Human Gene ABL1 (uc004bzv.3)
  Description: Homo sapiens c-abl oncogene 1, non-receptor tyrosine kinase (ABL1), transcript variant b, mRNA.
RefSeq Summary (NM_007313): This gene is a protooncogene that encodes a protein tyrosine kinase involved in a variety of cellular processes, including cell division, adhesion, differentiation, and response to stress. The activity of the protein is negatively regulated by its SH3 domain, whereby deletion of the region encoding this domain results in an oncogene. The ubiquitously expressed protein has DNA-binding activity that is regulated by CDC2-mediated phosphorylation, suggesting a cell cycle function. This gene has been found fused to a variety of translocation partner genes in various leukemias, most notably the t(9;22) translocation that results in a fusion with the 5' end of the breakpoint cluster region gene (BCR; MIM:151410). Alternative splicing of this gene results in two transcript variants, which contain alternative first exons that are spliced to the remaining common exons. [provided by RefSeq, Aug 2014].
Transcript (Including UTRs)
   Position: hg19 chr9:133,589,268-133,763,062 Size: 173,795 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr9:133,589,707-133,761,070 Size: 171,364 Coding Exon Count: 11 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
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 (chr9:133,589,268-133,763,062)mRNA (may differ from genome)Protein (1149 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMalacardsMGI
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  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): ABL1
CDC HuGE Published Literature: ABL1
Positive Disease Associations: clonal evolution of chronic myeloid leukemia , Lymphocytes , Neutrophils
Related Studies:
  1. clonal evolution of chronic myeloid leukemia
    Asimakopoulos FA et al. 1999, ABL1 methylation is a distinct molecular event associated with clonal evolution of chronic myeloid leukemia., Blood. 1999 Oct;94(7):2452-60. [PubMed 10498618]
  2. Lymphocytes
    , , . [PubMed 0]
  3. Neutrophils
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: ABL1
Diseases sorted by gene-association score: congenital heart defects and skeletal malformations syndrome* (900), leukemia, chronic myeloid, somatic* (215), heart disease* (200), leukemia, acute lymphoblastic 3* (118), abl1 kd-related altered drug metabolism* (100), precursor t-cell acute lymphoblastic leukemia* (94), myeloid leukemia (33), leukemia (29), myeloproliferative neoplasm (7), lymphoblastic leukemia (6), philadelphia-negative chronic myeloid leukemia (6), gastrointestinal stromal tumor (4), hypereosinophilic syndrome (4), bone marrow cancer (4), hematologic cancer (4), essential thrombocythemia (3), leukemia, acute lymphoblastic (3), childhood leukemia (2), chronic eosinophilic leukemia (2), cellular neurofibroma (2), t-cell prolymphocytic leukemia (2), myasthenic syndrome, congenital, 9, associated with acetylcholine receptor deficiency (1), myelofibrosis with myeloid metaplasia, somatic (1), artemis deficiency (1), leukemia, acute myeloid (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • C097613 imatinib
  • C488369 dasatinib
  • C498826 4-methyl-N-(3-(4-methylimidazol-1-yl)-5-(trifluoromethyl)phenyl)-3-((4-pyridin-3-ylpyrimidin-2-yl)amino)benzamide
  • C545373 AP24534
  • D002945 Cisplatin
  • D013629 Tamoxifen
  • D014212 Tretinoin
  • C017947 sodium arsenite
  • C576882 1-(2-trifluoromethoxyphenyl)-2-nitroethanone
  • C488288 2,5,7,8-tetramethyl-2R-(4R,8R,12-trimethyltridecyl)chroman-6-yloxy acetic acid
          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: 65.06 RPKM in Colon - Sigmoid
Total median expression: 1262.71 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 -105.20439-0.240 Picture PostScript Text
3' UTR -806.271992-0.405 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
  Pfam Domains:
PF00017 - SH2 domain
PF00018 - SH3 domain
PF00069 - Protein kinase domain
PF07653 - Variant SH3 domain
PF07714 - Protein tyrosine kinase
PF08919 - F-actin binding
PF14604 - Variant SH3 domain

SCOP Domains:
50044 - SH3-domain
56112 - Protein kinase-like (PK-like)
55550 - SH2 domain

ModBase Predicted Comparative 3D Structure on P00519-2
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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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Descriptions from all associated GenBank mRNAs
  AB209642 - Homo sapiens mRNA for Proto-oncogene tyrosine-protein kinase ABL1 variant protein.
