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Aliases for KHDC4 Gene

Aliases for KHDC4 Gene

  • KH Domain Containing 4, Pre-MRNA Splicing Factor 2 3 5
  • KIAA0907 2 3 4
  • Brings Lots Of Money 7 3 4
  • SNORA80EHG 3 4
  • BLOM7 3 4
  • Protein BLOM7 3

External Ids for KHDC4 Gene

Previous HGNC Symbols for KHDC4 Gene

  • KIAA0907

Summaries for KHDC4 Gene

GeneCards Summary for KHDC4 Gene

KHDC4 (KH Domain Containing 4, Pre-MRNA Splicing Factor) is a Protein Coding gene.

UniProtKB/Swiss-Prot for KHDC4 Gene

  • RNA-binding protein involved in pre-mRNA splicing (PubMed:19641227). Interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome (PubMed:19641227). Involved in regulating splice site selection (PubMed:19641227). Binds preferentially RNA with A/C rich sequences and poly-C stretches (PubMed:23144703).

Additional gene information for KHDC4 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KHDC4 Gene

Genomics for KHDC4 Gene

GeneHancer (GH) Regulatory Elements for KHDC4 Gene

Promoters and enhancers for KHDC4 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
GH01I155930 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 581.7 +1.6 1551 5.4 HDGF PKNOX1 CLOCK FOXA2 SMAD1 MLX ARNT ARID4B SIN3A DMAP1 KHDC4 GON4L RRNAD1 ISG20L2 CCT3 MSTO2P MSTO1 LOC101928120 CLK2 ENSG00000271267
GH01I155242 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 273.8 +690.2 690200 2.9 FEZF1 YBX1 IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 SP3 GBA KHDC4 GON4L CLK2 ENSG00000271267 MSTO1 MSTO2P RUSC1-AS1 THBS3 SHC1
GH01I155222 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 137 +708.7 708711 5.9 ZFP64 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC ZC3H11A MEF2D GBAP1 KHDC4 MSTO1 ENSG00000271267 GON4L MSTO2P CLK2 RUSC1-AS1 LOC101928120 THBS3
GH01I154998 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 68.7 +930.0 929991 11.3 CLOCK MLX YBX1 DMAP1 YY1 ZNF213 E2F8 ZNF416 ZNF143 SP3 ZBTB7B GON4L CLK2 UBAP2L KHDC4 ENSG00000271267 RUSC1-AS1 MSTO1 THBS3 MSTO2P
GH01I156111 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 61.3 -186.9 -186947 19.4 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 LMNA GON4L CLK2 RRNAD1 KHDC4 LOC246784 MSTO1 MSTO2P PRCC ISG20L2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around KHDC4 on UCSC Golden Path with GeneCards custom track

Genomic Locations for KHDC4 Gene

Genomic Locations for KHDC4 Gene
chr1:155,913,043-155,934,442
(GRCh38/hg38)
Size:
21,400 bases
Orientation:
Minus strand
chr1:155,882,834-155,904,191
(GRCh37/hg19)

Genomic View for KHDC4 Gene

Genes around KHDC4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KHDC4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KHDC4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KHDC4 Gene

Proteins for KHDC4 Gene

  • Protein details for KHDC4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z7F0-BLOM7_HUMAN
    Recommended name:
    Protein BLOM7
    Protein Accession:
    Q7Z7F0
    Secondary Accessions:
    • O94981
    • Q7L7Q2
    • Q7Z7E9
    • Q8TBQ0

    Protein attributes for KHDC4 Gene

    Size:
    614 amino acids
    Molecular mass:
    64845 Da
    Quaternary structure:
    • Interacts with PRPF19 (PubMed:19641227). Isoform 2: Interacts with U2AF65 (PubMed:19641227).
    SequenceCaution:
    • Sequence=BAA74930.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KHDC4 Gene

    Alternative splice isoforms for KHDC4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KHDC4 Gene

Post-translational modifications for KHDC4 Gene

No Post-translational modifications

Other Protein References for KHDC4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for KHDC4 Gene

Domains & Families for KHDC4 Gene

Gene Families for KHDC4 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for KHDC4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for KHDC4 Gene

Graphical View of Domain Structure for InterPro Entry

Q7Z7F0

UniProtKB/Swiss-Prot:

BLOM7_HUMAN :
  • The C-terminal part is necessary for the interaction with the PRP19C/Prp19 complex/NTC/Nineteen complex.
  • Belongs to the BLOM7 family.
Domain:
  • The C-terminal part is necessary for the interaction with the PRP19C/Prp19 complex/NTC/Nineteen complex.
  • The KH domains mediate RNA-binding.
Family:
  • Belongs to the BLOM7 family.
genes like me logo Genes that share domains with KHDC4: view

Function for KHDC4 Gene

Molecular function for KHDC4 Gene

UniProtKB/Swiss-Prot Function:
RNA-binding protein involved in pre-mRNA splicing (PubMed:19641227). Interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome (PubMed:19641227). Involved in regulating splice site selection (PubMed:19641227). Binds preferentially RNA with A/C rich sequences and poly-C stretches (PubMed:23144703).

