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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RSPH4A Gene

protein-coding   GIFtS: 49
GCID: GC06P116941

radial spoke head 4 homolog A (Chlamydomonas)

(Previous name: radial spokehead-like 3 )
(Previous symbol: RSHL3)
 Explore 6 diseases affiliated with
RSPH4A via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for RSPH4A    

Aliases
for RSPH4A gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Radial Spoke Head 4 Homolog A (Chlamydomonas)1 2     Radial Spokehead-Like 31 2
RSHL31 2 3     Radial Spoke Head-Like Protein 32 3
CILD111 2 5     FLJ379741
RSPH6B1 2     Radial Spoke Head Protein 4 Homolog A2
DJ412I7.11     

External Ids:    HGNC: 215581   Entrez Gene: 3458952   Ensembl: ENSG000001118347   OMIM: 6126475   UniProtKB: Q5TD943   

Export aliases for RSPH4A gene to outside databases

Previous GC identifers: GC06P117045 GC06P114517


Summaries
for RSPH4A gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for RSPH4A:
This gene encodes a protein that appears to be a component the radial spoke head, as determined by homology to similar
proteins in the biflagellate alga Chlamydomonas reinhardtii and other ciliates. Radial spokes, which are regularly
spaced along cilia, sperm, and flagella axonemes, consist of a thin 'stalk' and a bulbous 'head' that form a signal
transduction scaffold between the central pair of microtubules and dynein. Mutations in this gene cause primary
ciliary dyskinesia 1, a disease arising from dysmotility of motile cilia and sperm. Alternative splicing results in
multiple transcript variants. (provided by RefSeq, Sep 2009)

UniProtKB/Swiss-Prot: RSH4A_HUMAN, Q5TD94
Function: Probable component of the axonemal radial spoke head. Radial spokes are regularly spaced along cilia, sperm
and flagella axonemes. They consist of a thin stalk which is attached to a subfiber of the outer doublet microtubule,
and a bulbous head which is attached to the stalk and appears to interact with the projections from the central pair
of microtubules

Gene Wiki entry for RSPH4A


Genomic Views
for RSPH4A gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.1  NT_025741.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RSPH4A gene promoter:
         AhR   POU3F2   Gfi-1   RORalpha2   POU2F1   POU2F1a   FOXO1a   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: RSPH4A promoter sequence
   Search SABiosciences Chromatin IP Primers for RSPH4A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RSPH4A


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6q22.1   Ensembl cytogenetic band:  6q22.1   HGNC cytogenetic band: 6q22.1

RSPH4A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RSPH4A gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P116941:  view genomic region     (about GC identifiers)

Start:
 116,937,642 bp from pter      End:
 116,954,148 bp from pter
Size:
 16,507 bases      Orientation:
 plus strand

Proteins
for RSPH4A gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: RSH4A_HUMAN, Q5TD94 (See protein sequence)
Recommended Name: Radial spoke head protein 4 homolog A  
Size: 716 amino acids; 80733 Da
Subcellular location: Cytoplasm, cytoskeleton, cilium axoneme (Probable). Note=Radial spoke (Probable)
Secondary accessions: B4DSI1 Q3KP24 Q5TD95
Alternative splicing: 3 isoforms:  Q5TD94-1   Q5TD94-2   Q5TD94-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for RSPH4A: NX_Q5TD94

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q5TD94

    • RSPH4A Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001010892.1  NP_001155136.1  

    ENSEMBL proteins: 
     ENSP00000229554   ENSP00000357569   ENSP00000357570  

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    Uscn Proteins for RSPH4A

    Gene Ontology (GO): 5/7 cellular component terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001534radial spoke ISS--
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm ----
    GO:0005856cytoskeleton IEA--


    RSPH4A for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for RSPH4A gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    RSPH4A for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR006802 Radial_spoke

    Graphical View of Domain Structure for InterPro Entry Q5TD94

    ProtoNet protein and cluster: Q5TD94

    UniProtKB/Swiss-Prot: RSH4A_HUMAN, Q5TD94
    Similarity: Belongs to the flagellar radial spoke RSP4/6 family


