Human Gene ABRAXAS1 (ENST00000321945.12_7) from GENCODE V47lift37
  Description: abraxas 1, BRCA1 A complex subunit, transcript variant 1 (from RefSeq NM_139076.3)
Gencode Transcript: ENST00000321945.12_7
Gencode Gene: ENSG00000163322.14_12
Transcript (Including UTRs)
   Position: hg19 chr4:84,380,670-84,406,253 Size: 25,584 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr4:84,383,622-84,406,225 Size: 22,604 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:84,380,670-84,406,253)mRNA (may differ from genome)Protein (409 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
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-  Comments and Description Text from UniProtKB
  ID: F175A_HUMAN
DESCRIPTION: RecName: Full=BRCA1-A complex subunit Abraxas; AltName: Full=Coiled-coil domain-containing protein 98; AltName: Full=Protein FAM175A;
FUNCTION: Component of the BRCA1-A complex, a complex that specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSBs). The BRCA1-A complex also possesses deubiquitinase activity that specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX. In the BRCA1-A complex, it acts as a central scaffold protein that assembles the various components of the BRCA1-A complex and mediates the recruitment of BRCA1.
SUBUNIT: Component of the BRCA1-A complex, at least composed of the BRCA1, BARD1, UIMC1/RAP80, FAM175A/Abraxas, BRCC3/BRCC36, BRE/BRCC45 and BABAM1/NBA1. In the complex, interacts directly with UIMC1/RAP80, BRCC3/BRCC36 and BRE/BRCC45. Interacts directly (when phosphorylated at Ser-406) with BRCA1. Binds polyubiquitin.
INTERACTION: P38398:BRCA1; NbExp=10; IntAct=EBI-1263451, EBI-349905; Q96RL1:UIMC1; NbExp=9; IntAct=EBI-1263451, EBI-725300;
SUBCELLULAR LOCATION: Nucleus. Note=Localizes at sites of DNA damage at double-strand breaks (DSBs).
DOMAIN: The MPN-like region is similar to the MPN (JAB/Mov34) domain. Its presence reveals similarities between the structure of the 19S proteasome and the BRCA1-A complexes.
PTM: Phosphorylation of Ser-406 of the pSXXF motif by ATM or ATR constitutes a specific recognition motif for the BRCT domain of BRCA1. Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the FAM175 family. Abraxas subfamily.
SEQUENCE CAUTION: Sequence=AAH39573.1; Type=Erroneous initiation; Sequence=BAB14189.1; Type=Erroneous initiation; Sequence=BAB14635.1; 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: ABRAXAS1
Diseases sorted by gene-association score: breast cancer* (65)
* = Manually curated disease association

+  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: 2.79 RPKM in Ovary
Total median expression: 44.63 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -4.4028-0.157 Picture PostScript Text
3' UTR -937.002952-0.317 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
IPR023238 - FAM175
IPR023239 - FAM175_BRCA1-A_cplx_Abraxas_su

SCOP Domains:
103657 - BAR/IMD domain-like
57997 - Tropomyosin

ModBase Predicted Comparative 3D Structure on Q6UWZ7
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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0031593 polyubiquitin binding

Biological Process:
GO:0006281 DNA repair
GO:0006302 double-strand break repair
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0006325 chromatin organization
GO:0006974 cellular response to DNA damage stimulus
GO:0010212 response to ionizing radiation
GO:0016579 protein deubiquitination
GO:0045739 positive regulation of DNA repair
GO:0072425 signal transduction involved in G2 DNA damage checkpoint

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016604 nuclear body
GO:0070531 BRCA1-A complex


