Human Gene TONSL (ENST00000409379.8_7) from GENCODE V47lift37
  Description: tonsoku like, DNA repair protein (from RefSeq NM_013432.5)
Gencode Transcript: ENST00000409379.8_7
Gencode Gene: ENSG00000160949.18_10
Transcript (Including UTRs)
   Position: hg19 chr8:145,654,158-145,669,823 Size: 15,666 Total Exon Count: 26 Strand: -
Coding Region
   Position: hg19 chr8:145,654,526-145,669,797 Size: 15,272 Coding Exon Count: 26 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:145,654,158-145,669,823)mRNA (may differ from genome)Protein (1378 aa)
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TONSL_HUMAN
DESCRIPTION: RecName: Full=Tonsoku-like protein; AltName: Full=Inhibitor of kappa B-related protein; Short=I-kappa-B-related protein; Short=IkappaBR; AltName: Full=NF-kappa-B inhibitor-like protein 2; AltName: Full=Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2;
FUNCTION: Component of the MMS22L-TONSL complex, a complex that stimulates the recombination-dependent repair of stalled or collapsed replication forks. The MMS22L-TONSL complex is required to maintain genome integrity during DNA replication by promoting homologous recombination-mediated repair of replication fork- associated double-strand breaks. It may act by mediating the assembly of RAD51 filaments on ssDNA. Within the complex, may act as a scaffold.
SUBUNIT: Component of the MMS22L-TONSL complex, a complex at least composed of MMS22L and TONSL/NFKBIL2. Interacts with the MCM complex, the FACT complex and the RPA complex. Binds histones.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Mainly nuclear. Localizes to DNA damage sites, accumulates at stressed replication forks.
TISSUE SPECIFICITY: Expressed in heart, skeletal muscle and tracheal epithelial cells.
DOMAIN: The ANK repeats mediate the interaction with the MCM complex and histones, while the LRR repeats mediate the interaction with MMS22L.
SIMILARITY: Belongs to the Tonsoku family.
SIMILARITY: Contains 3 ANK repeats.
SIMILARITY: Contains 7 LRR (leucine-rich) repeats.
SIMILARITY: Contains 8 TPR repeats.
CAUTION: Was reported to share sequence similarities with IKBKB and therefore named 'NF-kappa-B inhibitor-like protein 2' (PubMed:7738005). However, the sequence similarity is remote and effects as regulator of NF-kappa-B are probably indirect and require additional evidence (PubMed:9242696).
SEQUENCE CAUTION: Sequence=AAA85819.1; Type=Frameshift; Positions=Several; Sequence=AAH08782.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAB63467.1; Type=Erroneous gene model prediction;

-  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

+  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: 8.75 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 101.75 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 -9.0026-0.346 Picture PostScript Text
3' UTR -131.10368-0.356 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
IPR002110 - Ankyrin_rpt
IPR020683 - Ankyrin_rpt-contain_dom
IPR013026 - TPR-contain_dom
IPR011990 - TPR-like_helical
IPR019734 - TPR_repeat

Pfam Domains:
PF00023 - Ankyrin repeat
PF07721 - Tetratricopeptide repeat
PF12796 - Ankyrin repeats (3 copies)
PF13176 - Tetratricopeptide repeat
PF13181 - Tetratricopeptide repeat
PF13516 - Leucine Rich repeat
PF13606 - Ankyrin repeat
PF13637 - Ankyrin repeats (many copies)
PF13857 - Ankyrin repeats (many copies)

SCOP Domains:
81901 - HCP-like
140860 - Pseudo ankyrin repeat-like
48452 - TPR-like
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1
48403 - Ankyrin repeat

ModBase Predicted Comparative 3D Structure on Q96HA7
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 orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
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 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003714 transcription corepressor activity
GO:0005515 protein binding
GO:0042393 histone binding

