SCGB1D4 Gene (Protein Coding)

Secretoglobin Family 1D Member 4

GC11M062297
GIFtS:
30

Aliases for SCGB1D4 Gene

Aliases for SCGB1D4 Gene

  • Secretoglobin Family 1D Member 4 2 3 4 5
  • IFN-Gamma-Inducible Secretoglobin 3 4
  • IIS 3 4
  • IFN-Gamma Inducible SCGB (IIS) 3

External Ids for SCGB1D4 Gene

Previous GeneCards Identifiers for SCGB1D4 Gene

  • GC00U916714
  • GC11M061820
  • GC11M062063
  • GC11M058392

Summaries for SCGB1D4 Gene

GeneCards Summary for SCGB1D4 Gene

SCGB1D4 (Secretoglobin Family 1D Member 4) is a Protein Coding gene. Diseases associated with SCGB1D4 include Landau-Kleffner Syndrome. An important paralog of this gene is SCGB1D2.

UniProtKB/Swiss-Prot Summary for SCGB1D4 Gene

  • Seems to be involved in the regulation of chemotactic cell migration and invasion.

Additional gene information for SCGB1D4 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SCGB1D4 Gene

Genomics for SCGB1D4 Gene

GeneHancer (GH) Regulatory Elements for SCGB1D4 Gene

Promoters and enhancers for SCGB1D4 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH11J062299 Promoter 0.3 EPDnew 750.6 0.0 -31 0.1 SCGB1D4 lnc-SCGB1D4-4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCGB1D4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCGB1D4 gene promoter:
  • Evi-1

Genomic Locations for SCGB1D4 Gene

Genomic Locations for SCGB1D4 Gene
chr11:62,296,277-62,299,064
(GRCh38/hg38)
Size:
2,788 bases
Orientation:
Minus strand
chr11:62,063,754-62,066,536
(GRCh37/hg19)
Size:
2,783 bases
Orientation:
Minus strand

Genomic View for SCGB1D4 Gene

Genes around SCGB1D4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCGB1D4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCGB1D4 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SCGB1D4 Gene

Proteins for SCGB1D4 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for SCGB1D4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6XE38-SG1D4_HUMAN
    Recommended name:
    Secretoglobin family 1D member 4
    Protein Accession:
    Q6XE38
    Secondary Accessions:
    • A1L4Q8

    Protein attributes for SCGB1D4 Gene

    Size:
    83 amino acids
    Molecular mass:
    9201 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SCGB1D4 Gene

Protein Expression for SCGB1D4 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SCGB1D4 Gene

No Post-translational modifications

Other Protein References for SCGB1D4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SCGB1D4 Gene

Domains & Families for SCGB1D4 Gene

Gene Families for SCGB1D4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted secreted proteins

Protein Domains for SCGB1D4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SCGB1D4 Gene

GenScript: Design optimal peptide antigens:
  • IFN-gamma-inducible secretoglobin (SG1D4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6XE38

UniProtKB/Swiss-Prot:

SG1D4_HUMAN :
  • Belongs to the secretoglobin family. Lipophilin subfamily.
Family:
  • Belongs to the secretoglobin family. Lipophilin subfamily.
genes like me logo Genes that share domains with SCGB1D4: view

Function for SCGB1D4 Gene

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  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for SCGB1D4 Gene

UniProtKB/Swiss-Prot Function:
Seems to be involved in the regulation of chemotactic cell migration and invasion.
UniProtKB/Swiss-Prot Induction:
By IFNG/IFN-gamma.

Phenotypes From GWAS Catalog for SCGB1D4 Gene

Phenotypes for SCGB1D4 Gene

GenomeRNAi human phenotypes for SCGB1D4:
genes like me logo Genes that share phenotypes with SCGB1D4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCGB1D4

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SCGB1D4 Gene

Localization for SCGB1D4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCGB1D4 Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCGB1D4 gene
Compartment Confidence
extracellular 5
plasma membrane 1
cytoskeleton 1
mitochondrion 1
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for SCGB1D4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IBA 21873635
genes like me logo Genes that share ontologies with SCGB1D4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SCGB1D4 Gene

Pathways & Interactions for SCGB1D4 Gene

PathCards logo

SuperPathways for SCGB1D4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCGB1D4 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for SCGB1D4 Gene

Drugs & Compounds for SCGB1D4 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for SCGB1D4 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for SCGB1D4 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(3) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCGB1D4

