NCAM1
neural cell adhesion molecule 1 | CD56, NCAM

This gene encodes a cell adhesion protein which is a member of the immunoglobulin superfamily. The encoded protein is involved in cell-to-cell interactions as well as cell-matrix interactions during development and differentiation. The encoded protein plays a role in the development of the nervous system by regulating neurogenesis, neurite outgrowth, and cell migration. This protein is also involved in the expansion of T lymphocytes, B lymphocytes and natural killer (NK) cells which play an important role in immune surveillance. This protein plays a role in signal transduction by interacting with fibroblast growth factor receptors, N-cadherin and other components of the extracellular matrix and by triggering signalling cascades involving FYN-focal adhesion kinase (FAK), mitogen-activated protein kinase (MAPK), and phosphatidylinositol 3-kinase (PI3K). One prominent isoform of this gene, cell surface molecule CD56, plays a role in several myeloproliferative disorders such as acute myeloid leukemia and differential expression of this gene is associated with differential disease progression. For example, increased expression of CD56 is correlated with lower survival in acute myeloid leukemia patients whereas increased severity of COVID-19 is correlated with decreased abundance of CD56-expressing NK cells in peripheral blood. Alternative splicing results in multiple transcript variants encoding distinct protein isoforms. [provided by RefSeq, Aug 2020]

Developmental clusters: GC6
Biological processes 19 terms
Expression (TPM)
NCAM1 — as a Regulated Gene

TFs regulating NCAM1 0 TFs

Transcription factors with Perturb-seq knockdown data for NCAM1. 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 = NCAM1 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 NCAM1

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of NCAM1, 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
chr11:112,777,149–112,777,871 183.8 kb Distal (>10kb) Multiome 156
chr11:112,822,243–112,823,337 138.7 kb Distal (>10kb) Multiome 248
chr11:112,881,288–112,881,988 79.8 kb Distal (>10kb) Multiome 129
chr11:112,922,248–112,923,197 38.6 kb Distal (>10kb) Multiome 140
chr11:112,960,780–112,961,661 137 bp At TSS Multiome 501
chr11:112,961,782–112,962,651 381 bp At TSS 215
chr11:112,962,791–112,963,595 1.4 kb Proximal (<10kb) 281
chr11:113,093,473–113,094,494 132.6 kb Distal (>10kb) Multiome 118
chr11:113,192,132–113,192,786 231.0 kb Distal (>10kb) Multiome 88
chr11:113,240,569–113,241,253 279.5 kb Distal (>10kb) Multiome 76

Genome Browser

Genomic view of the NCAM1 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.

chr11:112,767,149 – 113,251,253
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq