Human Gene SLX1B (ENST00000330181.10_9) from GENCODE V47lift37
  Description: SLX1 homolog B, structure-specific endonuclease subunit, transcript variant 1 (from RefSeq NM_024044.5)
Gencode Transcript: ENST00000330181.10_9
Gencode Gene: ENSG00000181625.18_12
Transcript (Including UTRs)
   Position: hg19 chr16:29,465,854-29,469,540 Size: 3,687 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr16:29,466,064-29,469,445 Size: 3,382 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsGene 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 (chr16:29,465,854-29,469,540)mRNA (may differ from genome)Protein (275 aa)
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WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SLX1_HUMAN
DESCRIPTION: RecName: Full=Structure-specific endonuclease subunit SLX1; EC=3.6.1.-; AltName: Full=GIY-YIG domain-containing protein 1;
FUNCTION: Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for 5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves HJs by generating two pairs of ligatable, nicked duplex products.
COFACTOR: Divalent cation.
SUBUNIT: Forms a heterodimer with SLX4.
INTERACTION: Q8IY92:SLX4; NbExp=10; IntAct=EBI-2370858, EBI-2370740;
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the SLX1 family.
SIMILARITY: Contains 1 GIY-YIG domain.
SIMILARITY: Contains 1 SLX1-type zinc finger.
CAUTION: Found in a segmental duplication on p arm of chromosome 16 giving rise to two identical copies of this gene sharing exons with SULT1A3 and SULT1A4.

-  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: SLX1B
Diseases sorted by gene-association score: fanconi anemia, complementation group a (1)

+  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: 0.07 RPKM in Spleen
Total median expression: 0.20 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 -76.30210-0.363 Picture PostScript Text
3' UTR -19.4095-0.204 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
IPR000305 - UvrC_N

Pfam Domains:
PF01541 - GIY-YIG catalytic domain

SCOP Domains:
53474 - alpha/beta-Hydrolases
82771 - GIY-YIG endonuclease

ModBase Predicted Comparative 3D Structure on Q9BQ83
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:0004518 nuclease activity
GO:0004519 endonuclease activity
GO:0004520 endodeoxyribonuclease activity
GO:0005515 protein binding
GO:0008821 crossover junction endodeoxyribonuclease activity
GO:0016787 hydrolase activity
GO:0017108 5'-flap endonuclease activity
GO:0046872 metal ion binding

Biological Process:
GO:0000724 double-strand break repair via homologous recombination
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0006974 cellular response to DNA damage stimulus
GO:0010792 DNA double-strand break processing involved in repair via single-strand annealing
GO:0010833 telomere maintenance via telomere lengthening
GO:0036297 interstrand cross-link repair
GO:0061820 telomeric D-loop disassembly
GO:0090305 nucleic acid phosphodiester bond hydrolysis
GO:0090656 t-circle formation
GO:1904357 negative regulation of telomere maintenance via telomere lengthening
GO:1904431 positive regulation of t-circle formation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0033557 Slx1-Slx4 complex


