Human Gene NPM1 (ENST00000296930.10_4) from GENCODE V47lift37
  Description: nucleophosmin 1, transcript variant 1 (from RefSeq NM_002520.7)
Gencode Transcript: ENST00000296930.10_4
Gencode Gene: ENSG00000181163.14_9
Transcript (Including UTRs)
   Position: hg19 chr5:170,814,853-170,837,904 Size: 23,052 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr5:170,814,953-170,837,569 Size: 22,617 Coding Exon Count: 11 

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Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:170,814,853-170,837,904)mRNA (may differ from genome)Protein (294 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NPM_HUMAN
DESCRIPTION: RecName: Full=Nucleophosmin; Short=NPM; AltName: Full=Nucleolar phosphoprotein B23; AltName: Full=Nucleolar protein NO38; AltName: Full=Numatrin;
FUNCTION: Involved in diverse cellular processes such as ribosome biogenesis, centrosome duplication, protein chaperoning, histone assembly, cell proliferation, and regulation of tumor suppressors p53/TP53 and ARF. Binds ribosome presumably to drive ribosome nuclear export. Associated with nucleolar ribonucleoprotein structures and bind single-stranded nucleic acids. Acts as a chaperonin for the core histones H3, H2B and H4. Stimulates APEX1 endonuclease activity on apurinic/apyrimidinic (AP) double- stranded DNA but inhibits APEX1 endonuclease activity on AP single-stranded RNA. May exert a control of APEX1 endonuclease activity within nucleoli devoted to repair AP on rDNA and the removal of oxidized rRNA molecules. In concert with BRCA2, regulates centrosome duplication. Regulates centriole duplication: phosphorylation by PLK2 is able to trigger centriole replication.
SUBUNIT: Decamer formed by two pentameric rings associated in a head-to-head fashion. Disulfide-linked dimers under certain conditions. The SWAP complex consists of NPM1, NCL, PARP1 and SWAP70 (By similarity). Interacts with NSUN2 and SENP3. Interacts with hepatitis delta virus S-HDAg. Interacts with HTLV1 Rex protein (via N-terminal nuclear localization signal). Interacts with the methylated form of RPS10. Interacts (via N-terminal domain) with APEX1; the interaction is RNA-dependent and decreases in hydrogen peroxide-damaged cells. Interacts with isoform 1 of NEK2. Interacts with ROCK2 and BRCA2. Interacts with RPGR. Interacts with CENPW.
INTERACTION: Q98147:- (xeno); NbExp=2; IntAct=EBI-78579, EBI-626601; Q00987:MDM2; NbExp=3; IntAct=EBI-78579, EBI-389668; P04637:TP53; NbExp=3; IntAct=EBI-354150, EBI-366083;
SUBCELLULAR LOCATION: Nucleus, nucleolus. Nucleus, nucleoplasm. Cytoplasm, cytoskeleton, centrosome. Note=Generally nucleolar, but is translocated to the nucleoplasm in case of serum starvation or treatment with anticancer drugs. Has been found in the cytoplasm in patients with primary acute myelogenous leukemia (AML), but not with secondary AML. Can shuttle between cytoplasm and nucleus. Co- localizes with the methylated form of RPS10 in the granular component (GC) region of the nucleolus. Colocalized with nucleolin and APEX1 in nucleoli. Isoform 1 of NEK2 is required for its localization to the centrosome during mitosis.
PTM: Acetylated at C-terminal lysine residues, thereby increasing affinity to histones.
PTM: ADP-ribosylated.
PTM: Phosphorylated at Ser-4 by PLK1 and PLK2. Phosphorylation at Ser-4 by PLK2 in S phase is required for centriole duplication and is sufficient to trigger centriole replication. Phosphorylation at Ser-4 by PLK1 takes place during mitosis. Phosphorylated by CDK2 at Ser-125 and Thr-199. Phosphorylation at Thr-199 may trigger initiation of centrosome duplication. Phosphorylated by CDK1 at Thr-199, Thr-219, Thr-234 and Thr-237 during cell mitosis. When these four sites are phosphorated, RNA-binding activity seem to be abolished. May be phosphorylated at Ser-70 by NEK2. The Thr-199 phosphorylated form has higher affinity for ROCK2. CDK6 triggers Thr-199 phosphorylation when complexed to Kaposi's sarcoma herpesvirus (KSHV) V-cyclin, leading to viral reactivation by reducing viral LANA levels.
PTM: Sumoylated by ARF.
DISEASE: Note=A chromosomal aberration involving NPM1 is found in a form of non-Hodgkin lymphoma. Translocation t(2;5)(p23;q35) with ALK. The resulting chimeric NPM1-ALK protein homodimerize and the kinase becomes constitutively activated.
DISEASE: Note=A chromosomal aberration involving NPM1 is found in a form of acute promyelocytic leukemia. Translocation t(5;17)(q32;q11) with RARA.
DISEASE: Note=A chromosomal aberration involving NPM1 is a cause of myelodysplastic syndrome (MDS). Translocation t(3;5)(q25.1;q34) with MLF1.
DISEASE: Note=Defects in NPM1 are associated with acute myelogenous leukemia (AML). Mutations in exon 12 affecting the C- terminus of the protein are associated with an aberrant cytoplasmic location.
SIMILARITY: Belongs to the nucleoplasmin family.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/NPM1.html";

