ProteinestablishedQ92-kmt2a-sarcoma

Vimentin domain coordinates (P08670) - so the VIM::KMT2A breakpoint can actually be drawn

also called vimentin domains · VIM domain map · P08670 domains

This is just the map of vimentin's parts by residue number, fetched from the protein database. It exists so that the picture of the VIM-KMT2A sarcoma fusion can be drawn with real coordinates instead of words.

The same thing, for a scientist

Coordinate atlas for vimentin (P08670, 466 aa), written because the existing gene-vim entry carries no domain coordinates and the VIM::KMT2A fusion lane therefore could not resolve in this graph's 3D domain viewer. Vimentin is a type III intermediate filament with the canonical IF architecture: a head (aa 2-95), the IF rod comprising coil 1A (96-131), linker 1 (132-153), coil 1B (154-245), linker 12 (246-268) and coil 2 (269-407), and a tail (408-466); UniProt annotates the whole rod as one domain at aa 103-411. The exon structure of the canonical transcript ENST00000544301 puts aa 1-240 in CDS exons 2-4 (exon 1 is untranslated), which is exactly the portion retained in the VIM(ex4)::KMT2A(ex2) sarcoma fusion - head, coil 1A, linker 1 and most of coil 1B, with the distal coil 1B, linker 12, coil 2 and tail lost. This entry asserts coordinates only; it makes no claim about vimentin as a KMT2A-fusion interactor, which gene-vim already adjudicates and this entry does not revisit.

What it looks like

VIM466 aa

No three-dimensional model is available for this protein, so the map above is the whole picture. That is itself informative: AlphaFold does not model chains this long, and the parts that have been crystallised are held under the entries for the individual domains.

Go deeper

The map

element	residues	UniProt feature type
Head	2-95	Region
Coil 1A	96-131	Region
Linker 1	132-153	Region
Coil 1B	154-245	Region
Linker 12	246-268	Region
Coil 2	269-407	Region
Tail	408-466	Region
IF rod	103-411	Domain

Coordinates 1. CDS exon boundaries 2: exon 2 = aa 1-188, exon 3 = 188-208, exon 4 = 209-240, exon 5 = 241-294, exon 6 = 295-336, exon 7 = 337-410, exon 8 = 410-425, exon 9 = 425-453, exon 10 = 454-467; exon 1 is untranslated.

The fusion boundary falls at aa 240, inside coil 1B - so the sarcoma fusion carries a truncated rod that cannot complete a coiled-coil dimer the way full-length vimentin does.

Facts and figures

uniprot	P08670
length AA	466
gene symbol	VIM
ensembl gene ID	ENSG00000026025
ensembl transcript ID	ENST00000544301
resolution note	fetched by accession; primary gene name (VIM) and length (466) read back from the fetched record, 2026-09-21. gene_exact was not used. The VIM literature-register hazard (Verona integron-encoded metallo-beta-lactamase; the VIM-2 antibody clone) does not affect an accession-keyed fetch.
why this entry exists	gene-vim carries no data.domains, so the VIM::KMT2A fusion lane could not resolve in the 3D domain viewer. This is a coordinates-only companion, following the existing protein-*-domains pattern, and it does not revisit gene-vim's interactome adjudication.
scope note	no biological claim is made here beyond residue boundaries

domains

domains — the numbers behind the chart

[
  {
    "name": "IF rod",
    "start": 103,
    "end": 411
  },
  {
    "name": "Head",
    "start": 2,
    "end": 95
  },
  {
    "name": "Coil 1A",
    "start": 96,
    "end": 131
  },
  {
    "name": "Linker 1",
    "start": 132,
    "end": 153
  },
  {
    "name": "Coil 1B",
    "start": 154,
    "end": 245
  },
  {
    "name": "Linker 12",
    "start": 246,
    "end": 268
  },
  {
    "name": "Coil 2",
    "start": 269,
    "end": 407
  },
  {
    "name": "Tail",
    "start": 408,
    "end": 466
  }
]

exon AA ranges

{
  "1": "untranslated",
  "2": [
    1,
    188
  ],
  "3": [
    188,
    208
  ],
  "4": [
    209,
    240
  ],
  "5": [
    241,
    294
  ],
  "6": [
    295,
    336
  ],
  "7": [
    337,
    410
  ],
  "8": [
    410,
    425
  ],
  "9": [
    425,
    453
  ],
  "10": [
    454,
    467
  ]
}

How this could bite us back

A coordinates-only entry is the kind that gets cited for more than it says. It asserts residue boundaries from UniProt and nothing about vimentin's role in any fusion complex; gene-vim's verdict on that question stands unaltered.

