Ig

Immunoglobulin Locus Explorer

Zoom the whole locus down to single codons · build a V(D)J rearrangement

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V D J C · isotypes

scroll to zoom · drag to pan · double-click a segment to dive in

Segment inspector

Hover or click a segment on the map.

V(D)J Recombinator heavy · V-D-J

Quick reference

12/23 rule. RAG joins a 12-spacer RSS only to a 23-spacer RSS. In IGH the V (23) and J (23) can't join directly — the D (12/12) is obligatory.
P-nucleotides. Palindromic; templated by the coding end when RAG opens the hairpin off-centre.
N-nucleotides. Non-templated; added by TdT (GC-biased), mostly at IGH junctions.
CDR3. Spans the conserved Cys (from V) to the conserved Trp (IGH) / Phe (IGK/IGL) in J — the junction sits right in it.
Productive. Junction length a multiple of 3 and no premature stop.

How to use this explorer

Navigate the locus

Scroll to zoom toward the cursor; drag to pan.
Four zoom levels reveal themselves automatically: locus bands → named segments → RSS & exons → nucleotides + protein.
Use the V / D / J / C chips to jump to a region, Fit to see everything, and the minimap to stay oriented.
Double-click a segment to dive to its sequence.

Read the colours

Each V family has its own hue — the same hue marks the homologous family in the other species, so you can compare mouse ↔ human at a glance.
Paler blocks are pseudogenes; the warm blocks on the right are C-region isotypes (IgM, IgG, IgA…).
Blue/orange triangles below segments are RSS spacers (12 vs 23).

Build a rearrangement

The Recombinator guides you to pick a V, (D), and J — click them on the map or in the slots. The guide never locks you in; toggle it off for free mode.
Then trim the ends, add P- and N-nucleotides, and watch the CDR3 and productivity update live.

Teaching model. Family structure, segment order, isotype order and RSS architecture are biologically faithful; individual synthetic V sequences and intergenic spacing are schematic. D and J segments and the family-consensus V backbones are IMGT-derived reference sequences.