-  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: NPM1
Diseases sorted by gene-association score: leukemia, acute myeloid* (416), lymphomatoid papulosis* (377), acute myeloblastic leukemia with maturation* (350), acute myeloblastic leukemia without maturation* (350), primary cutaneous anaplastic large cell lymphoma* (350), acute myeloid leukemia with npm1 somatic mutations* (350), acute myeloid leukemia, flt3-related* (163), leukemia, acute promyelocytic, somatic* (153), npm1-related acute myeloid leukemia* (100), leukemia (24), anaplastic large cell lymphoma (23), reticulosarcoma (19), hodgkin lymphoma (18), aleukemic leukemia cutis (15), myelodysplastic syndrome (15), alk-positive anaplastic large cell lymphoma (14), cytogenetically normal acute myeloid leukemia (14), lymphatic system cancer (13), myeloid sarcoma (10), lymphoma (10), shwachman-diamond syndrome (9), fibrosclerosis of breast (7), myeloid leukemia (7), inflammatory myofibroblastic tumor (6), non-proliferative fibrocystic change of the breast (6), lymphoma, non-hodgkin (6), hematologic cancer (6), blastic plasmacytoid dendritic cell (6), multiple enchondromatosis, maffucci type (3), fanconi anemia, complementation group a (1)
* = Manually curated disease association

-  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: 334.92 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 3957.26 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 -17.40100-0.174 Picture PostScript Text
3' UTR -69.90335-0.209 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
IPR004301 - Nucleoplasmin
IPR024057 - Nucleoplasmin_core

Pfam Domains:
PF03066 - Nucleoplasmin/nucleophosmin domain
PF16276 - Nucleophosmin C-terminal domain

SCOP Domains:
48371 - ARM repeat
47819 - HRDC-like
69203 - Nucleoplasmin-like core domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2LLH - NMR MuPIT 2P1B - X-ray MuPIT 2VXD - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P06748
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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 Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001047 core promoter binding
GO:0001105 RNA polymerase II transcription coactivator activity
GO:0003676 nucleic acid binding
GO:0003713 transcription coactivator activity
GO:0003723 RNA binding
GO:0004860 protein kinase inhibitor activity
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0019901 protein kinase binding
GO:0030957 Tat protein binding
GO:0033613 activating transcription factor binding
GO:0042393 histone binding
GO:0042803 protein homodimerization activity
GO:0043023 ribosomal large subunit binding
GO:0043024 ribosomal small subunit binding
GO:0046982 protein heterodimerization activity
GO:0051059 NF-kappaB binding
GO:0051082 unfolded protein binding

