Human Gene NBR1 (ENST00000590996.6_6) from GENCODE V47lift37
  Description: NBR1 autophagy cargo receptor, transcript variant 1 (from RefSeq NM_005899.5)
Gencode Transcript: ENST00000590996.6_6
Gencode Gene: ENSG00000188554.15_9
Transcript (Including UTRs)
   Position: hg19 chr17:41,323,231-41,363,707 Size: 40,477 Total Exon Count: 21 Strand: +
Coding Region
   Position: hg19 chr17:41,327,817-41,362,093 Size: 34,277 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:41,323,231-41,363,707)mRNA (may differ from genome)Protein (966 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NBR1_HUMAN
DESCRIPTION: RecName: Full=Next to BRCA1 gene 1 protein; AltName: Full=Cell migration-inducing gene 19 protein; AltName: Full=Membrane component chromosome 17 surface marker 2; AltName: Full=Neighbor of BRCA1 gene 1 protein; AltName: Full=Protein 1A1-3B;
FUNCTION: Acts probably as a receptor for selective autophagosomal degradation of ubiquitinated targets.
SUBUNIT: Homooligomer and heterooligomer. Interacts with TRIM55 (By similarity). Interacts with SQSTM1, titin/TTN, RNF29, USP8, SQSTM1, MAP1LC3A, MAP1LC3B, MAP1LC3C, GABARAP, GABARAPL1 and GABARAPL2. Binds to ubiquitin and ubiquitinated proteins.
INTERACTION: P38182:ATG8 (xeno); NbExp=6; IntAct=EBI-742698, EBI-2684; O95166:GABARAP; NbExp=5; IntAct=EBI-742698, EBI-712001; Q9H0R8:GABARAPL1; NbExp=4; IntAct=EBI-742698, EBI-746969; P60520:GABARAPL2; NbExp=10; IntAct=EBI-742698, EBI-720116; P42858:HTT; NbExp=3; IntAct=EBI-742698, EBI-466029; Q9H492:MAP1LC3A; NbExp=2; IntAct=EBI-742698, EBI-720768; Q9GZQ8:MAP1LC3B; NbExp=8; IntAct=EBI-742698, EBI-373144; Q9BXW4:MAP1LC3C; NbExp=3; IntAct=EBI-742698, EBI-2603996; Q13501:SQSTM1; NbExp=5; IntAct=EBI-742698, EBI-307104;
SUBCELLULAR LOCATION: Cytoplasm. Cytoplasmic vesicle, autophagosome. Lysosome. Cytoplasm, myofibril, sarcomere, M line (By similarity). Note=In cardiac muscles localizes to the sarcomeric M line (By similarity). Is targeted to lysosomes for degradation.
DOMAIN: The OPR domain mediates interaction with SQSTM1.
SIMILARITY: Contains 1 OPR domain.
SIMILARITY: Contains 1 UBA domain.
SIMILARITY: Contains 1 ZZ-type zinc finger.
CAUTION: Was originally (PubMed:8069304) thought to be the ovarian carcinoma antigen CA125.
SEQUENCE CAUTION: Sequence=BAA06417.2; 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: NBR1
Diseases sorted by gene-association score: inclusion body myositis (3), synucleinopathy (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D002945 Cisplatin
  • D004997 Ethinyl Estradiol
  • D013749 Tetrachlorodibenzodioxin
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C009505 4,4'-diaminodiphenylmethane
  • D000082 Acetaminophen
  • D016604 Aflatoxin B1
  • D000393 Air Pollutants
  • D002994 Clofibrate
          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: 64.71 RPKM in Testis
Total median expression: 1394.63 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 -38.3098-0.391 Picture PostScript Text
3' UTR -430.901614-0.267 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
IPR000270 - OPR_PB1
IPR009060 - UBA-like
IPR015940 - UBA/transl_elong_EF1B_N_euk
IPR000433 - Znf_ZZ

Pfam Domains:
PF00564 - PB1 domain
PF00569 - Zinc finger, ZZ type
PF16158 - Ig-like domain from next to BRCA1 gene

SCOP Domains:
46934 - UBA-like
54277 - CAD & PB1 domains
57850 - RING/U-box
57889 - Cysteine-rich domain
57903 - FYVE/PHD zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1WJ6 - NMR MuPIT 2BKF - X-ray MuPIT 2CP8 - NMR MuPIT 2G4S - X-ray MuPIT 2L8J - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q14596
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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    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0043130 ubiquitin binding
GO:0046872 metal ion binding
GO:0051019 mitogen-activated protein kinase binding

Biological Process:
GO:0016236 macroautophagy
GO:0030500 regulation of bone mineralization
GO:0032872 regulation of stress-activated MAPK cascade
GO:0045668 negative regulation of osteoblast differentiation
GO:0051259 protein oligomerization

Cellular Component:
GO:0000407 pre-autophagosomal structure
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005770 late endosome
GO:0005776 autophagosome
GO:0005829 cytosol
GO:0016020 membrane
GO:0016604 nuclear body
GO:0031410 cytoplasmic vesicle
GO:0031430 M band
GO:0043231 intracellular membrane-bounded organelle
GO:0005739 mitochondrion


