Human Gene NHLRC3 (ENST00000379599.6_3) from GENCODE V47lift37
  Description: NHL repeat containing 3, transcript variant 2 (from RefSeq NM_001017370.3)
Gencode Transcript: ENST00000379599.6_3
Gencode Gene: ENSG00000188811.14_8
Transcript (Including UTRs)
   Position: hg19 chr13:39,612,528-39,624,246 Size: 11,719 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr13:39,612,777-39,622,063 Size: 9,287 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene 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 (chr13:39,612,528-39,624,246)mRNA (may differ from genome)Protein (280 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NHLC3_HUMAN
DESCRIPTION: RecName: Full=NHL repeat-containing protein 3; Flags: Precursor;
SUBCELLULAR LOCATION: Secreted (Potential).
SIMILARITY: Contains 4 NHL repeats.

-  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
  • D016604 Aflatoxin B1
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • D000082 Acetaminophen
  • D001564 Benzo(a)pyrene
  • D019327 Copper Sulfate
  • D016572 Cyclosporine
  • D003993 Dibutyl Phthalate
  • C028473 N-acetyl-4-benzoquinoneimine
  • D011078 Polychlorinated Biphenyls
  • D013749 Tetrachlorodibenzodioxin
          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: 14.48 RPKM in Thyroid
Total median expression: 407.54 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 -104.10249-0.418 Picture PostScript Text
3' UTR -514.102183-0.236 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
IPR011042 - 6-blade_b-propeller_TolB-like
IPR001258 - NHL_repeat
IPR013017 - NHL_repeat_subgr

Pfam Domains:
PF01436 - NHL repeat

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50956 - Thermostable phytase (3-phytase)
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
117289 - Nucleoporin domain
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Peptidase/esterase 'gauge' domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - DPP6 N-terminal domain-like

ModBase Predicted Comparative 3D Structure on Q5JS37
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0043312 neutrophil degranulation

Cellular Component:
GO:0005576 extracellular region
GO:0035578 azurophil granule lumen


-  Descriptions from all associated GenBank mRNAs
  AL833329 - Homo sapiens mRNA; cDNA DKFZp686G2033 (from clone DKFZp686G2033).
LF206116 - JP 2014500723-A/13619: Polycomb-Associated Non-Coding RNAs.
BX648122 - Homo sapiens mRNA; cDNA DKFZp686E1140 (from clone DKFZp686E1140).
BC052492 - Homo sapiens similar to RIKEN cDNA 8030451K01, mRNA (cDNA clone IMAGE:4822701).
BC140877 - Homo sapiens NHL repeat containing 3, mRNA (cDNA clone MGC:176554 IMAGE:9021745), complete cds.
BC140878 - Homo sapiens NHL repeat containing 3, mRNA (cDNA clone MGC:176555 IMAGE:9021746), complete cds.
CR749318 - Homo sapiens mRNA; cDNA DKFZp313A0825 (from clone DKFZp313A0825).
AK300260 - Homo sapiens cDNA FLJ52655 complete cds.
AK299198 - Homo sapiens cDNA FLJ50047 complete cds.
BX647872 - Homo sapiens mRNA; cDNA DKFZp313M1221 (from clone DKFZp313M1221).
JD404588 - Sequence 385612 from Patent EP1572962.
JD257411 - Sequence 238435 from Patent EP1572962.
JD525964 - Sequence 506988 from Patent EP1572962.
JD255642 - Sequence 236666 from Patent EP1572962.
KJ896176 - Synthetic construct Homo sapiens clone ccsbBroadEn_05570 NHLRC3 gene, encodes complete protein.
LF351544 - JP 2014500723-A/159047: Polycomb-Associated Non-Coding RNAs.
LF351539 - JP 2014500723-A/159042: Polycomb-Associated Non-Coding RNAs.
LF351538 - JP 2014500723-A/159041: Polycomb-Associated Non-Coding RNAs.
LF351537 - JP 2014500723-A/159040: Polycomb-Associated Non-Coding RNAs.
LF351536 - JP 2014500723-A/159039: Polycomb-Associated Non-Coding RNAs.
LF351535 - JP 2014500723-A/159038: Polycomb-Associated Non-Coding RNAs.
MA587121 - JP 2018138019-A/159047: Polycomb-Associated Non-Coding RNAs.
MA587116 - JP 2018138019-A/159042: Polycomb-Associated Non-Coding RNAs.
MA587115 - JP 2018138019-A/159041: Polycomb-Associated Non-Coding RNAs.
MA587114 - JP 2018138019-A/159040: Polycomb-Associated Non-Coding RNAs.
MA587113 - JP 2018138019-A/159039: Polycomb-Associated Non-Coding RNAs.
MA587112 - JP 2018138019-A/159038: Polycomb-Associated Non-Coding RNAs.
MA441693 - JP 2018138019-A/13619: Polycomb-Associated Non-Coding RNAs.

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

Protein Q5JS37 (Reactome details) participates in the following event(s):

R-HSA-6798751 Exocytosis of azurophil granule lumen proteins
R-HSA-6798695 Neutrophil degranulation
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B2RTZ2, B4DTL0, ENST00000379599.1, ENST00000379599.2, ENST00000379599.3, ENST00000379599.4, ENST00000379599.5, NHLC3_HUMAN, NM_001017370, Q5JS37, Q69YI9, uc318pbq.1, uc318pbq.2
UCSC ID: ENST00000379599.6_3
RefSeq Accession: NM_001017370.3
Protein: Q5JS37 (aka NHLC3_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.