Mouse T-Cell Receptor Repertoire Analyzer

Comprehensive, client-side WebAssembly analysis for mature Mouse T-cell receptor sequences across TRA (Alpha), TRB (Beta), TRG (Gamma), and TRD (Delta) loci. Features automated V/J alignment, CDR3 anchor extraction (Cys104 & Phe118), biophysical characterization, synthesis boundary compliance, and live 2D PaCMAP projection.

290

V-Genes

D-Genes

J-Genes

4 Loci

αβ & γδ

🛡️ Immunogenomic Rule: The 12/23 RSS Molecular Diode Suppresses TCR D-Inversion (<0.1%) vs BCR (10%)

In antibody heavy chains (IGH), the D-segment is flanked on both sides by 12-bp spacer RSSs (12-D-12), allowing RAG1/2 recombinase to pair in forward or reverse orientations and producing ~10% inverted D-genes in BCR repertoires. In stark contrast, Mouse TCR D-segments (TRBD & TRDD) are asymmetrically flanked by a 5' 12-RSS and a 3' 23-RSS (12-D-23). Inversion would force illegal 23-to-23 or 12-to-12 pairings, which are biochemically forbidden. Consequently, TCR D-inversion is virtually non-existent (<0.1%); instead, TCR achieves CDR3 hypervariability through tandem forward concatenation (e.g. TRDD1–TRDD2–TRDD3 in TRD), flexible forward reading frames, and hyperactive TdT N-addition.

🔬 Paste Mouse TCR Sequence (Nucleotide or Amino Acid)

Automatic V/J assignment • IMGT numbering • Biophysics

Engine: Client WebAssembly (dnaplot_wasm.js)

📊 Clonotype Analysis Report

TRA / TRB

Assigned V-Gene

Matched J-Gene

CDR3 Length

Net Charge (pH 7.4)

Hydropathy (GRAVY)

Isoelectric Point (pI)

TCR Lineage & Recombination

Annotated Domain Architecture (FR1 - CDR1 - FR2 - CDR2 - FR3 - CDR3 - FR4):

Extracted CDR3 Sequence (Cys104 → Phe118):

J-Synthesis Boundary Motif: - ✓ Compliant

📊 Multi-Clonotype Batch Profiler (Mouse TCR)

Paste multiple FASTA or plain sequences

Paste up to 100 TCR sequences (one per line or FASTA format). The WASM engine will rapidly classify locus, extract CDR3 loops, and evaluate biophysical properties.

🧬 Mouse TCR Diversity (D) & Joining (J) Elements

Canonical Recombination Signals (RSS) & Synthesis Boundaries

Diversity Elements (TRBD & TRDD)

Gene ID	Locus	5' RSS (Spacer)	Coding DNA	3' RSS (Spacer)	Orientation Rule
*mus_TRBD101**	TRB	`CACAGTG-12-ACAAAAACC`	`GGGACAGGGGGC`	`GGTTTTTGT-23-CACTGTG`	Strict Forward Only (12/23 Diode)
*mus_TRBD201**	TRB	`CACAGTG-12-ACAAAAACC`	`GGGACTGGGGGGGC`	`GGTTTTTGT-23-CACTGTG`	Strict Forward Only (12/23 Diode)
*mus_TRDD101**	TRD	`CACAGTG-12-ACAAAAACC`	`GAAATAG`	`GGTTTTTGT-12-CACTGTG`	Strict Forward Only (12/23 Diode)
*mus_TRDD201**	TRD	`CACAGTG-12-ACAAAAACC`	`ATCGGAGGGATAC`	`GGTTTTTGT-23-CACTGTG`	Strict Forward Only (12/23 Diode)

Joining Elements (TRAJ, TRBJ, TRGJ, TRDJ) — Sample (15 of 16)

Gene ID	Locus	5' RSS	Canonical J-Motif	Boundary Sequence
*mus_TRBJ1-101**	TRB	`12-RSS`	LTVV	`NTEVFFGKGTRLTVV...`
*mus_TRBJ1-201**	TRB	`12-RSS`	LTVV	`NYGYTFGSGTRLTVV...`
*mus_TRBJ1-301**	TRB	`12-RSS`	LTVV	`SGNTLYFGEGSRLTVV...`
*mus_TRBJ1-401**	TRB	`12-RSS`	LSVL	`SNERLFFGHGTKLSVL...`
*mus_TRBJ1-501**	TRB	`12-RSS`	LSVL	`NQAPLFGEGTRLSVL...`
*mus_TRBJ1-601**	TRB	`12-RSS`	LTVT	`SYNSPLYFAAGTRLTVT...`
*mus_TRBJ2-101**	TRB	`12-RSS`	LTVL	`NYAEQFFGPGTRLTVL...`
*mus_TRBJ2-201**	TRB	`12-RSS`	LTVL	`NTGQLYFGEGSKLTVL...`
*mus_TRBJ2-301**	TRB	`12-RSS`	LTVL	`SAETLYFGSGTRLTVL...`
*mus_TRBJ2-401**	TRB	`12-RSS`	LSVL	`SQNTLYFGAGTRLSVL...`
*mus_TRBJ2-501**	TRB	`12-RSS`	LLVL	`DTQYFGPGTRLLVL...`
*mus_TRBJ2-701**	TRB	`12-RSS`	LTVT	`SYEQYFGPGTRLTVT...`
*mus_TRDJ101**	TRD	`12-RSS`	VTVE	`TDKLIFGKGTRVTVE...`
*mus_TRDJ201**	TRD	`12-RSS`	LTVL	`TAQLFFGKGTRLTVL...`
*mus_TRGJ101**	TRG	`12-RSS`	LVVI	`NYYKKLFGSGTTLVVI...`

🗺️ Mouse TCR Manifold (PaCMAP 2D Projection • 290 Genes)

TRA (Green), TRB (Blue), TRG (Purple), TRD (Amber)