Human Gene JAGN1 (uc003btt.4) Description and Page Index
  Description: Homo sapiens jagunal homolog 1 (Drosophila) (JAGN1), mRNA.
RefSeq Summary (NM_032492): The protein encoded by this gene is a transmembrane protein. It functions in the early secretory pathway and is necessary for neutrophil differentiation and survival. Mutations in this gene result in severe congenital neutropenia. [provided by RefSeq, Oct 2014].
Transcript (Including UTRs)
   Position: hg19 chr3:9,932,271-9,936,031 Size: 3,761 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr3:9,932,407-9,935,061 Size: 2,655 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr3:9,932,271-9,936,031)mRNA (may differ from genome)Protein (183 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Protein jagunal homolog 1;
FUNCTION: May be required for endoplasmic reticulum organization (By similarity).
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein (By similarity).
SIMILARITY: Belongs to the jagunal family.

-  MalaCards Disease Associations
  MalaCards Gene Search: JAGN1
Diseases sorted by gene-association score: neutropenia, severe congenital, 6, autosomal recessive* (1680), severe congenital neutropenia* (301), neutropenia (28), t cell deficiency (4), omenn syndrome (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 35.08 RPKM in Adrenal Gland
Total median expression: 780.26 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -53.70136-0.395 Picture PostScript Text
3' UTR -282.11970-0.291 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
IPR009787 - DUF1352

Pfam Domains:
PF07086 - Jagunal, ER re-organisation during oogenesis

ModBase Predicted Comparative 3D Structure on Q8N5M9
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 orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  Protein SequenceProtein SequenceProtein Sequence 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0002376 immune system process
GO:0002446 neutrophil mediated immunity
GO:0006887 exocytosis
GO:0007029 endoplasmic reticulum organization
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0030223 neutrophil differentiation
GO:0038158 granulocyte colony-stimulating factor signaling pathway
GO:0050832 defense response to fungus
GO:0061179 negative regulation of insulin secretion involved in cellular response to glucose stimulus
GO:1904577 cellular response to tunicamycin
GO:1990266 neutrophil migration

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane

-  Descriptions from all associated GenBank mRNAs
  LF384165 - JP 2014500723-A/191668: Polycomb-Associated Non-Coding RNAs.
AK074760 - Homo sapiens cDNA FLJ90279 fis, clone NT2RP1000448.
AK225756 - Homo sapiens mRNA for jagunal homolog 1 variant, clone: FCC135D03.
BC032101 - Homo sapiens jagunal homolog 1 (Drosophila), mRNA (cDNA clone MGC:20680 IMAGE:4554225), complete cds.
LF365122 - JP 2014500723-A/172625: Polycomb-Associated Non-Coding RNAs.
AK027508 - Homo sapiens cDNA FLJ14602 fis, clone NT2RP1000191.
AF212230 - Homo sapiens GL009 mRNA, complete cds.
DQ892281 - Synthetic construct clone IMAGE:100004911; FLH184826.01X; RZPDo839C04146D jagunal homolog 1 (Drosophila) (JAGN1) gene, encodes complete protein.
DQ895481 - Synthetic construct Homo sapiens clone IMAGE:100009941; FLH184822.01L; RZPDo839C04145D jagunal homolog 1 (Drosophila) (JAGN1) gene, encodes complete protein.
CU689272 - Synthetic construct Homo sapiens gateway clone IMAGE:100021855 5' read JAGN1 mRNA.
KJ899803 - Synthetic construct Homo sapiens clone ccsbBroadEn_09197 JAGN1 gene, encodes complete protein.
LF365123 - JP 2014500723-A/172626: Polycomb-Associated Non-Coding RNAs.
BC008507 - Homo sapiens jagunal homolog 1 (Drosophila), mRNA (cDNA clone IMAGE:3461248), with apparent retained intron.
LF365124 - JP 2014500723-A/172627: Polycomb-Associated Non-Coding RNAs.
JD157696 - Sequence 138720 from Patent EP1572962.
LF365125 - JP 2014500723-A/172628: Polycomb-Associated Non-Coding RNAs.
JD257292 - Sequence 238316 from Patent EP1572962.
JD506496 - Sequence 487520 from Patent EP1572962.
JD464535 - Sequence 445559 from Patent EP1572962.
JD427595 - Sequence 408619 from Patent EP1572962.
MA619742 - JP 2018138019-A/191668: Polycomb-Associated Non-Coding RNAs.
MA600699 - JP 2018138019-A/172625: Polycomb-Associated Non-Coding RNAs.
MA600700 - JP 2018138019-A/172626: Polycomb-Associated Non-Coding RNAs.
MA600701 - JP 2018138019-A/172627: Polycomb-Associated Non-Coding RNAs.
MA600702 - JP 2018138019-A/172628: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: JAGN1_HUMAN, NM_032492, NP_115881, Q8N5M9, Q8NCF6, Q96SW1
UCSC ID: uc003btt.4
RefSeq Accession: NM_032492
Protein: Q8N5M9 (aka JAGN1_HUMAN)
CCDS: CCDS2588.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_032492.3
exon count: 2CDS single in 3' UTR: no RNA size: 1660
ORF size: 552CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1304.00frame shift in genome: no % Coverage: 99.88
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.