Biological Process:
GO:0000724 double-strand break repair via homologous recombination
GO:0006281 DNA repair
GO:0006974 cellular response to DNA damage stimulus
GO:0031297 replication fork processing
GO:0042994 cytoplasmic sequestering of transcription factor
GO:1903507 negative regulation of nucleic acid-templated transcription

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0016604 nuclear body
GO:0043596 nuclear replication fork
GO:0005662 DNA replication factor A complex
GO:0035101 FACT complex
GO:0042555 MCM complex


-  Descriptions from all associated GenBank mRNAs
  AB209126 - Homo sapiens mRNA for I-kappa-B-related protein variant protein.
BC008782 - Homo sapiens nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2, mRNA (cDNA clone MGC:3398 IMAGE:3628374), complete cds.
AK097406 - Homo sapiens cDNA FLJ40087 fis, clone TESTI2003089.
JD366482 - Sequence 347506 from Patent EP1572962.
JD145067 - Sequence 126091 from Patent EP1572962.
JD313435 - Sequence 294459 from Patent EP1572962.
JD079520 - Sequence 60544 from Patent EP1572962.
JD243194 - Sequence 224218 from Patent EP1572962.
JD136154 - Sequence 117178 from Patent EP1572962.
JD106616 - Sequence 87640 from Patent EP1572962.
JD436979 - Sequence 418003 from Patent EP1572962.
JD468817 - Sequence 449841 from Patent EP1572962.
JD561323 - Sequence 542347 from Patent EP1572962.
JD101915 - Sequence 82939 from Patent EP1572962.
JD101914 - Sequence 82938 from Patent EP1572962.
JD481317 - Sequence 462341 from Patent EP1572962.
JD561321 - Sequence 542345 from Patent EP1572962.
JD101913 - Sequence 82937 from Patent EP1572962.
JD393233 - Sequence 374257 from Patent EP1572962.
KJ901603 - Synthetic construct Homo sapiens clone ccsbBroadEn_10997 TONSL gene, encodes complete protein.
DQ892694 - Synthetic construct clone IMAGE:100005324; FLH188957.01X; RZPDo839H1173D nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2 (NFKBIL2) gene, encodes complete protein.
DQ895937 - Synthetic construct Homo sapiens clone IMAGE:100010397; FLH188953.01L; RZPDo839H1163D nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2 (NFKBIL2) gene, encodes complete protein.
U16258 - Human I kappa BR mRNA, complete cds.
CU679105 - Synthetic construct Homo sapiens gateway clone IMAGE:100020584 5' read NFKBIL2 mRNA.
JD444539 - Sequence 425563 from Patent EP1572962.
JD471002 - Sequence 452026 from Patent EP1572962.
JD274122 - Sequence 255146 from Patent EP1572962.
JD107915 - Sequence 88939 from Patent EP1572962.
JD099832 - Sequence 80856 from Patent EP1572962.
JD115613 - Sequence 96637 from Patent EP1572962.
JD066106 - Sequence 47130 from Patent EP1572962.
JD156095 - Sequence 137119 from Patent EP1572962.
JD051375 - Sequence 32399 from Patent EP1572962.
JD338670 - Sequence 319694 from Patent EP1572962.
JD351894 - Sequence 332918 from Patent EP1572962.
JD419748 - Sequence 400772 from Patent EP1572962.
JD269414 - Sequence 250438 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B5MDP0, C9JKB1, C9JNV8, ENST00000409379.1, ENST00000409379.2, ENST00000409379.3, ENST00000409379.4, ENST00000409379.5, ENST00000409379.6, ENST00000409379.7, IKBR , NFKBIL2, NM_013432, Q13006, Q96HA7, Q9UGJ2, TONSL , TONSL_HUMAN, uc319fqm.1, uc319fqm.2
UCSC ID: ENST00000409379.8_7
RefSeq Accession: NM_013432.5
Protein: Q96HA7 (aka TONSL_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.