-  Descriptions from all associated GenBank mRNAs
  BC015990 - Homo sapiens GIY-YIG domain containing 2, mRNA (cDNA clone MGC:2631 IMAGE:3503887), complete cds.
BC071688 - Homo sapiens cDNA clone IMAGE:5243747, **** WARNING: chimeric clone ****.
BC000754 - Homo sapiens GIY-YIG domain containing 2, mRNA (cDNA clone MGC:2532 IMAGE:2823474), complete cds.
BC019306 - Homo sapiens GIY-YIG domain containing 2, mRNA (cDNA clone MGC:4202 IMAGE:2823474), complete cds.
AK027092 - Homo sapiens cDNA: FLJ23439 fis, clone HSI00184.
AK225436 - Homo sapiens mRNA for GIY-YIG domain containing 2 isoform 1 variant, clone: HSI00184.
BC130545 - Homo sapiens GIY-YIG domain containing 2, mRNA (cDNA clone MGC:163417 IMAGE:40146576), complete cds.
BC130547 - Homo sapiens GIY-YIG domain containing 2, mRNA (cDNA clone MGC:163419 IMAGE:40146578), complete cds.
BC144462 - Homo sapiens GIY-YIG domain containing 1, mRNA (cDNA clone MGC:178005 IMAGE:9052988), complete cds.
BC069007 - Homo sapiens GIY-YIG domain containing 2, mRNA (cDNA clone MGC:78508 IMAGE:4335620), complete cds.
JD126502 - Sequence 107526 from Patent EP1572962.
BC000803 - Homo sapiens GIY-YIG domain containing 2, mRNA (cDNA clone MGC:5178 IMAGE:3452236), complete cds.
JD128287 - Sequence 109311 from Patent EP1572962.
AB463685 - Synthetic construct DNA, clone: pF1KB7367, Homo sapiens GIYD2 gene for GIY-YIG domain containing 2, without stop codon, in Flexi system.
BC141497 - Synthetic construct Homo sapiens clone IMAGE:100014746, MGC:175364 GIY-YIG domain containing 1 (GIYD1) mRNA, encodes complete protein.
BC148777 - Synthetic construct Homo sapiens clone IMAGE:100015825, MGC:183186 GIY-YIG domain containing 1 (GIYD1) mRNA, encodes complete protein.
HQ258083 - Synthetic construct Homo sapiens clone IMAGE:100072392 GIY-YIG domain containing 1 (GIYD1), transcript variant 2 (GIYD2) gene, encodes complete protein.
KJ894628 - Synthetic construct Homo sapiens clone ccsbBroadEn_04022 SLX1B gene, encodes complete protein.
KJ894629 - Synthetic construct Homo sapiens clone ccsbBroadEn_04023 SLX1B gene, encodes complete protein.
L19956 - Human aryl sulfotransferase mRNA, complete cds.
AK122707 - Homo sapiens cDNA FLJ16185 fis, clone BRTHA2005864, highly similar to Monoamine-sulfating phenol sulfotransferase (EC 2.8.2.1).
AK097386 - Homo sapiens cDNA FLJ40067 fis, clone TESOP2000527, moderately similar to MONOAMINE-SULFATING PHENOL SULFOTRANSFERASE (EC 2.8.2.1).
AK122733 - Homo sapiens cDNA FLJ16248 fis, clone HCHON2010543, highly similar to Human aryl sulfotransferase.
BC111011 - Homo sapiens sulfotransferase family, cytosolic, 1A, phenol-preferring, member 4, mRNA (cDNA clone MGC:117469 IMAGE:5768190), complete cds.
AK094769 - Homo sapiens cDNA FLJ37450 fis, clone BRAWH2010354, highly similar to Monoamine-sulfating phenol sulfotransferase (EC 2.8.2.1).
JD549245 - Sequence 530269 from Patent EP1572962.
JD234257 - Sequence 215281 from Patent EP1572962.
BC014471 - Homo sapiens sulfotransferase family, cytosolic, 1A, phenol-preferring, member 4, mRNA (cDNA clone MGC:23115 IMAGE:4907290), complete cds.
JD474402 - Sequence 455426 from Patent EP1572962.
JD186379 - Sequence 167403 from Patent EP1572962.
JD061786 - Sequence 42810 from Patent EP1572962.
JD265779 - Sequence 246803 from Patent EP1572962.
X84653 - H.sapiens mRNA for monoamine-sulfating phenosulfotransferase.
JD515955 - Sequence 496979 from Patent EP1572962.
JD054690 - Sequence 35714 from Patent EP1572962.
JD269478 - Sequence 250502 from Patent EP1572962.

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

Protein Q9BQ83 (Reactome details) participates in the following event(s):

R-HSA-5686475 SLX1A:SLX4 binds MUS81:EME1,(MUS81:EME2)
R-HSA-6785732 DNA nucleases bind monoubiquitinated ID2 complex
R-HSA-5693584 Cleavage of Holliday junctions by GEN1 or SLX1A:SLX4:MUS81:EME1,(MUS81:EME2)
R-HSA-5693568 Resolution of D-loop Structures through Holliday Junction Intermediates
R-HSA-6783310 Fanconi Anemia Pathway
R-HSA-5693537 Resolution of D-Loop Structures
R-HSA-73894 DNA Repair
R-HSA-5685942 HDR through Homologous Recombination (HRR)
R-HSA-5693567 HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
R-HSA-5693538 Homology Directed Repair
R-HSA-5693532 DNA Double-Strand Break Repair

-  Other Names for This Gene
  Alternate Gene Symbols: B7ZME1, ENST00000330181.1, ENST00000330181.2, ENST00000330181.3, ENST00000330181.4, ENST00000330181.5, ENST00000330181.6, ENST00000330181.7, ENST00000330181.8, ENST00000330181.9, GIYD1 , GIYD2, NM_024044, Q6NTG6, Q9BQ83, SLX1, SLX1A , SLX1B , SLX1_HUMAN, uc317sxg.1, uc317sxg.2
UCSC ID: ENST00000330181.10_9
RefSeq Accession: NM_024044.5
Protein: Q9BQ83 (aka SLX1_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.