The Gene

Name: B-Raf Proto-oncogene, serine/threonine kinase (synonyms: NS7, B-raf, BRAF1, RAFB1, B-RAF1) (3)

Official Symbol: BRAF (3)

Gene ID: 673 (3)

Accession numbers from National Center for Biotechnology Information:

Protein: NP_004324.2 (8)
Genomic: NC_000007.14 (6)
mRNA: NM_004333.4 (5)

Description of Gene Structure:

According to Ensembl, there are five different known isoforms of our BRAF1 gene. The first isoform, depicted directly below, is the main and most common form and has 18 exons and 17 introns. The second isoform, BRAF-003, has 10 exons and 9 introns. The third isoform, BRAF-002, has 19 exons but only five 5 exons are coding due to a nonsense mediated decay, and 4 introns. The fourth isoform, BRAF-003, has 6 exons though only 4 are coding due to a nonsense mediated decay, and 5 introns. The last isoform has 3 exons and 2 introns, but none of its exons are coding and it is the only isoform of BRAF1 to not produce a protein.

The main gene and isoform 1 are the only complete protein coding versions of this gene, and their introns and exons do differ greatly in size due to alternative splicing. The first exon of each isoform are of similar size, but still terminate at different areas, and the introns of the main gene encompass many of the exons from isoform 1, while many of isoform 2's exon and intron pairs exist within the first couple exon and introns of the main gene. The size of the UTRs of these isoforms cannot be accurately compared as both are incomplete. Isoform 1 is truncated, while isoform 2 also has an incomplete CDS as a result of nonsense mediated decay, as stated earlier. These different forms have vastly different sizes of CDSs as the main gene is 190,753 base pairs long while isoform 1 is only 63,831 base pairs long, and isoform 2 is 19,691 base pairs long and thus isoform 1 produces a much smaller protein, while isoform 2 produces no protein at all. However, isoform 1's CDS is also listed as incomplete as the protein is truncated. Since this form of the protein is incomplete it may be that the mRNA coding for it will be largely prevented from leaving the cell nucleus, but if it were to get out and be translated into a protein then this protein will likely cause cancerous growth or other disorders as described in the Mutations and Disease Association section later on.

Main Gene: BRAF-001 (10)

Isoform 1: BRAF-003 (11)

This isoform was selected because it is the largest existing isoform of BRAF and it is the only isoform to code for a functioning, though still incorrect, protein.

Isoform 2: BRAF-005 (12)

This isoform was chosen for investigation because it is the smallest form of nonsense mediated decay.

Comparison of Isoform Domains: (BRAF-003 [11] and BRAF-005 [12])

Gene Expression:

BRAF-001 (aAUG 10) is expressed (7) in thirty different tissues which are nervous tumor, testis, germinal center B cell, nervous normal, breast, kidney, blastocyst, liver and spleen, liver, PCR rescued clones, mammary adenocarcinoma, cell line, melanocyte, pancreas, placenta normal, pluripotent cell line derived from blastocyst inner cell mass, pooled germ cell tumors, prostate, purified pancreatic islet, stomach, thalamus, breast cancer, breast, mammary adenocarcinoma, breast normal, embryonal carcinoma, cell line, head neck, hippocampus, human embryonic stem cells, kidney tumor, mammary gland (cancer tissue), ovary, pooled human melanocyte, fetal heart, and pregnant uterus, testes, thymus.

BRAF-003 did not have information on what tissues it is expressed in.

BRAF-005 (eAUG 10) is said to be expressed (7) in the testis and nervous tumor tissue, though it did not how how this is possible since it is supposed to be non-protein coding due to nonsense mediated decay.

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