Biological Process:
GO:0006281 DNA repair
GO:0006334 nucleosome assembly
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0006886 intracellular protein transport
GO:0006913 nucleocytoplasmic transport
GO:0007098 centrosome cycle
GO:0007165 signal transduction
GO:0007569 cell aging
GO:0008104 protein localization
GO:0008284 positive regulation of cell proliferation
GO:0008285 negative regulation of cell proliferation
GO:0010826 negative regulation of centrosome duplication
GO:0016032 viral process
GO:0032071 regulation of endodeoxyribonuclease activity
GO:0034080 CENP-A containing nucleosome assembly
GO:0034644 cellular response to UV
GO:0042255 ribosome assembly
GO:0043066 negative regulation of apoptotic process
GO:0044387 negative regulation of protein kinase activity by regulation of protein phosphorylation
GO:0045727 positive regulation of translation
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0046599 regulation of centriole replication
GO:0051092 positive regulation of NF-kappaB transcription factor activity
GO:0051259 protein oligomerization
GO:0060699 regulation of endoribonuclease activity
GO:0060735 regulation of eIF2 alpha phosphorylation by dsRNA
GO:1902629 regulation of mRNA stability involved in cellular response to UV
GO:1902751 positive regulation of cell cycle G2/M phase transition

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0031616 spindle pole centrosome
GO:0032991 macromolecular complex
GO:0032993 protein-DNA complex
GO:1990904 ribonucleoprotein complex