-  Descriptions from all associated GenBank mRNAs
  LF209356 - JP 2014500723-A/16859: Polycomb-Associated Non-Coding RNAs.
D30756 - Homo sapiens KIAA0049 mRNA.
AF227189 - Homo sapiens NBR1 mRNA, partial cds; alternatively spliced.
AK299328 - Homo sapiens cDNA FLJ55359 complete cds, highly similar to Next to BRCA1 gene 1 protein.
LF213993 - JP 2014500723-A/21496: Polycomb-Associated Non-Coding RNAs.
AK290005 - Homo sapiens cDNA FLJ75601 complete cds, highly similar to Homo sapiens neighbor of BRCA1 gene 1 (NBR1), transcript variant 1, mRNA.
LF209357 - JP 2014500723-A/16860: Polycomb-Associated Non-Coding RNAs.
BC012591 - Homo sapiens, clone IMAGE:4297209, mRNA.
AK297425 - Homo sapiens cDNA FLJ55105 complete cds, highly similar to Next to BRCA1 gene 1 protein.
X76952 - H.sapiens IAI.3B mRNA.
BC009808 - Homo sapiens neighbor of BRCA1 gene 1, mRNA (cDNA clone MGC:1377 IMAGE:2989212), complete cds.
AY450308 - Homo sapiens migration-inducing protein 19 mRNA, complete cds.
CU679501 - Synthetic construct Homo sapiens gateway clone IMAGE:100020535 5' read NBR1 mRNA.
AB383726 - Synthetic construct DNA, clone: pF1KSDA0049, Homo sapiens NBR1 gene for neighbor of BRCA1 gene 1, complete cds, without stop codon, in Flexi system.
LF327967 - JP 2014500723-A/135470: Polycomb-Associated Non-Coding RNAs.
AK128512 - Homo sapiens cDNA FLJ46669 fis, clone TRACH3008042, highly similar to Membrane component, chromosome 17, surface marker 2.
AK308324 - Homo sapiens cDNA, FLJ98272.
LF327972 - JP 2014500723-A/135475: Polycomb-Associated Non-Coding RNAs.
LF327973 - JP 2014500723-A/135476: Polycomb-Associated Non-Coding RNAs.
LF327974 - JP 2014500723-A/135477: Polycomb-Associated Non-Coding RNAs.
AK093172 - Homo sapiens cDNA FLJ35853 fis, clone TESTI2007078, highly similar to MEMBRANE COMPONENT, CHROMOSOME 17, SURFACE MARKER 2.
LF327975 - JP 2014500723-A/135478: Polycomb-Associated Non-Coding RNAs.
BC012847 - Homo sapiens neighbor of BRCA1 gene 1, mRNA (cDNA clone IMAGE:3858519), with apparent retained intron.
JD313136 - Sequence 294160 from Patent EP1572962.
JD239404 - Sequence 220428 from Patent EP1572962.
JD245320 - Sequence 226344 from Patent EP1572962.
JD235085 - Sequence 216109 from Patent EP1572962.
LF327977 - JP 2014500723-A/135480: Polycomb-Associated Non-Coding RNAs.
JD318668 - Sequence 299692 from Patent EP1572962.
JD208198 - Sequence 189222 from Patent EP1572962.
JD347633 - Sequence 328657 from Patent EP1572962.
JD272402 - Sequence 253426 from Patent EP1572962.
LF327978 - JP 2014500723-A/135481: Polycomb-Associated Non-Coding RNAs.
JD427325 - Sequence 408349 from Patent EP1572962.
JD290673 - Sequence 271697 from Patent EP1572962.
LF327979 - JP 2014500723-A/135482: Polycomb-Associated Non-Coding RNAs.
MA449570 - JP 2018138019-A/21496: Polycomb-Associated Non-Coding RNAs.
MA563544 - JP 2018138019-A/135470: Polycomb-Associated Non-Coding RNAs.
MA563549 - JP 2018138019-A/135475: Polycomb-Associated Non-Coding RNAs.
MA563550 - JP 2018138019-A/135476: Polycomb-Associated Non-Coding RNAs.
MA563551 - JP 2018138019-A/135477: Polycomb-Associated Non-Coding RNAs.
MA563552 - JP 2018138019-A/135478: Polycomb-Associated Non-Coding RNAs.
MA563554 - JP 2018138019-A/135480: Polycomb-Associated Non-Coding RNAs.
MA563555 - JP 2018138019-A/135481: Polycomb-Associated Non-Coding RNAs.
MA563556 - JP 2018138019-A/135482: Polycomb-Associated Non-Coding RNAs.
MA444933 - JP 2018138019-A/16859: Polycomb-Associated Non-Coding RNAs.
MA444934 - JP 2018138019-A/16860: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: 1A13B, ENST00000590996.1, ENST00000590996.2, ENST00000590996.3, ENST00000590996.4, ENST00000590996.5, KIAA0049, M17S2, MIG19, NBR1_HUMAN, NM_005899, Q13173, Q14596, Q15026, Q5J7Q8, Q96GB6, Q9NRF7, uc326vuk.1, uc326vuk.2
UCSC ID: ENST00000590996.6_6
RefSeq Accession: NM_005899.5
Protein: Q14596 (aka NBR1_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.