E1BL04 (bovine XIRP2): comparison with characterized Xin-family proteins
Script: compare_xin_family.py (run with uv run python compare_xin_family.py;
raw output in compare_xin_family.out). Sequences are fetched live from UniProt
REST; global pairwise alignment, BLOSUM62, gap open -10, extend -0.5.
Results (2026-10-20 run)
| Reference |
PANTHER subfamily |
Length |
Identity over aligned |
Reference coverage |
Ref C-term 300 aa covered |
| A4UGR9 human XIRP2 |
PTHR22591:SF1 |
3374 |
0.805 |
0.992 |
0.993 |
| Q4U4S6 mouse Xirp2 (isoform 1) |
PTHR22591:SF1 |
3784 |
0.707 |
0.860 |
0.047 |
| Q702N8 human XIRP1 |
PTHR22591:SF2 |
1843 |
0.378 |
0.916 |
0.833 |
| O70373 mouse Xirp1 |
PTHR22591:SF2 |
1813 |
0.359 |
0.949 |
0.957 |
LIM check: a local alignment of the mouse Xirp2 isoform-1 LIM zinc-binding
domain (Q4U4S6 residues 3255-3315) against E1BL04 gave only a 13-residue
alignment with 5 identities (score 33), i.e. no LIM domain is present in E1BL04.
Interpretation
- E1BL04 is a full-length XIRP2 long (Xin-repeat) product: it covers 99% of
human XIRP2 (A4UGR9) including both termini, with 80.5% identity, and is far
less similar to XIRP1 (36-38%), consistent with its PANTHER SF1 placement.
- E1BL04 lacks the C-terminal LIM domain / C-terminal domain (CTD) carried by
mouse Xirp2 isoform 1 and by the short stereocilia isoform (XEPLIN, isoform 3).
It therefore corresponds to the LIM-less long isoform class (like human
A4UGR9 canonical and mouse isoform 2), not to the isoform whose LIM/CTD
mediates force-dependent recruitment and monomeric gamma-actin enrichment
at stereocilia gaps (PMID:37294664).
- It is not a fragment. A UniProt search (gene:XIRP2, organism 9913, 2026-10-20)
returns three unreviewed entries: E1BL04 (3561 aa) and two short products,
A0AAA9SWG7 (936 aa) and A0AAA9SUE1 (957 aa), which were not analysed here and
may represent short-isoform gene models. No reviewed (Swiss-Prot) bovine XIRP2
entry exists, so E1BL04 is the de facto canonical long product.