-  Descriptions from all associated GenBank mRNAs
  AY347529 - Homo sapiens nucleophosmin mRNA, complete cds.
HM005441 - Homo sapiens clone HTL-T-128 testicular tissue protein Li 128 mRNA, complete cds.
D28343 - Homo sapiens mRNA for nucleolar phosphoprotein B23, 5'UTR region.
AK290652 - Homo sapiens cDNA FLJ76122 complete cds, highly similar to Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin) (NPM1), transcript variant 1, mRNA.
BC107754 - Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin), mRNA (cDNA clone MGC:104254 IMAGE:6736004), complete cds.
BC008495 - Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin), mRNA (cDNA clone MGC:14826 IMAGE:4276604), complete cds.
BC012566 - Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin), mRNA (cDNA clone MGC:13433 IMAGE:4097025), complete cds.
BC021668 - Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin), mRNA (cDNA clone MGC:22695 IMAGE:3930893), complete cds.
DQ303464 - Homo sapiens mutant nucleolar phosphoprotein B23 (NPM1) mRNA, complete cds.
BC016768 - Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin), mRNA (cDNA clone MGC:22724 IMAGE:4081364), complete cds.
BC016824 - Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin), mRNA (cDNA clone MGC:24544 IMAGE:4106286), complete cds.
BC016716 - Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin), mRNA (cDNA clone MGC:24404 IMAGE:4068167), complete cds.
BC021983 - Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin), mRNA (cDNA clone MGC:22736 IMAGE:4106023), complete cds.
BC014349 - Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin), mRNA (cDNA clone MGC:24185 IMAGE:3511037), complete cds.
BC009623 - Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin), mRNA (cDNA clone MGC:17308 IMAGE:3877633), complete cds.
LP947257 - Sequence 3 from Patent EP3203239.
LZ177443 - JP 2017138189-A/1: Determination method of atrial fibrillation.
M23613 - Human nucleophosmin mRNA, complete cds.
M26697 - Human nucleolar protein (B23) mRNA, complete cds.
BC002398 - Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin), mRNA (cDNA clone MGC:8463 IMAGE:2821577), complete cds.
BC050628 - Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin), mRNA (cDNA clone MGC:60104 IMAGE:5575414), complete cds.
BC020467 - Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin), mRNA (cDNA clone IMAGE:3872185).
BC071891 - Homo sapiens cDNA clone IMAGE:4579479, **** WARNING: chimeric clone ****.
M28699 - Homo sapiens nucleolar phosphoprotein B23 (NPM1) mRNA, complete cds.
AY740634 - Homo sapiens nucleophosmin (NPM1) mRNA, NPM1-A allele, complete cds.
AY740635 - Homo sapiens nucleophosmin (NPM1) mRNA, complete cds.
AY740636 - Homo sapiens nucleophosmin (NPM1) mRNA, complete cds.
AY740637 - Homo sapiens nucleophosmin (NPM1) mRNA, complete cds.
AY740638 - Homo sapiens nucleophosmin (NPM1) mRNA, complete cds.
AY740639 - Homo sapiens nucleophosmin (NPM1) mRNA, complete cds.
AY740640 - Homo sapiens nucleophosmin (NPM1) mRNA, complete cds.
LP947258 - Sequence 4 from Patent EP3203239.
LZ177444 - JP 2017138189-A/2: Determination method of atrial fibrillation.
BC063542 - Homo sapiens cDNA clone IMAGE:4525305, **** WARNING: chimeric clone ****.
CU676967 - Synthetic construct Homo sapiens gateway clone IMAGE:100016987 5' read NPM1 mRNA.
CU677717 - Synthetic construct Homo sapiens gateway clone IMAGE:100018085 5' read NPM1 mRNA.
AB042278 - Homo sapiens mRNA for nucleophosmin/B23.2, complete cds.
EF429251 - Homo sapiens truncated nucleolar phosphoprotein B23 (NPM1) mRNA, complete cds.
CU680364 - Synthetic construct Homo sapiens gateway clone IMAGE:100023350 5' read NPM1 mRNA.
CU692436 - Synthetic construct Homo sapiens gateway clone IMAGE:100018083 5' read NPM1 mRNA.
AB451361 - Homo sapiens NPM1 mRNA for nucleophosmin 1 isoform 1, partial cds, clone: FLJ08034AAAF.
AB463949 - Synthetic construct DNA, clone: pF1KB8236, Homo sapiens NPM1 gene for nucleophosmin, without stop codon, in Flexi system.
KU178236 - Homo sapiens nucleophosmin isoform 1 (NPM1) mRNA, partial cds.
KU178237 - Homo sapiens nucleophosmin isoform 2 (NPM1) mRNA, partial cds.
DQ895223 - Synthetic construct Homo sapiens clone IMAGE:100009683; FLH182507.01L; RZPDo839G12137D nucleophosmin (nucleolar phosphoprotein B23, numatrin) (NPM1) gene, encodes complete protein.
KJ905840 - Synthetic construct Homo sapiens clone ccsbBroadEn_15510 NPM1 gene, encodes complete protein.
KJ905841 - Synthetic construct Homo sapiens clone ccsbBroadEn_15511 NPM1 gene, encodes complete protein.
BT007011 - Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin) mRNA, complete cds.
DQ892032 - Synthetic construct clone IMAGE:100004662; FLH182511.01X; RZPDo839G12138D nucleophosmin (nucleolar phosphoprotein B23, numatrin) (NPM1) gene, encodes complete protein.
KJ891713 - Synthetic construct Homo sapiens clone ccsbBroadEn_01107 NPM1 gene, encodes complete protein.
KJ897260 - Synthetic construct Homo sapiens clone ccsbBroadEn_06654 NPM1 gene, encodes complete protein.
KJ897261 - Synthetic construct Homo sapiens clone ccsbBroadEn_06655 NPM1 gene, encodes complete protein.
AB451236 - Homo sapiens NPM1 mRNA for nucleophosmin 1 isoform 1, complete cds, clone: FLJ08034AAAN.
X16934 - Human hB23 gene for B23 nucleophosmin.
DQ579020 - Homo sapiens piRNA piR-47132, complete sequence.
AK000472 - Homo sapiens cDNA FLJ20465 fis, clone KAT06236.
BC003670 - Homo sapiens nucleophosmin (nucleolar phosphoprotein B23, numatrin), mRNA (cDNA clone IMAGE:3932340), partial cds.
KJ905842 - Synthetic construct Homo sapiens clone ccsbBroadEn_15512 NPM1 gene, encodes complete protein.
DL492405 - Novel nucleic acids.
DL492406 - Novel nucleic acids.
DL490887 - Novel nucleic acids.
JD437096 - Sequence 418120 from Patent EP1572962.
JD310793 - Sequence 291817 from Patent EP1572962.
M31004 - Human nuclear phosphoprotein B23 mRNA, clone hpB2.
J02590 - Human nucleolar phosphoprotein B23 mRNA, clone hpB1.
BC024716 - Homo sapiens cDNA clone IMAGE:3856933, with apparent retained intron.
JD299587 - Sequence 280611 from Patent EP1572962.
JD299586 - Sequence 280610 from Patent EP1572962.
JD233784 - Sequence 214808 from Patent EP1572962.
JD562621 - Sequence 543645 from Patent EP1572962.
JD562620 - Sequence 543644 from Patent EP1572962.
JD449611 - Sequence 430635 from Patent EP1572962.
JD354959 - Sequence 335983 from Patent EP1572962.
JD336921 - Sequence 317945 from Patent EP1572962.
JD492400 - Sequence 473424 from Patent EP1572962.