Phenotypes From GWAS Catalog for KHDC4 Gene

Gene Ontology (GO) - Molecular Function for KHDC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 19641227
GO:0005515 protein binding IPI 19641227
genes like me logo Genes that share ontologies with KHDC4: view
genes like me logo Genes that share phenotypes with KHDC4: view

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for KHDC4 Gene

Localization for KHDC4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for KHDC4 Gene

Nucleus. Cytoplasm.

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 KHDC4 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for KHDC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IDA 19641227
GO:0005681 colocalizes_with spliceosomal complex IDA 19641227
GO:0005737 cytoplasm IDA,IEA 19641227
genes like me logo Genes that share ontologies with KHDC4: view

Pathways & Interactions for KHDC4 Gene

SuperPathways for KHDC4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for KHDC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006376 mRNA splice site selection IDA 19641227
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with KHDC4: view

No data available for Pathways by source and SIGNOR curated interactions for KHDC4 Gene

Drugs & Compounds for KHDC4 Gene

No Compound Related Data Available

Transcripts for KHDC4 Gene

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for KHDC4 Gene

No ASD Table

Relevant External Links for KHDC4 Gene

GeneLoc Exon Structure for
KHDC4
ECgene alternative splicing isoforms for
KHDC4

Expression for KHDC4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of KHDC4 Gene:

KHDC4

mRNA Expression by UniProt/SwissProt for KHDC4 Gene:

Q7Z7F0-BLOM7_HUMAN
Tissue specificity: Ubiquitous. Expressed at high level in skeletal muscle, kidney, heart, brain and liver.

Evidence on tissue expression from TISSUES for KHDC4 Gene

  • Lung(5)
  • Nervous system(4.6)
  • Liver(4.4)
  • Adrenal gland(4.2)
genes like me logo Genes that share expression patterns with KHDC4: view

Primer Products

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for KHDC4 Gene

Orthologs for KHDC4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for KHDC4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KIAA0907 34
  • 100 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia KIAA0907 34
  • 94 (a)
OneToOne
cow
(Bos Taurus)
Mammalia KIAA0907 33 34
  • 93.69 (n)
dog
(Canis familiaris)
Mammalia KIAA0907 33 34
  • 92.62 (n)
rat
(Rattus norvegicus)
Mammalia RGD1565775 33
  • 90.8 (n)
mouse
(Mus musculus)
Mammalia 2810403A07Rik 33 16 34
  • 90.66 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia KIAA0907 34
  • 63 (a)
OneToOne
chicken
(Gallus gallus)
Aves KIAA0907 33 34
  • 80.49 (n)
lizard
(Anolis carolinensis)
Reptilia KIAA0907 34
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kiaa0907 33
  • 67.79 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.14194 33
zebrafish
(Danio rerio)
Actinopterygii kiaa0907 33 34
  • 61.04 (n)
Dr.1618 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5853 33
Species where no ortholog for KHDC4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for KHDC4 Gene

ENSEMBL:
Gene Tree for KHDC4 (if available)
TreeFam:
Gene Tree for KHDC4 (if available)

Paralogs for KHDC4 Gene

No data available for Paralogs for KHDC4 Gene

Variants for KHDC4 Gene

Sequence variations from dbSNP and Humsavar for KHDC4 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000006697 -- 155,932,886(-) G/A/C intron_variant
rs1000124773 -- 155,935,244(-) ACA/A upstream_transcript_variant
rs1000323098 -- 155,928,816(-) G/A intron_variant
rs1000938679 -- 155,919,923(-) C/T intron_variant
rs1001187392 -- 155,933,214(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for KHDC4 Gene

Variant ID Type Subtype PubMed ID
nsv509513 CNV insertion 20534489
esv33869 CNV loss 17666407

Variation tolerance for KHDC4 Gene

Residual Variation Intolerance Score: 10.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.79; 16.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KHDC4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
KHDC4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KHDC4 Gene

Disorders for KHDC4 Gene

Additional Disease Information for KHDC4

No disorders were found for KHDC4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for KHDC4 Gene

Publications for KHDC4 Gene

  1. Inhibition of pre-mRNA splicing by a synthetic Blom7α-interacting small RNA. (PMID: 23144703) Löscher M … Grillari J (PloS one 2012) 2 3 4 58
  2. Blom7alpha is a novel heterogeneous nuclear ribonucleoprotein K homology domain protein involved in pre-mRNA splicing that interacts with SNEVPrp19-Pso4. (PMID: 19641227) Grillari J … Grillari-Voglauer R (The Journal of biological chemistry 2009) 2 3 4 58
  3. Small nucleolar RNA 42 acts as an oncogene in lung tumorigenesis. (PMID: 21986946) Mei YP … Jiang F (Oncogene 2012) 2 3 58
  4. Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10048485) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for KHDC4 Gene

Sources for KHDC4 Gene

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