RBM4
RNA binding motif protein 4 | LARK, RBM4A, ZCCHC21, ZCRB3A

Enables RNA binding activity and cyclin binding activity. Involved in several processes, including IRES-dependent translational initiation of linear mRNA; negative regulation of translation; and regulation of alternative mRNA splicing, via spliceosome. Located in cytoplasmic stress granule; cytosol; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2025]

Member of: DE-1 DE-1.2 Developmental clusters: GC5
Biological processes 46 terms
IRES-dependent translational initiation of linear mRNA (GO:0002192)RNA binding (GO:0003723)RNA binding (GO:0003723)RNA binding (GO:0003723)RNA binding (GO:0003723)RNA processing (GO:0006396)cap-independent translational initiation (GO:0002190)circadian regulation of translation (GO:0097167)circadian regulation of translation (GO:0097167)circadian rhythm (GO:0007623)cyclin binding (GO:0030332)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasmic stress granule (GO:0010494)entrainment of circadian clock by photoperiod (GO:0043153)entrainment of circadian clock by photoperiod (GO:0043153)mRNA 3'-UTR binding (GO:0003730)mRNA 3'-UTR binding (GO:0003730)mRNA binding (GO:0003729)mRNA binding (GO:0003729)miRNA binding (GO:0035198)miRNA-mediated gene silencing by inhibition of translation (GO:0035278)negative regulation of translation (GO:0017148)negative regulation of translation in response to stress (GO:0032055)negative regulation of translational initiation (GO:0045947)nuclear speck (GO:0016607)nuclear speck (GO:0016607)nuclear speck (GO:0016607)nucleic acid binding (GO:0003676)nucleolus (GO:0005730)nucleolus (GO:0005730)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)perinuclear region of cytoplasm (GO:0048471)positive regulation of muscle cell differentiation (GO:0051149)pre-mRNA binding (GO:0036002)pre-mRNA intronic binding (GO:0097157)pre-mRNA intronic pyrimidine-rich binding (GO:0097158)protein binding (GO:0005515)regulation of alternative mRNA splicing, via spliceosome (GO:0000381)regulation of alternative mRNA splicing, via spliceosome (GO:0000381)regulation of nucleocytoplasmic transport (GO:0046822)regulation of nucleocytoplasmic transport (GO:0046822)response to arsenic-containing substance (GO:0046685)zinc ion binding (GO:0008270)
Expression (TPM)
RBM4 — as a Regulated Gene

TFs regulating RBM4 0 TFs

Transcription factors with Perturb-seq knockdown data for RBM4. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = RBM4 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to RBM4

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of RBM4, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Accessibility Element Dist. to TSS Link type TFs
chr11:66,344,804–66,345,488 293.6 kb Distal (>10kb) Multiome 731
chr11:66,347,078–66,348,463 290.9 kb Distal (>10kb) Multiome 866
chr11:66,370,733–66,372,576 266.8 kb Distal (>10kb) Multiome 800
chr11:66,408,467–66,409,206 230.0 kb Distal (>10kb) Multiome 569
chr11:66,421,258–66,422,129 216.9 kb Distal (>10kb) Multiome 1190
chr11:66,438,544–66,439,241 199.7 kb Distal (>10kb) Multiome 756
chr11:66,466,155–66,467,634 171.9 kb Distal (>10kb) Multiome 579
chr11:66,479,578–66,480,947 158.3 kb Distal (>10kb) Multiome 937
chr11:66,510,277–66,510,954 128.0 kb Distal (>10kb) Multiome 787
chr11:66,545,631–66,547,072 92.5 kb Distal (>10kb) Multiome 753
chr11:66,568,061–66,568,910 70.2 kb Distal (>10kb) Multiome 392
chr11:66,592,561–66,593,452 45.6 kb Distal (>10kb) Multiome 857
chr11:66,616,078–66,617,408 22.2 kb Distal (>10kb) Multiome 1011
chr11:66,637,919–66,639,003 159 bp At TSS Multiome 872
chr11:66,677,182–66,678,796 39.2 kb Distal (>10kb) Multiome 926
chr11:66,728,259–66,728,943 89.8 kb Distal (>10kb) Multiome 275
chr11:66,744,354–66,745,291 106.0 kb Distal (>10kb) Multiome 747
chr11:66,842,896–66,843,952 204.7 kb Distal (>10kb) Multiome 843
chr11:66,855,758–66,857,980 217.7 kb Distal (>10kb) Multiome 795
chr11:66,882,995–66,883,462 244.6 kb Distal (>10kb) Multiome 277

Genome Browser

Genomic view of the RBM4 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.

chr11:66,334,804 – 66,893,462
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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