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    CALML4 calmodulin like 4 [ Homo sapiens (human) ]

    Gene ID: 91860, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CALML4provided by HGNC
    Official Full Name
    calmodulin like 4provided by HGNC
    Primary source
    HGNC:HGNC:18445
    See related
    Ensembl:ENSG00000129007 MIM:620520; AllianceGenome:HGNC:18445
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NY-BR-20
    Summary
    Enables myosin head/neck binding activity. Involved in brush border assembly. Located in microvillus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in colon (RPKM 15.5), duodenum (RPKM 14.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CALML4 in Genome Data Viewer
    Location:
    15q23
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (68190705..68206110, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (66009455..66024859, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (68483043..68498448, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein S15a pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:68299513-68300103 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:68301209-68302094 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:68302095-68302980 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:68308948-68309655 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68312077-68312615 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68312616-68313153 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68314382-68315165 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68337310-68337830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68337831-68338350 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6583 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68361989-68362489 Neighboring gene protein inhibitor of activated STAT 1 Neighboring gene uncharacterized LOC105370871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:68492859-68493630 Neighboring gene Sharpr-MPRA regulatory region 569 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:68503536-68504076 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9641 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9642 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:68521930-68522109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9643 Neighboring gene CLN6 transmembrane ER protein Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:68549209-68549856 Neighboring gene uncharacterized LOC124903593 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 40

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. The small EF-hand protein CALML4 functions as a critical myosin light chain within the intermicrovillar adhesion complex. Choi MS, et al. J Biol Chem, 2020 Jul 10. PMID 32209652, Free PMC Article
    2. Humoral immunity to human breast cancer: antigen definition and quantitative analysis of mRNA expression. Scanlan MJ, et al. Cancer Immun, 2001 Mar 30. PMID 12747765
    3. Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies. GENDEP Investigators, et al. Am J Psychiatry, 2013 Feb. PMID 23377640, Free PMC Article
    4. ΔNp63α Suppresses TGFB2 Expression and RHOA Activity to Drive Cell Proliferation in Squamous Cell Carcinomas. Abraham CG, et al. Cell Rep, 2018 Sep 18. PMID 30232004, Free PMC Article
    5. Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers. Ito T, et al. Nat Genet, 2021 Dec. PMID 34857952

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The small EF-hand protein CALML4 functions as a critical myosin light chain within the intermicrovillar adhesion complex.
      Title: The small EF-hand protein CALML4 functions as a critical myosin light chain within the intermicrovillar adhesion complex.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC4809

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables enzyme regulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables myosin head/neck binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in brush border assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in microtubule cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in microvillus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    calmodulin-like protein 4
    Names
    serologically defined breast cancer antigen NY-BR-20

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001031733.3 → NP_001026903.3  calmodulin-like protein 4 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AC107871
      Consensus CDS
      CCDS42052.2
      UniProtKB/TrEMBL
      A0A804D2Q3
      Related
      ENSP00000400755.3, ENST00000448060.7
      Conserved Domains (1) summary
      PTZ00184
      Location:7 → 96
      PTZ00184; calmodulin; Provisional

    2. NM_001286694.1 → NP_001273623.1  calmodulin-like protein 4 isoform 3

      See identical proteins and their annotated locations for NP_001273623.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in its 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC107871, BC009516, BX439220, BX640702, BX640817
      Consensus CDS
      CCDS66808.1
      UniProtKB/Swiss-Prot
      Q96GE6
      Related
      ENSP00000435285.2, ENST00000395463.3
      Conserved Domains (1) summary
      cl25352
      Location:4 → 110
      EFh_PEF; The penta-EF hand (PEF) family

    3. NM_001286695.1 → NP_001273624.1  calmodulin-like protein 4 isoform 4

      See identical proteins and their annotated locations for NP_001273624.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in its 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC107871, BX439220, BX640702, BX640817
      Consensus CDS
      CCDS92031.1
      UniProtKB/Swiss-Prot
      Q96GE6
      Related
      ENSP00000438177.2, ENST00000540479.6
      Conserved Domains (1) summary
      cl08302
      Location:20 → 72
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    4. NM_033429.3 → NP_219501.3  calmodulin-like protein 4 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC107871
      Consensus CDS
      CCDS10226.3
      UniProtKB/TrEMBL
      A0A804DNR1
      Related
      ENSP00000419081.2, ENST00000467889.3
      Conserved Domains (1) summary
      PTZ00184
      Location:1 → 143
      PTZ00184; calmodulin; Provisional

    RNA

    1. NR_104583.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks three internal exons, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AC107871, BX439220, BX640702, BX640817
      Related
      ENST00000395465.3

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      68190705..68206110 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      66009455..66024859 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96GE6.3 GenPept UniProtKB/Swiss-Prot:Q96GE6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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