Human Gene IGSF3 (uc031pnr.1) Description and Page Index
  Description: Homo sapiens immunoglobulin superfamily, member 3 (IGSF3), transcript variant 1, mRNA.
RefSeq Summary (NM_001542): The protein encoded by this gene is an immunoglobulin-like membrane protein containing several V-type Ig-like domains. A mutation in this gene has been associated with bilateral nasolacrimal duct obstruction (LCDD). [provided by RefSeq, Jun 2016].
Transcript (Including UTRs)
   Position: hg19 chr1:117,117,020-117,209,578 Size: 92,559 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr1:117,119,934-117,208,948 Size: 89,015 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:117,117,020-117,209,578)mRNA (may differ from genome)Protein (1214 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
OMIMPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: SubName: Full=Immunoglobulin superfamily member 3;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  MalaCards Disease Associations
  MalaCards Gene Search: IGSF3
Diseases sorted by gene-association score: lacrimal duct defect* (1319)
* = 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
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 15.51 RPKM in Esophagus - Mucosa
Total median expression: 150.29 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 -227.70630-0.361 Picture PostScript Text
3' UTR -959.342914-0.329 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
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003599 - Ig_sub
IPR013106 - Ig_V-set

Pfam Domains:
PF07686 - Immunoglobulin V-set domain

SCOP Domains:
48726 - Immunoglobulin

ModBase Predicted Comparative 3D Structure on A6NJZ6
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 Details     
Gene Sorter     

-  Descriptions from all associated GenBank mRNAs
  AB007935 - Homo sapiens KIAA0466 mRNA for KIAA0466 protein.
BC130279 - Homo sapiens immunoglobulin superfamily, member 3, mRNA (cDNA clone MGC:163151 IMAGE:40146310), complete cds.
BC144132 - Homo sapiens immunoglobulin superfamily, member 3, mRNA (cDNA clone MGC:177669 IMAGE:9052652), complete cds.
BC110651 - Homo sapiens immunoglobulin superfamily, member 3, mRNA (cDNA clone MGC:117164 IMAGE:6166346), complete cds.
AF031174 - Homo sapiens Ig-like membrane protein (IGSF3) mRNA, complete cds.
AB383889 - Synthetic construct DNA, clone: pF1KSDA0466, Homo sapiens IGSF3 gene for immunoglobulin superfamily, member 3 isoform 2, complete cds, without stop codon, in Flexi system.
EU832096 - Synthetic construct Homo sapiens clone HAIB:100067125; DKFZo008A0925 immunoglobulin superfamily, member 3 protein (IGSF3) gene, encodes complete protein.
EU832189 - Synthetic construct Homo sapiens clone HAIB:100067218; DKFZo004A0926 immunoglobulin superfamily, member 3 protein (IGSF3) gene, encodes complete protein.
BC071861 - Homo sapiens cDNA clone IMAGE:4551895, partial cds.
JD436008 - Sequence 417032 from Patent EP1572962.
AK097809 - Homo sapiens cDNA FLJ40490 fis, clone TESTI2044276, highly similar to Homo sapiens Ig-like membrane protein (IGSF3) mRNA.
JD298637 - Sequence 279661 from Patent EP1572962.
JD511136 - Sequence 492160 from Patent EP1572962.
JD175183 - Sequence 156207 from Patent EP1572962.
JD340145 - Sequence 321169 from Patent EP1572962.
JD382013 - Sequence 363037 from Patent EP1572962.
JD474384 - Sequence 455408 from Patent EP1572962.
LF206261 - JP 2014500723-A/13764: Polycomb-Associated Non-Coding RNAs.
LF352769 - JP 2014500723-A/160272: Polycomb-Associated Non-Coding RNAs.
MA588346 - JP 2018138019-A/160272: Polycomb-Associated Non-Coding RNAs.
MA441838 - JP 2018138019-A/13764: Polycomb-Associated Non-Coding RNAs.
JD158160 - Sequence 139184 from Patent EP1572962.
DL492048 - Novel nucleic acids.
JD269769 - Sequence 250793 from Patent EP1572962.
DL490597 - Novel nucleic acids.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NJZ6, A6NJZ6_HUMAN, NM_001542, NP_001533, uc001egq.1
UCSC ID: uc031pnr.1
RefSeq Accession: NM_001542
Protein: A6NJZ6 CCDS: CCDS30813.1, CCDS30814.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001542.3
exon count: 11CDS single in 3' UTR: no RNA size: 7206
ORF size: 3645CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 7196.50frame shift in genome: no % Coverage: 99.76
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
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.