Human Gene ABLIM2 (uc003gkj.4)
  Description: Homo sapiens actin binding LIM protein family, member 2 (ABLIM2), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr4:7,967,037-8,160,559 Size: 193,523 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg19 chr4:7,968,717-8,160,416 Size: 191,700 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:7,967,037-8,160,559)mRNA (may differ from genome)Protein (645 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
OMIMPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: E9PF39_HUMAN
DESCRIPTION: SubName: Full=Actin-binding LIM protein 2;
SIMILARITY: Contains 4 LIM zinc-binding domains.
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ABLIM2
CDC HuGE Published Literature: ABLIM2
Positive Disease Associations: Basophils , Coronary Artery Disease , Prostatic Neoplasms
Related Studies:
  1. Basophils
    , , . [PubMed 0]
  2. Coronary Artery Disease
    , , . [PubMed 0]
  3. Prostatic Neoplasms
    , , . [PubMed 0]
           more ... click here to view the complete list

-  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: 61.78 RPKM in Muscle - Skeletal
Total median expression: 296.17 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 -84.90143-0.594 Picture PostScript Text
3' UTR -667.811680-0.398 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)

ModBase Predicted Comparative 3D Structure on E9PF39
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 orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Descriptions from all associated GenBank mRNAs
  AK301060 - Homo sapiens cDNA FLJ52773 complete cds, highly similar to Actin-binding LIM protein 2.
HM005542 - Homo sapiens clone HTL-S-2 testis tissue sperm-binding protein Li 35a mRNA, complete cds.
AL834195 - Homo sapiens mRNA; cDNA DKFZp761F129 (from clone DKFZp761F129).
AK094754 - Homo sapiens cDNA FLJ37435 fis, clone BRAWH2002811, moderately similar to Homo sapiens actin-binding double-zinc-finger protein (abLIM) mRNA.
AK094798 - Homo sapiens cDNA FLJ37479 fis, clone BRAWH2013748, moderately similar to Actin binding LIM protein 1.
AB058711 - Homo sapiens mRNA for KIAA1808 protein, partial cds.
AJ748600 - Homo sapiens mRNA for actin binding LIM protein family member 2 (ABLIM2 gene), isoform b.
AJ748601 - Homo sapiens mRNA for actin binding LIM protein family member 2 (ABLIM2 gene), isoform a.
BC122567 - Homo sapiens actin binding LIM protein family, member 2, mRNA (cDNA clone MGC:141918 IMAGE:40085570), complete cds.
DQ413176 - Homo sapiens actin-binding LIM protein 2 splice variant 1 (ABLIM2) mRNA, complete cds, alternatively spliced.
DQ413177 - Homo sapiens actin-binding LIM protein 2 splice variant 2 (ABLIM2) mRNA, complete cds, alternatively spliced.
KJ899797 - Synthetic construct Homo sapiens clone ccsbBroadEn_09191 ABLIM2 gene, encodes complete protein.
BC067214 - Homo sapiens actin binding LIM protein family, member 2, mRNA (cDNA clone IMAGE:6188753), partial cds.
AK097003 - Homo sapiens cDNA FLJ39684 fis, clone SMINT2010326.
JD357065 - Sequence 338089 from Patent EP1572962.
JD036882 - Sequence 17906 from Patent EP1572962.
JD437817 - Sequence 418841 from Patent EP1572962.
JD282868 - Sequence 263892 from Patent EP1572962.
JD550580 - Sequence 531604 from Patent EP1572962.
JD051967 - Sequence 32991 from Patent EP1572962.
JD536413 - Sequence 517437 from Patent EP1572962.
JD273304 - Sequence 254328 from Patent EP1572962.
JD487690 - Sequence 468714 from Patent EP1572962.
JD378325 - Sequence 359349 from Patent EP1572962.
JD119503 - Sequence 100527 from Patent EP1572962.
JD314243 - Sequence 295267 from Patent EP1572962.
JD196372 - Sequence 177396 from Patent EP1572962.
JD494076 - Sequence 475100 from Patent EP1572962.
JD143612 - Sequence 124636 from Patent EP1572962.
JD214971 - Sequence 195995 from Patent EP1572962.
JD459814 - Sequence 440838 from Patent EP1572962.
JD450909 - Sequence 431933 from Patent EP1572962.
JD473448 - Sequence 454472 from Patent EP1572962.
JD408078 - Sequence 389102 from Patent EP1572962.
JD483763 - Sequence 464787 from Patent EP1572962.
JD283762 - Sequence 264786 from Patent EP1572962.
JD475543 - Sequence 456567 from Patent EP1572962.
JD215696 - Sequence 196720 from Patent EP1572962.
JD276572 - Sequence 257596 from Patent EP1572962.
JD437856 - Sequence 418880 from Patent EP1572962.
JD230853 - Sequence 211877 from Patent EP1572962.
JD397339 - Sequence 378363 from Patent EP1572962.
JD054848 - Sequence 35872 from Patent EP1572962.
JD210512 - Sequence 191536 from Patent EP1572962.
JD077300 - Sequence 58324 from Patent EP1572962.
JD462778 - Sequence 443802 from Patent EP1572962.
JD434894 - Sequence 415918 from Patent EP1572962.
AJ431609 - Homo sapiens mRNA adjacent to 3' end of integrated HPV16 (INT259).
AK130044 - Homo sapiens cDNA FLJ26534 fis, clone KDN09135.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04360 - Axon guidance

-  Other Names for This Gene
  Alternate Gene Symbols: E9PF39, E9PF39_HUMAN, NM_001130083, NP_001123555
UCSC ID: uc003gkj.4
RefSeq Accession: NM_001130083
Protein: E9PF39 CCDS: CCDS47014.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001130083.1
exon count: 21CDS single in 3' UTR: no RNA size: 3774
ORF size: 1938CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4076.00frame shift in genome: no % Coverage: 99.66
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.