-  Descriptions from all associated GenBank mRNAs
  KM576717 - Homo sapiens clone FAM175A-HELQ_F8-H3 mRNA sequence.
CU675034 - Synthetic construct Homo sapiens gateway clone IMAGE:100016694 3' read MRPS18C mRNA.
JD472270 - Sequence 453294 from Patent EP1572962.
JD294062 - Sequence 275086 from Patent EP1572962.
JD198983 - Sequence 180007 from Patent EP1572962.
JD327184 - Sequence 308208 from Patent EP1572962.
JD406847 - Sequence 387871 from Patent EP1572962.
JD378236 - Sequence 359260 from Patent EP1572962.
JD057350 - Sequence 38374 from Patent EP1572962.
JD455082 - Sequence 436106 from Patent EP1572962.
JD139088 - Sequence 120112 from Patent EP1572962.
JD533679 - Sequence 514703 from Patent EP1572962.
JD056827 - Sequence 37851 from Patent EP1572962.
JD291723 - Sequence 272747 from Patent EP1572962.
JD421878 - Sequence 402902 from Patent EP1572962.
JD421876 - Sequence 402900 from Patent EP1572962.
JD294027 - Sequence 275051 from Patent EP1572962.
JD067980 - Sequence 49004 from Patent EP1572962.
AK023676 - Homo sapiens cDNA FLJ13614 fis, clone PLACE1010857.
JD296323 - Sequence 277347 from Patent EP1572962.
BC039573 - Homo sapiens family with sequence similarity 175, member A, mRNA (cDNA clone MGC:48664 IMAGE:6045433), complete cds.
AK022704 - Homo sapiens cDNA FLJ12642 fis, clone NT2RM4001965.
JD363059 - Sequence 344083 from Patent EP1572962.
JD469443 - Sequence 450467 from Patent EP1572962.
JD047449 - Sequence 28473 from Patent EP1572962.
JD238679 - Sequence 219703 from Patent EP1572962.
JD503088 - Sequence 484112 from Patent EP1572962.
JD358849 - Sequence 339873 from Patent EP1572962.
AY358576 - Homo sapiens clone DNA56410 EGES496 (UNQ496) mRNA, complete cds.
JD313686 - Sequence 294710 from Patent EP1572962.
AK021582 - Homo sapiens cDNA FLJ11520 fis, clone HEMBA1002381.
JD117216 - Sequence 98240 from Patent EP1572962.
JD441462 - Sequence 422486 from Patent EP1572962.
JD551653 - Sequence 532677 from Patent EP1572962.
JD499229 - Sequence 480253 from Patent EP1572962.
JD468422 - Sequence 449446 from Patent EP1572962.
JD099937 - Sequence 80961 from Patent EP1572962.
JD512697 - Sequence 493721 from Patent EP1572962.
EF531340 - Homo sapiens abraxas protein (ABRA1) mRNA, complete cds.
KJ903390 - Synthetic construct Homo sapiens clone ccsbBroadEn_12784 FAM175A gene, encodes complete protein.
CU691726 - Synthetic construct Homo sapiens gateway clone IMAGE:100021103 5' read CCDC98 mRNA.
JD304636 - Sequence 285660 from Patent EP1572962.
BC016905 - Homo sapiens family with sequence similarity 175, member A, mRNA (cDNA clone IMAGE:4392057), complete cds.
JD155333 - Sequence 136357 from Patent EP1572962.
JD490570 - Sequence 471594 from Patent EP1572962.
JD367005 - Sequence 348029 from Patent EP1572962.
JD485343 - Sequence 466367 from Patent EP1572962.

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

Protein Q6UWZ7 (Reactome details) participates in the following event(s):

R-HSA-5683384 UIMC1 and FAM175A bind DNA DSBs
R-HSA-5684071 RNF4 ubiquitinates MDC1
R-HSA-5686685 RIF1 and PAX1IP bind TP53BP1 at DNA DSBs
R-HSA-5683385 Formation of BRCA1-A complex at DNA DSBs
R-HSA-5693551 Phosphorylation of BRCA1-A complex at multiple sites by ATM
R-HSA-5691411 BRCA1-A complex deubiquitinates K63polyUb-histone H2A
R-HSA-5683735 CHEK2 is recruited to DNA DSBs
R-HSA-5683801 CHEK2 phosphorylates BRCA1
R-HSA-69891 Phosphorylation and activation of CHEK2 by ATM
R-HSA-5684052 PIAS4 SUMOylates MDC1
R-HSA-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-HSA-5693607 Processing of DNA double-strand break ends
R-HSA-5693571 Nonhomologous End-Joining (NHEJ)
R-HSA-5693606 DNA Double Strand Break Response
R-HSA-5693567 HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
R-HSA-5693532 DNA Double-Strand Break Repair
R-HSA-5689901 Metalloprotease DUBs
R-HSA-69473 G2/M DNA damage checkpoint
R-HSA-5693538 Homology Directed Repair
R-HSA-73894 DNA Repair
R-HSA-5688426 Deubiquitination
R-HSA-69481 G2/M Checkpoints
R-HSA-597592 Post-translational protein modification
R-HSA-69620 Cell Cycle Checkpoints
R-HSA-392499 Metabolism of proteins
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: A5JJ07, ABRA1 , ABRAXAS1 , ABRX1_HUMAN, CCDC98, ENST00000321945.1, ENST00000321945.10, ENST00000321945.11, ENST00000321945.2, ENST00000321945.3, ENST00000321945.4, ENST00000321945.5, ENST00000321945.6, ENST00000321945.7, ENST00000321945.8, ENST00000321945.9, FAM175A , NM_139076, Q6UWZ7, Q9H8I1, Q9H9N4, uc317ref.1, uc317ref.2, UNQ496/PRO1013
UCSC ID: ENST00000321945.12_7
RefSeq Accession: NM_139076.3
Protein: Q6UWZ7 (aka F175A_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.