    Function
    for RSPH4A gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: RSH4A_HUMAN, Q5TD94
    Function: Probable component of the axonemal radial spoke head. Radial spokes are regularly spaced along cilia, sperm
    and flagella axonemes. They consist of a thin stalk which is attached to a subfiber of the outer doublet microtubule,
    and a bulbous head which is attached to the stalk and appears to interact with the projections from the central pair
    of microtubules

    miRNA
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    SwitchGear 3'UTR luciferase reporter plasmid: RSPH4A 3' UTR sequence
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    Gene Editing
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    Clone
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    In Situ Assay
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--


    RSPH4A for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for RSPH4A:
     Decreased cilium length after  


    Pathways & Interactions
    for RSPH4A gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RSPH4A

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003341cilium movement IMP19200523
    GO:0035083cilium axoneme assembly IMP19200523


    RSPH4A for ontologies           About GeneDecksing



    Drugs & Compounds
    for RSPH4A gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RSPH4A
    Search CenterWatch for drugs/clinical trials and news about RSPH4A / RSH4A 

    Transcripts
    for RSPH4A gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for RSPH4A gene (2 alternative transcripts): 
    NM_001010892.2  NM_001161664.1  

    Unigene Cluster for RSPH4A:

    Radial spoke head 4 homolog A (Chlamydomonas)
    Hs.160380  [show with all ESTs]
    Unigene Representative Sequence: NM_001010892
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000229554(uc003pxe.2) ENST00000368580 ENST00000368581(uc010kee.2)


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    2 QIAGEN miScript miRNA Assays for microRNAs that regulate RSPH4A:
    hsa-miR-875-3p hsa-miR-589*
    SwitchGear 3'UTR luciferase reporter plasmid: RSPH4A 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AK095293.1 AK299754.1 BC022879.1 BC106949.2 

    3 DOTS entries:

    DT.91788117  DT.121313988  DT.100015191 

    22 AceView cDNA sequences:

    BX643918 AI422005 BC022879 AK095293 CD108647 BI836803 CA313625 BG717128 
    BF196823 CB305529 BX280339 AW105181 CD703851 CB851663 BU686996 CA311499 
    CD697912 AI222073 AA723541 CD693265 CD702532 CD683627 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for RSPH4A    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b
    SP1:                                                
    SP2:                          -                     


    ECgene alternative splicing isoforms for RSPH4A

    Expression
    for RSPH4A gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RSPH4A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GTCCAGGTGA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    RSPH4A expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 2 LifeMap Cells 
    NameCategory
    Intermediate limb mesenchymal cells (ILM cells) (Primary Cell)Bone, Cartilage, Limb
    Posterior foregut-like cells (A scalable, suspensi...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See RSPH4A Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RSPH4A

    SOURCE GeneReport for Unigene cluster: Hs.160380
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    In Situ
    Assay Products:     
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    Orthologs
    for RSPH4A gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for RSPH4A gene from 4/19 species (see all 19)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves RSPH4A1 radial spoke head 4 homolog A (Chlamydomonas) 69.4(n)
    66.29(a)    		   422717  XM_420671.3  XP_420671.3 
    tropical clawed frog
    (Xenopus tropicalis)    		 Amphibia Str.118032 Transcribed sequence with weak similarity to protein more 79.13(n)    BX707088.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii wufj17d052 Transcribed sequence with weak similarity to protein more 76.08(n)    57072739 
    fruit fly
    (Drosophila melanogaster)    		 Insecta CG31211 CG3121 48.87(n)
    40(a)    		   37831  NM_138025.2  NP_611869.1 


    ENSEMBL Gene Tree for RSPH4A (if available)
    TreeFam Gene Tree for RSPH4A (if available) 

    Paralogs
    for RSPH4A gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RSPH4A gene
    RSPH6A2  
    2 SIMAP similar genes for RSPH4A using alignment to 1 protein entry:     RSH4A_HUMAN:
    RSHL1    RSPH6A