M14753 - Human abl mRNA containing alternative first exons.
AB209456 - Homo sapiens mRNA for v-abl Abelson murine leukemia viral oncogene homolog 1 isoform b variant protein.
BC117451 - Homo sapiens c-abl oncogene 1, receptor tyrosine kinase, mRNA (cDNA clone MGC:151060 IMAGE:40126002), complete cds.
AB384952 - Synthetic construct DNA, clone: pF1KB4477, Homo sapiens ABL1 gene for proto-oncogene tyrosine-protein kinase ABL1, complete cds, without stop codon, in Flexi system.
EU447303 - Homo sapiens BCR/ABL fusion protein (BCR/ABL fusion) mRNA, partial cds.
KY284159 - Homo sapiens Bcr/Abl fusion protein e13a2 mRNA, partial cds.
EU394716 - Homo sapiens BCR/ABL e18-int1b-a2 fusion protein (BCR/ABL fusion) mRNA, exons, 2 and partial cds.
M14752 - Human c-abl gene, complete cds.
M30833 - Human abl protein mRNA, 5' end.
X16416 - Human c-abl mRNA encoding p150 protein.
M14754 - Human abl mRNA containing alternative first exons.
AY789120 - Homo sapiens BCR/ABL fusion mRNA sequence.
M14755 - Homo sapiens ABL1 protein (ABL1) mRNA, partial cds.
MH743144 - Homo sapiens BCR/ABL1 e1a2 fusion protein mRNA, partial cds.
MH401088 - Homo sapiens BCR-ABL1 p190 mRNA, partial cds.
AF113911 - Homo sapiens BCR-ABL1 e1a2 chimeric protein (BCR/ABL fusion) mRNA, partial cds.
DL225921 - METHOD AND REAGENT FOR INHIBITING THE EXPRESSION OF DISEASE RELATED GENES.
DL225922 - METHOD AND REAGENT FOR INHIBITING THE EXPRESSION OF DISEASE RELATED GENES.
MF925339 - Homo sapiens BCR/ABL e8a2 fusion mRNA, partial sequence.
EF158045 - Homo sapiens BCR/ABL p210 fusion protein (BCR/ABL fusion) mRNA, partial cds.
KU375572 - Homo sapiens BCR/ABL1 fusion protein (bcr/abl1) mRNA, partial cds.
KU705509 - Homo sapiens Bcr/Abl fusion protein (Bcr/Abl fusion) mRNA, partial cds.
KU705510 - Homo sapiens Bcr/Abl fusion protein (Bcr/Abl fusion) mRNA, partial cds.
AJ131467 - Homo sapiens partial mRNA for bcr-abl1 e13a2 chimeric protein.
EU216066 - Homo sapiens BCR/ABL fusion protein isoform X9 (BCR/ABL fusion) mRNA, complete cds.
EF423615 - Homo sapiens BCR/ABL fusion protein (BCR/ABL fusion) mRNA, partial cds.
MH401089 - Homo sapiens nonfunctional BCR-ABL1 p210 mRNA, partial sequence.
M13096 - Human chimeric bcr/c-abl fusion protein gene, exons 2-5.
M25946 - Human chronic myelocytic leukemia c-abl oncogene breakpoint cluster region (bcr) DNA, partial cds.
AJ131466 - Homo sapiens partial mRNA for bcr-abl1 e14a2 chimeric protein.
EU216071 - Homo sapiens BCR/ABL fusion protein isoform Y5 (BCR/ABL fusion) mRNA, complete cds.
EU394718 - Homo sapiens BCR/ABL e14a2 fusion protein (BCR/ABL fusion) mRNA, exons 12 through 14, a2, a3, a2 and partial cds.
AM491360 - Homo sapiens partial mRNA for bcr-abl1 e14a3 chimeric protein.
AM491361 - Homo sapiens partial mRNA for bcr-abl1 e1a3 chimeric protein.