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

Protein P06748 (Reactome details) participates in the following event(s):

R-HSA-8869568 NPM1 binds TFAP2A homodimer
R-HSA-180736 Disassembly of the Rev-importin beta-B23:Ran-GTP complex
R-HSA-180725 Rev associates with B23
R-HSA-6801675 PLK2 phosphorylates NPM1
R-HSA-180728 Association of Ran-GTP with importin-beta
R-HSA-180732 Translocation of Rev:importin-beta:B23 to the nucleus
R-HSA-606326 HJURP:CENPA complex localizes to the centromere
R-HSA-8869542 TFPA2A homodimer and NPM1 bind the HSPD1 gene promoter
R-HSA-8869543 TFPA2A homodimer and NPM1 bind the NOP2 gene promoter
R-HSA-8869549 TFPA2A homodimer and NPM1 bind the MYBL2 gene promoter
R-HSA-180710 Rev:importin beta:B23 recruited to the nuclear pore
R-HSA-8869496 TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation
R-HSA-180746 Nuclear import of Rev protein
R-HSA-6804115 TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain
R-HSA-606279 Deposition of new CENPA-containing nucleosomes at the centromere
R-HSA-8864260 Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors
R-HSA-177243 Interactions of Rev with host cellular proteins
R-HSA-6791312 TP53 Regulates Transcription of Cell Cycle Genes
R-HSA-774815 Nucleosome assembly
R-HSA-212436 Generic Transcription Pathway
R-HSA-162909 Host Interactions of HIV factors
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-73886 Chromosome Maintenance
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-162906 HIV Infection
R-HSA-1640170 Cell Cycle
R-HSA-74160 Gene expression (Transcription)
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: A8K3N7, B5BU00, D3DQL6, ENST00000296930.1, ENST00000296930.2, ENST00000296930.3, ENST00000296930.4, ENST00000296930.5, ENST00000296930.6, ENST00000296930.7, ENST00000296930.8, ENST00000296930.9, NM_002520, NPM, NPM_HUMAN, P06748, P08693, Q12826, Q13440, Q13441, Q14115, Q5EU94, Q5EU95, Q5EU96, Q5EU97, Q5EU98, Q5EU99, Q6V962, Q8WTW5, Q96AT6, Q96DC4, Q96EA5, Q9BYG9, Q9UDJ7, uc317lxp.1, uc317lxp.2
UCSC ID: ENST00000296930.10_4
RefSeq Accession: NM_002520.7
Protein: P06748 (aka NPM_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.