Human Gene SCGB3A1 (uc003mly.3)
  Description: Homo sapiens secretoglobin, family 3A, member 1 (SCGB3A1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr5:180,017,105-180,018,487 Size: 1,383 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr5:180,017,231-180,018,462 Size: 1,232 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:180,017,105-180,018,487)mRNA (may differ from genome)Protein (104 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SG3A1_HUMAN
DESCRIPTION: RecName: Full=Secretoglobin family 3A member 1; AltName: Full=Cytokine HIN-1; AltName: Full=High in normal 1; AltName: Full=Pneumo secretory protein 2; Short=PnSP-2; AltName: Full=Uteroglobin-related protein 2; Flags: Precursor;
FUNCTION: Potential growth inhibitory cytokine.
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Highly expressed in breast tissues. Absent in breast cancer cell lines.
SIMILARITY: Belongs to the secretoglobin family. UGRP subfamily.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SCGB3A1
CDC HuGE Published Literature: SCGB3A1

-  MalaCards Disease Associations
  MalaCards Gene Search: SCGB3A1
Diseases sorted by gene-association score: breast cancer (2)

-  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: 241.21 RPKM in Minor Salivary Gland
Total median expression: 372.58 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 -6.8025-0.272 Picture PostScript Text
3' UTR -39.70126-0.315 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
  ModBase Predicted Comparative 3D Structure on Q96QR1
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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 Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005125 cytokine activity

Biological Process:
GO:0010469 regulation of receptor activity
GO:0030308 negative regulation of cell growth
GO:0042127 regulation of cell proliferation
GO:1901741 positive regulation of myoblast fusion

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BC029176 - Homo sapiens secretoglobin, family 3A, member 1, mRNA (cDNA clone MGC:34758 IMAGE:5180304), complete cds.
AF086152 - Homo sapiens full length insert cDNA clone ZB52D10.
BC072673 - Homo sapiens secretoglobin, family 3A, member 1, mRNA (cDNA clone MGC:87867 IMAGE:5753142), complete cds.
AY359064 - Homo sapiens clone DNA64884 SCGB3A1 (UNQ629) mRNA, complete cds.
AF436839 - Homo sapiens pneumo secretory protein 2 mRNA, complete cds.
AY040564 - Homo sapiens HIN-1 putative cytokine mRNA, complete cds.
AF313458 - Homo sapiens UGRP2 mRNA, complete cds.
KJ895180 - Synthetic construct Homo sapiens clone ccsbBroadEn_04574 SCGB3A1 gene, encodes complete protein.
AB590701 - Synthetic construct DNA, clone: pFN21AE1603, Homo sapiens SCGB3A1 gene for secretoglobin, family 3A, member 1, without stop codon, in Flexi system.

-  Other Names for This Gene
  Alternate Gene Symbols: HIN1, NM_052863, NP_443095, PNSP2, Q96PL0, Q96QR1, SG3A1_HUMAN, UGRP2, UNQ629/PRO1245
UCSC ID: uc003mly.3
RefSeq Accession: NM_052863
Protein: Q96QR1 (aka SG3A1_HUMAN)
CCDS: CCDS4456.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_052863.2
exon count: 3CDS single in 3' UTR: no RNA size: 517
ORF size: 315CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 821.00frame shift in genome: no % Coverage: 90.14
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.