Still open

Do the sarcoma reports number VIM exons from the transcription start or from the first coding exon? The answer moves the fusion junction from aa 240 to aa 294 and nobody has stated it.
Does a vimentin fragment ending inside coil 1B dimerise, oligomerise, or neither? That determines whether the VIM contribution to the fusion is a dimerisation module or an inert N-terminal extension.

Every source behind this entry (2)

E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
Fetched from live UniProt (2026-09-21): P08670, primary gene name read back as VIM, 466 aa, Vimentin, with an IF rod domain at aa 103-411 and regions head 2-95, coil 1A 96-131, linker 1 132-153, coil 1B 154-245, linker 12 246-268, coil 2 269-407 and tail 408-466.
UniProtKB P08670 (VIME_HUMAN), Vimentin, feature table and sequence · UniProt Consortium · UniProtKB 2026
What this evidence cannot show
Coordinates only. This entry deliberately makes no claim about vimentin's biology, its localisation or whether it contacts a KMT2A fusion protein - gene-vim adjudicates all of that and reaches a 'probably contamination, as an interactor' verdict that this entry neither supports nor disputes.
Evidence that argues against this (1)
- UniProt's boundaries for the IF rod (103-411) and for the coil/linker series do not tile exactly - the rod domain starts at 103 while coil 1A starts at 96 - so a figure that draws both will show a small overlap. That is a curation artefact of two annotation layers, not an error in either. Ensembl (EMBL-EBI) 2026
E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
Computed here from live Ensembl REST (2026-09-21): VIM canonical transcript ENST00000544301 has 10 exons of which exon 1 is untranslated, and CDS exons 2-4 together encode exactly aa 1-240 (720 CDS bp), which is the portion retained in a VIM(exon 4)::KMT2A(exon 2) fusion.
Ensembl REST API lookup, VIM (ENSG00000026025), canonical transcript ENST00000544301 with exon and translation coordinates · Ensembl (EMBL-EBI) · Ensembl REST 2026
What this evidence cannot show
Codon ranges computed by cumulative CDS length; codon 188 is split across exons 2 and 3 and so appears in both. The sarcoma reports do not name a VIM transcript accession, so mapping their 'VIM exon 4' to this transcript needed checking. It was checked against RefSeq NM_003380.5 (see the counter-note): that accession also carries an untranslated exon 1 and identical CDS exon lengths, so both numbering systems give aa 1-240 and the mapping is not an inference.
Evidence that argues against this (1)
- The obvious worry is that the reports might number VIM exons from the first CODING exon, which would move 'VIM exon 4' to this transcript's exon 5 and the junction from aa 240 to aa 294. CHECKED AND RESOLVED: RefSeq NM_003380.5, the accession this literature works from, also has an untranslated first exon (exon 1 = bases 1-284, CDS begins at base 432 inside exon 2), and its exon 2-4 CDS lengths are 563, 61 and 96 bp - identical to Ensembl's. Both numbering systems therefore agree and VIM exons 1-4 encode aa 1-240 in either. The ambiguity does not exist. National Center for Biotechnology Information 2026

Connected to

part of →VIM / vimentin (P08670) - a pan-MLL-fusion prey with a clean negative control, and separately a genuine KMT2A rearrangement partner in sarcoma, which are two different facts
coordinates-only companion; gene-vim carries no data.domains so the VIM::KMT2A lane could not resolve
supports →VIM::KMT2A - the one KMT2A rearrangement that keeps the SET domain and still throws away the menin-binding exon
the residue boundaries that place the fusion junction at vimentin aa 240, inside coil 1B