AB020650 - Homo sapiens KIAA0843 mRNA for KIAA0843 protein.
AK225769 - Homo sapiens mRNA for actin binding LIM protein family, member 3 variant, clone: FCC133E06.
BC014463 - Homo sapiens actin binding LIM protein family, member 3, mRNA (cDNA clone IMAGE:4908608), with apparent retained intron.
BC001665 - Homo sapiens actin binding LIM protein family, member 3, mRNA (cDNA clone MGC:1835 IMAGE:2988043), complete cds.
DQ413174 - Homo sapiens actin-binding LIM protein 3 (ABLIM3) mRNA, complete cds.
AK289736 - Homo sapiens cDNA FLJ76333 complete cds, highly similar to Homo sapiens actin binding LIM protein family, member 3 (ABLIM3), mRNA.
AM392595 - Synthetic construct Homo sapiens clone IMAGE:100002722 for hypothetical protein (ABLIM3 gene).
AM392703 - Synthetic construct Homo sapiens clone IMAGE:100002725 for hypothetical protein (ABLIM3 gene).
AM392846 - Synthetic construct Homo sapiens clone IMAGE:100002796 for hypothetical protein (ABLIM3 gene).
AM392865 - Synthetic construct Homo sapiens clone IMAGE:100002794 for hypothetical protein (ABLIM3 gene).
AM392930 - Synthetic construct Homo sapiens clone IMAGE:100002724 for hypothetical protein (ABLIM3 gene).
AM392963 - Synthetic construct Homo sapiens clone IMAGE:100002801 for hypothetical protein (ABLIM3 gene).
AM392998 - Synthetic construct Homo sapiens clone IMAGE:100002802 for hypothetical protein (ABLIM3 gene).
AM393099 - Synthetic construct Homo sapiens clone IMAGE:100002727 for hypothetical protein (ABLIM3 gene).
AM393161 - Synthetic construct Homo sapiens clone IMAGE:100002729 for hypothetical protein (ABLIM3 gene).
AM393223 - Synthetic construct Homo sapiens clone IMAGE:100002800 for hypothetical protein (ABLIM3 gene).
AM393284 - Synthetic construct Homo sapiens clone IMAGE:100002803 for hypothetical protein (ABLIM3 gene).
AM393405 - Synthetic construct Homo sapiens clone IMAGE:100002795 for hypothetical protein (ABLIM3 gene).
AM393422 - Synthetic construct Homo sapiens clone IMAGE:100002728 for hypothetical protein (ABLIM3 gene).
AM393563 - Synthetic construct Homo sapiens clone IMAGE:100002726 for hypothetical protein (ABLIM3 gene).
AM393655 - Synthetic construct Homo sapiens clone IMAGE:100002731 for hypothetical protein (ABLIM3 gene).
AM393682 - Synthetic construct Homo sapiens clone IMAGE:100002798 for hypothetical protein (ABLIM3 gene).
AM393722 - Synthetic construct Homo sapiens clone IMAGE:100002799 for hypothetical protein (ABLIM3 gene).
AM393756 - Synthetic construct Homo sapiens clone IMAGE:100002730 for hypothetical protein (ABLIM3 gene).
AM393757 - Synthetic construct Homo sapiens clone IMAGE:100002723 for hypothetical protein (ABLIM3 gene).
AM392890 - Synthetic construct Homo sapiens clone IMAGE:100002975 for hypothetical protein (ABLIM3 gene).
AM393101 - Synthetic construct Homo sapiens clone IMAGE:100003052 for hypothetical protein (ABLIM3 gene).
AM393116 - Synthetic construct Homo sapiens clone IMAGE:100002974 for hypothetical protein (ABLIM3 gene).
AM393153 - Synthetic construct Homo sapiens clone IMAGE:100002977 for hypothetical protein (ABLIM3 gene).
AM393412 - Synthetic construct Homo sapiens clone IMAGE:100002976 for hypothetical protein (ABLIM3 gene).
AM393431 - Synthetic construct Homo sapiens clone IMAGE:100002972 for hypothetical protein (ABLIM3 gene).
AM393524 - Synthetic construct Homo sapiens clone IMAGE:100003051 for hypothetical protein (ABLIM3 gene).
AM393554 - Synthetic construct Homo sapiens clone IMAGE:100003049 for hypothetical protein (ABLIM3 gene).
AM393559 - Synthetic construct Homo sapiens clone IMAGE:100002971 for hypothetical protein (ABLIM3 gene).