Alternative Splicing Database (ASD) splice patterns (SP) for SCGB1D4 Gene

No ASD Table

Relevant External Links for SCGB1D4 Gene

GeneLoc Exon Structure for
SCGB1D4
ECgene alternative splicing isoforms for
SCGB1D4

Expression for SCGB1D4 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCGB1D4 Gene

mRNA expression in normal human tissues for SCGB1D4 Gene
mRNA expression by GTEx for SCGB1D4 GenemRNA expression by BioGPS for SCGB1D4 Gene

mRNA differential expression in normal tissues according to GTEx for SCGB1D4 Gene

This gene is overexpressed in Cervix - Endocervix (x22.6), Fallopian Tube (x17.0), and Uterus (x9.9).

Protein differential expression in normal tissues from HIPED for SCGB1D4 Gene

This gene is overexpressed in Platelet (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SCGB1D4 Gene



Protein tissue co-expression partners for SCGB1D4 Gene

NURSA nuclear receptor signaling pathways regulating expression of SCGB1D4 Gene:

SCGB1D4

SOURCE GeneReport for Unigene cluster for SCGB1D4 Gene:

Hs.473247

mRNA Expression by UniProt/SwissProt for SCGB1D4 Gene:

Q6XE38-SG1D4_HUMAN
Tissue specificity: Expressed in all tissues; the highest level of expression is detectable in lymph nodes, tonsil, cultured lymphoblasts and ovary.

Evidence on tissue expression from TISSUES for SCGB1D4 Gene

  • Nervous system(2.2)
genes like me logo Genes that share expression patterns with SCGB1D4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCGB1D4 Gene

Orthologs for SCGB1D4 Gene

This gene was present in the common ancestor of mammals.

Orthologs for SCGB1D4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia SCGB1D4 33 32
  • 96.2 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia SCGB1D 33
  • 42 (a)
 OneToMany
dog
(Canis familiaris)
 Mammalia -- 33
  • 42 (a)
 ManyToMany
-- 33
  • 41 (a)
 ManyToMany
Species where no ortholog for SCGB1D4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for SCGB1D4 Gene

ENSEMBL:
Gene Tree for SCGB1D4 (if available)
TreeFam:
Gene Tree for SCGB1D4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SCGB1D4: view image

Paralogs for SCGB1D4 Gene

Paralogs for SCGB1D4 Gene

(2) SIMAP similar genes for SCGB1D4 Gene using alignment to 1 proteins:

  • SG1D4_HUMAN

Pseudogenes.org Pseudogenes for SCGB1D4 Gene

genes like me logo Genes that share paralogs with SCGB1D4: view

Variants for SCGB1D4 Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for SCGB1D4 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000450885 -- 62,299,530(-) AAA/AA upstream_transcript_variant
rs1000592393 -- 62,297,411(-) T/G intron_variant
rs1001171455 -- 62,297,826(-) A/G intron_variant
rs1001271993 -- 62,299,122(-) G/C upstream_transcript_variant
rs1002096912 -- 62,297,754(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SCGB1D4 Gene

Variant ID Type Subtype PubMed ID
esv33305 CNV loss 17666407

Variation tolerance for SCGB1D4 Gene

Residual Variation Intolerance Score: 59.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.59; 12.64% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCGB1D4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCGB1D4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCGB1D4 Gene

Disorders for SCGB1D4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SCGB1D4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
landau-kleffner syndrome
  • acquired epileptic aphasia
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SCGB1D4

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SCGB1D4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCGB1D4 Gene

Publications for SCGB1D4 Gene

  1. IFN-gamma stimulates the expression of a novel secretoglobin that regulates chemotactic cell migration and invasion. (PMID: 15034037) Choi MS … Mukherjee AB (Journal of immunology (Baltimore, Md. : 1950) 2004) 2 3 4 23 56
  2. Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PMID: 15340161) Zhang Z … Henzel WJ (Protein science : a publication of the Protein Society 2004) 2 3 4 56
  3. Update of the human secretoglobin (SCGB) gene superfamily and an example of 'evolutionary bloom' of androgen-binding protein genes within the mouse Scgb gene superfamily. (PMID: 22155607) Jackson BC … Vasiliou V (Human genomics 2011) 2 3 56
  4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4 56
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 56

ExternalLinks

View latest publications for SCGB1D4 gene in Mastermind

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