AY043457 - Homo sapiens BCR-ABL fusion protein (BCR-ABL fusion) mRNA, partial cds.
AM491359 - Homo sapiens partial mRNA for bcr-abl1 e13a3 chimeric protein.
KY287767 - Homo sapiens BCR-ABL1 fusion protein e13a3 mRNA, partial cds.
EU216060 - Homo sapiens BCR/ABL fusion protein isoform X3 (BCR/ABL fusion) mRNA, complete cds.
DQ898314 - Homo sapiens isolate e13a4 BCR/ABL fusion protein (BCR/ABL fusion) mRNA, partial cds, alternatively spliced.
JX565024 - Homo sapiens isolate c-abl D276N c-ABL1 mRNA, partial cds.
JX565025 - Homo sapiens isolate c-abl E279A c-ABL1 mRNA, partial cds.
JF272500 - Homo sapiens isolate PTS2010 mutant BCR/ABL fusion protein mRNA, partial cds.
FJ785401 - Homo sapiens isolate RRC2008 mutant BCR/ABL fusion protein mRNA, partial cds.
AK095344 - Homo sapiens cDNA FLJ38025 fis, clone CTONG2013128.
AK294983 - Homo sapiens cDNA FLJ58117 complete cds, highly similar to Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2).
BC107069 - Homo sapiens c-abl oncogene 1, receptor tyrosine kinase, mRNA (cDNA clone IMAGE:40009788), partial cds.
BC107070 - Homo sapiens c-abl oncogene 1, receptor tyrosine kinase, mRNA (cDNA clone IMAGE:40009791), partial cds.
X51945 - H.sapiens c-abl mRNA 3'-fragment.
JD022796 - Sequence 3820 from Patent EP1572962.
JD027931 - Sequence 8955 from Patent EP1572962.
JD486266 - Sequence 467290 from Patent EP1572962.
JD346336 - Sequence 327360 from Patent EP1572962.
JD210026 - Sequence 191050 from Patent EP1572962.
JD416025 - Sequence 397049 from Patent EP1572962.
JD510645 - Sequence 491669 from Patent EP1572962.
JD423633 - Sequence 404657 from Patent EP1572962.
JD123547 - Sequence 104571 from Patent EP1572962.
JD209600 - Sequence 190624 from Patent EP1572962.
JD516697 - Sequence 497721 from Patent EP1572962.
JD070818 - Sequence 51842 from Patent EP1572962.
JD403574 - Sequence 384598 from Patent EP1572962.
JD422762 - Sequence 403786 from Patent EP1572962.
JD045485 - Sequence 26509 from Patent EP1572962.
JD426968 - Sequence 407992 from Patent EP1572962.
JD023907 - Sequence 4931 from Patent EP1572962.
JD035571 - Sequence 16595 from Patent EP1572962.
JD309915 - Sequence 290939 from Patent EP1572962.
JD187990 - Sequence 169014 from Patent EP1572962.
JD495158 - Sequence 476182 from Patent EP1572962.
JD078046 - Sequence 59070 from Patent EP1572962.
JD492322 - Sequence 473346 from Patent EP1572962.
JD415897 - Sequence 396921 from Patent EP1572962.
JD063328 - Sequence 44352 from Patent EP1572962.
JD077070 - Sequence 58094 from Patent EP1572962.
JD469811 - Sequence 450835 from Patent EP1572962.
JD437438 - Sequence 418462 from Patent EP1572962.
JD072548 - Sequence 53572 from Patent EP1572962.
JD269260 - Sequence 250284 from Patent EP1572962.
JD493853 - Sequence 474877 from Patent EP1572962.
JD456863 - Sequence 437887 from Patent EP1572962.
JD127029 - Sequence 108053 from Patent EP1572962.
JD106158 - Sequence 87182 from Patent EP1572962.
JD069263 - Sequence 50287 from Patent EP1572962.
JD487760 - Sequence 468784 from Patent EP1572962.
JD227259 - Sequence 208283 from Patent EP1572962.
JD255630 - Sequence 236654 from Patent EP1572962.
AF533988 - Homo sapiens BCRE3/ABL1A11 fusion protein (BCR/ABL1 fusion) mRNA, partial cds.