    RSPH4A for paralogs           About GeneDecksing



    Genomic Variants
    for RSPH4A gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/363 NCBI SNPs in RSPH4A are shown (see all 363)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 6 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1182040421,2
    		Cpathogenic195728108(+) CACCTC/TAGTCG 4 Q * stg11Minor allele frequency- T:0.00NA 4548
    rs40314641,2
    		C,F,H,--114515945(+) GGGGA/GAAAAA 2 -- us2k1 trp312Minor allele frequency- G:0.19NS EA 1932
    rs729504741,2
    		C,F,--114517048(+) AAGACT/AGGTCG 2 -- us2k11Minor allele frequency- A:0.03NA 120
    rs7841241,2
    		H,--114517146(+) TCTCTT/GAGTCT 2 -- us2k15Minor allele frequency- G:0.00MN NS EA 604
    rs131981581,2
    		C,H--114517181(+) CGCGGT/GGAGTT 2 -- us2k14Minor allele frequency- G:0.00NS EA 420
    rs132124991,2
    		H--114517190(+) TTTTTC/TTGAGA 2 -- us2k1 tfbs34Minor allele frequency- T:0.00NS EA 420
    rs132125051,2
    		A,H--114517202(+) GAACCC/GGGCCT 2 -- us2k14Minor allele frequency- G:0.00NS EA 418
    rs1996610891,2
    		C--114518250(+) TTAACC/TTTTTT 2 -- int10--------
    rs729504751,2
    		C,F,--114518276(+) TCCTCC/TAGCTT 2 -- int11Minor allele frequency- T:0.03NA 120
    rs729504781,2
    		C,F,--114518407(+) TGTCTA/GCCAGT 2 -- int12Minor allele frequency- G:0.02WA NA 238

    HapMap Linkage Disequilibrium report for RSPH4A (116937642 - 116954148 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for RSPH4A: --
    Human Gene Mutation Database (HGMD): RSPH4A

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    DNA2.0 Custom Variant and Variant Library Synthesis for RSPH4A

    Disorders / Diseases
    for RSPH4A gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    RSPH4A for disorders           About GeneDecksing

    OMIM gene information: 612647   
    OMIM disorders: 612649  
    UniProtKB/Swiss-Prot: RSH4A_HUMAN, Q5TD94
  • Defects in RSPH4A are the cause of primary ciliary dyskinesia type 11 (CILD11) [MIM:612649]. CILD is an
    • autosomal recessive disorder characterized by axonemal abnormalities of motile cilia. Respiratory infections leading
    to chronic inflammation and bronchiectasis are recurrent, due to defects in the respiratory cilia; reduced fertility
    is often observed in male patients due to abnormalities of sperm tails. Half of the patients exhibit situs inversus,
    due to dysfunction of monocilia at the embryonic node and randomization of left-right body asymmetry. Primary ciliary
    dyskinesia associated with situs inversus is referred to as Kartagener syndrome

    6 diseases for RSPH4A:    About MalaCards
    ciliary dyskinesia    primary ciliary dyskinesia    ciliary dyskinesia, primary, 11    situs inversus
    kartagener syndrome    bronchiectasis

    1 disease from the University of Copenhagen DISEASES database for RSPH4A:
    Primary ciliary dyskinesia
    GeneTests: RSPH4A
    Primary Ciliary Dyskinesia


    Export disorders for RSPH4A gene to outside databases

    Publications
    for RSPH4A gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for RSPH4A gene integrated from 9 sources:
    (articles sorted by number of sources associating them with RSPH4A)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutations in radial spoke head protein genes RSPH9 and RSPH4A cause primary ciliary dyskinesia with central-microtubular-pair abnormalities. (PubMed id 19200523)1, 2, 3 Castleman V.H.... Mitchison H.M. (2009)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. Mutations in radial spoke head genes and ultrastructur al cilia defects in East-European cohort of primary ciliary dyskinesia patients. (PubMed id 22448264)1 Zietkiewicz E....Witt M. (2012)
    4. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    6. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)2 Mungall A.J.... Beck S. (2003)
    7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    8. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (1996)
    9. Primary Ciliary Dyskinesia (PubMed id 20301301)1 Zariwala M.A....Leigh M.W. (1993)

    External Searches for RSPH4A gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Genome Databases showing RSPH4A gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 345895 HGNC: 21558 AceView: RSHL3 Ensembl:ENSG00000111834 euGenes: HUgn345895
    ECgene: RSPH4A H-InvDB: RSPH4A

    Other Databases showing RSPH4A gene

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    Specialized Databases showing RSPH4A gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for RSPH4A Pharmacogenomics, SNPs, Pathways

    Intellectual Property
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