AM393658 - Synthetic construct Homo sapiens clone IMAGE:100002970 for hypothetical protein (ABLIM3 gene).
AM393820 - Synthetic construct Homo sapiens clone IMAGE:100002973 for hypothetical protein (ABLIM3 gene).
AM393401 - Synthetic construct Homo sapiens clone IMAGE:100002797 for hypothetical protein (ABLIM3 gene).
AB384009 - Synthetic construct DNA, clone: pF1KSDA0843, Homo sapiens ABLIM3 gene for actin-binding LIM protein 3, complete cds, without stop codon, in Flexi system.
KJ902248 - Synthetic construct Homo sapiens clone ccsbBroadEn_11642 ABLIM3 gene, encodes complete protein.
AL833021 - Homo sapiens mRNA; cDNA DKFZp666D088 (from clone DKFZp666D088).
AB075881 - Homo sapiens mRNA for putative protein product of HMFN1661, complete cds.
AK098469 - Homo sapiens cDNA FLJ25603 fis, clone JTH14023.
JD310214 - Sequence 291238 from Patent EP1572962.
JD263096 - Sequence 244120 from Patent EP1572962.
JD154643 - Sequence 135667 from Patent EP1572962.
JD520913 - Sequence 501937 from Patent EP1572962.
JD062786 - Sequence 43810 from Patent EP1572962.
JD230637 - Sequence 211661 from Patent EP1572962.
JD164759 - Sequence 145783 from Patent EP1572962.
JD523962 - Sequence 504986 from Patent EP1572962.
JD288832 - Sequence 269856 from Patent EP1572962.
JD560581 - Sequence 541605 from Patent EP1572962.
JD111844 - Sequence 92868 from Patent EP1572962.
JD436521 - Sequence 417545 from Patent EP1572962.
JD525407 - Sequence 506431 from Patent EP1572962.
JD108680 - Sequence 89704 from Patent EP1572962.
JD146186 - Sequence 127210 from Patent EP1572962.
JD092869 - Sequence 73893 from Patent EP1572962.
JD060526 - Sequence 41550 from Patent EP1572962.
JD462194 - Sequence 443218 from Patent EP1572962.
JD556810 - Sequence 537834 from Patent EP1572962.
JD398538 - Sequence 379562 from Patent EP1572962.
JD418459 - Sequence 399483 from Patent EP1572962.
JD271615 - Sequence 252639 from Patent EP1572962.
JD322044 - Sequence 303068 from Patent EP1572962.
JD427525 - Sequence 408549 from Patent EP1572962.
JD416354 - Sequence 397378 from Patent EP1572962.
JD385036 - Sequence 366060 from Patent EP1572962.
JD272419 - Sequence 253443 from Patent EP1572962.
JD155441 - Sequence 136465 from Patent EP1572962.
JD268742 - Sequence 249766 from Patent EP1572962.
JD439346 - Sequence 420370 from Patent EP1572962.
JD448952 - Sequence 429976 from Patent EP1572962.
JD315128 - Sequence 296152 from Patent EP1572962.
JD268193 - Sequence 249217 from Patent EP1572962.
JD419873 - Sequence 400897 from Patent EP1572962.
JD057937 - Sequence 38961 from Patent EP1572962.
JD174267 - Sequence 155291 from Patent EP1572962.
JD075225 - Sequence 56249 from Patent EP1572962.
JD224415 - Sequence 205439 from Patent EP1572962.
JD353796 - Sequence 334820 from Patent EP1572962.
JD209327 - Sequence 190351 from Patent EP1572962.
JD133878 - Sequence 114902 from Patent EP1572962.

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

Protein O94929 (Reactome details) participates in the following event(s):

R-HSA-418865 Recruitment of ABLIM to the plasma membrane
R-HSA-418885 DCC mediated attractive signaling
R-HSA-373752 Netrin-1 signaling
R-HSA-422475 Axon guidance
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: A8K121, ABLM3_HUMAN, ENST00000309868.1, ENST00000309868.10, ENST00000309868.11, ENST00000309868.2, ENST00000309868.3, ENST00000309868.4, ENST00000309868.5, ENST00000309868.6, ENST00000309868.7, ENST00000309868.8, ENST00000309868.9, HMFN1661, KIAA0843, NM_014945, O94929, Q19VH3, Q658S1, Q68CI5, Q9BV32, uc317opr.1, uc317opr.2
UCSC ID: ENST00000309868.12_4
RefSeq Accession: NM_014945.5
Protein: O94929 (aka ABLM3_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.