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CALML4 calmodulin like 4 [ Homo sapiens (human) ]

Gene ID: 91860, updated on 5-Mar-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
Predicted to enable calcium ion binding activity and enzyme regulator activity. Predicted to be involved in regulation of catalytic activity. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in colon (RPKM 15.5), duodenum (RPKM 14.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
15q23
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (68190705..68206110, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (66009455..66024859, complement)
105.20220307 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
  • 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. High-throughput analyses of hnRNP H1 dissects its multi-functional aspect. Uren PJ, et al. RNA Biol, 2016. PMID 26760575, Free PMC Article

See all (10) 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)

Genotypes

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 muscle contraction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
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_2023_10

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.

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