JD193841 - Sequence 174865 from Patent EP1572962.
JD128034 - Sequence 109058 from Patent EP1572962.
JD219751 - Sequence 200775 from Patent EP1572962.
JD452490 - Sequence 433514 from Patent EP1572962.
JD190905 - Sequence 171929 from Patent EP1572962.
JD136593 - Sequence 117617 from Patent EP1572962.
JD464359 - Sequence 445383 from Patent EP1572962.
MP015186 - Sequence 389 from Patent WO2019016252.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04012 - ErbB signaling pathway
hsa04110 - Cell cycle
hsa04360 - Axon guidance
hsa04722 - Neurotrophin signaling pathway
hsa05130 - Pathogenic Escherichia coli infection
hsa05131 - Shigellosis
hsa05200 - Pathways in cancer
hsa05220 - Chronic myeloid leukemia
hsa05416 - Viral myocarditis

BioCarta from NCI Cancer Genome Anatomy Project
h_g1Pathway - Cell Cycle: G1/S Check Point
h_arfPathway - Tumor Suppressor Arf Inhibits Ribosomal Biogenesis
h_atmPathway - ATM Signaling Pathway
h_Lis1Pathway - Lissencephaly gene (LIS1) in neuronal migration and development

Reactome (by CSHL, EBI, and GO)

Protein P00519 (Reactome details) participates in the following event(s):

R-HSA-449200 Interaction of ABL1 with CDO complex
R-HSA-1013833 Cables link CDK5 and ABL1
R-HSA-5686578 Activated ATM phosphorylates ABL1
R-HSA-448957 Interaction of p38 MAPK with JLP
R-HSA-376141 Interaction of ABL with ROBO1:SLIT2
R-HSA-2130194 ABL phosphorylates WAVEs
R-HSA-5686587 ABL1 phosphorylates RAD52
R-HSA-8956659 ABL1 phosphorylates YAP1
R-HSA-428888 Phosphorylation of ROBO1 by ABL kinase
R-HSA-428883 Recruitment of CAP to ABL
R-HSA-428885 Activation of CLASP
R-HSA-8942607 Tyrosine kinases phosphorylate Cip/Kip inhibitors bound to CDK4/6:CCND complexes
R-HSA-375170 CDO in myogenesis
R-HSA-983231 Factors involved in megakaryocyte development and platelet production
R-HSA-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-HSA-428890 Role of ABL in ROBO-SLIT signaling
R-HSA-525793 Myogenesis
R-HSA-109582 Hemostasis
R-HSA-2029482 Regulation of actin dynamics for phagocytic cup formation
R-HSA-5663213 RHO GTPases Activate WASPs and WAVEs
R-HSA-5693606 DNA Double Strand Break Response
R-HSA-5685938 HDR through Single Strand Annealing (SSA)
R-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-HSA-376176 Signaling by ROBO receptors
R-HSA-1266738 Developmental Biology
R-HSA-2029480 Fcgamma receptor (FCGR) dependent phagocytosis
R-HSA-195258 RHO GTPase Effectors
R-HSA-5693532 DNA Double-Strand Break Repair
R-HSA-5693567 HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-69231 Cyclin D associated events in G1
R-HSA-422475 Axon guidance
R-HSA-168249 Innate Immune System
R-HSA-194315 Signaling by Rho GTPases
R-HSA-73894 DNA Repair
R-HSA-5693538 Homology Directed Repair
R-HSA-212436 Generic Transcription Pathway
R-HSA-69236 G1 Phase
R-HSA-168256 Immune System
R-HSA-162582 Signal Transduction
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-453279 Mitotic G1-G1/S phases
R-HSA-74160 Gene expression (Transcription)
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: ABL, JTK7, NM_007313, NP_009297, P00519-2
UCSC ID: uc004bzv.3
RefSeq Accession: NM_007313
Protein: P00519-2, splice isoform of P00519 CCDS: CCDS35166.1, CCDS35165.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_007313.2
exon count: 11CDS single in 3' UTR: no RNA size: 5881
ORF size: 3450CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6203.50frame shift in genome: no % Coverage: 100.00
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.