Twintron Candidate Report

Generated 2026-08-03 09:43 · U12-guided de novo twintron detection · genome build hg38
Case replicates: 2 · Control replicates: 2 · 20 worker process(es)
min_inner_reads=3 · min_outer_reads=5 · GENCODE/RefSeq reference: provided · Mappability: soft-mask heuristic only
32
Total candidates
0
High-confidence
12
Probable
18
Genes affected
6
Differential (case vs ctrl)

Summary figures

Scoring methodology

Each candidate receives a Twintron Evidence Score (0-100) from 8 independently-capped components. Differential case-vs-control usage is deliberately excluded from this score -- a real twintron can be used equally in both cell lines, so differential usage is reported as a separate column, not a requirement.

ComponentMaxWhat it checks
Splice-site strength (PWM)20Continuous donor+acceptor/PPT strength, not just canonical y/n
Inner split-read support15Pooled, BAM-validated inner-junction depth
Outer junction validated10Parent U12 boundary itself well-supported
BAM ↔ junction.bed agreement10Confirmed by both direct CIGAR parsing and the aligner's own calls
Novelty vs GENCODE/RefSeq10Novel scores higher; neutral (5) if no reference supplied
Inner fraction10inner / (inner + outer) reads
Recurrence across replicates15Seen in >1 biological replicate; neutral if only 1 replicate/condition
Mappability / non-repetitive10Soft-mask heuristic or bigWig track; full credit if unassessable

Tiers: ≥90 High-confidence 70-89 Probable 50-69 Possible <50 Likely false positive

Note: before any candidate is scored, its parent outer U12 junction must have at least min_outer_reads (see header above) pooled reads in at least one condition -- this is a hard filter, separate from the "Outer junction validated" scoring component above (which further rewards especially well-supported outer junctions beyond that minimum).

Caveat: this is a heuristic evidence aggregator, not a statistical test, and the splice-site PWMs are illustrative consensus approximations (not a literal MaxEntScan reproduction). Sensitivity is kept deliberately high -- treat this as a shortlist for manual UCSC/IGV inspection and RT-PCR validation, not a confirmed call set.

Candidates by gene → U12 intron

Filter by tier: (click any column header to sort within its table; * IGV links require IGV desktop running locally with Preferences > Advanced > "Enable port" checked)
ACTL6A — 1 candidate(s) across 1 U12 intron(s)
ACTL6A;Homo_sapiens_3_179574468_179576216_F — 1 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr3:179574502-179575402+GT-AGU2-type50Possible Twintron4 (1,3) / 0 (0,0)161 / 1240.024 / 0.000NoAnnotatedmotif_strength=7, inner_reads=5, outer_validated=10, cross_validation=10, novelty=0, inner_fraction=0, recurrence=8, mappability=10 UCSC ↗ IGV*
C15orf41 — 1 candidate(s) across 1 U12 intron(s)
C15orf41;Homo_sapiens_15_36692176_36697322_F — 1 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr15:36694752-36695029+GT-AGU2-type63Possible Twintron3 (3,0) / 0 (0,0)9 / 00.250 / 0.000YesNovelmotif_strength=8, inner_reads=5, outer_validated=5, cross_validation=10, novelty=10, inner_fraction=7, recurrence=8, mappability=10 UCSC ↗ IGV*
CCDC28B — 1 candidate(s) across 1 U12 intron(s)
CCDC28B;Homo_sapiens_1_32204621_32205193_F — 1 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr1:32205014-32205123-GT-AGU2-type68Possible Twintron4 (1,3) / 0 (0,0)15 / 50.211 / 0.000YesNovelmotif_strength=8, inner_reads=5, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=7, recurrence=8, mappability=10 UCSC ↗ IGV*
DERL2 — 1 candidate(s) across 1 U12 intron(s)
DERL2;Homo_sapiens_17_5480583_5482808_R — 1 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr17:5481140-5481295-GT-AGU2-type44Likely False Positive4 (2,2) / 0 (0,0)44 / 00.083 / 0.000NoAnnotatedmotif_strength=6, inner_reads=5, outer_validated=10, cross_validation=10, novelty=0, inner_fraction=3, recurrence=0, mappability=10 UCSC ↗ IGV*
GAK — 1 candidate(s) across 1 U12 intron(s)
GAK;Homo_sapiens_4_911788_912734_R — 1 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr4:911843-912029-GT-AGU2-type58Possible Twintron9 (7,2) / 0 (0,0)118 / 360.071 / 0.000NoAnnotatedmotif_strength=7, inner_reads=10, outer_validated=10, cross_validation=10, novelty=0, inner_fraction=3, recurrence=8, mappability=10 UCSC ↗ IGV*
KANSL2 — 1 candidate(s) across 1 U12 intron(s)
KANSL2;Homo_sapiens_12_48660620_48667692_R — 1 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr12:48661244-48662559-GT-AGU2-type56Possible Twintron5 (0,5) / 0 (0,0)107 / 210.045 / 0.000NoAnnotatedmotif_strength=8, inner_reads=10, outer_validated=10, cross_validation=10, novelty=0, inner_fraction=0, recurrence=8, mappability=10 UCSC ↗ IGV*
LSM8 — 4 candidate(s) across 1 U12 intron(s)
LSM8;Homo_sapiens_7_118184255_118185653_F — 4 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr7:118184281-118185646+GT-AGU2-type70Probable Twintron191 (118,73) / 5 (1,4)2612 / 1270.068 / 0.038NoAnnotatedmotif_strength=7, inner_reads=15, outer_validated=10, cross_validation=10, novelty=0, inner_fraction=3, recurrence=15, mappability=10 UCSC ↗ IGV*
chr7:118185104-118185646+GT-AGU2-type60Possible Twintron4 (4,0) / 0 (0,0)2612 / 1270.002 / 0.000NoNovelmotif_strength=7, inner_reads=5, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=0, recurrence=8, mappability=10 UCSC ↗ IGV*
chr7:118184326-118185646+GT-AGU2-type60Possible Twintron3 (3,0) / 0 (0,0)2612 / 1270.001 / 0.000NoNovelmotif_strength=7, inner_reads=5, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=0, recurrence=8, mappability=10 UCSC ↗ IGV*
chr7:118184518-118185646+GT-AGU2-type52Possible Twintron3 (2,1) / 0 (0,0)2612 / 1270.001 / 0.000NoNovelmotif_strength=7, inner_reads=5, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=0, recurrence=0, mappability=10 UCSC ↗ IGV*
MAP4K4 — 2 candidate(s) across 1 U12 intron(s)
MAP4K4;Homo_sapiens_2_101859865_101864929_F — 2 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr2:101860987-101863826+GT-AGU2-type79Probable Twintron14 (7,7) / 0 (0,0)261 / 670.051 / 0.000NoNovelmotif_strength=6, inner_reads=15, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=3, recurrence=15, mappability=10 UCSC ↗ IGV*
chr2:101860987-101863820+GT-AGU2-type74Probable Twintron90 (45,45) / 5 (5,0)261 / 670.256 / 0.069YesAnnotatedmotif_strength=7, inner_reads=15, outer_validated=10, cross_validation=10, novelty=0, inner_fraction=7, recurrence=15, mappability=10 UCSC ↗ IGV*
MAPK14 — 5 candidate(s) across 2 U12 intron(s)
MAPK14;Homo_sapiens_6_36076609_36095986_F — 4 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr6:36083114-36089680+GT-AGU2-type84Probable Twintron94 (54,40) / 0 (0,0)441 / 540.176 / 0.000YesNovelmotif_strength=7, inner_reads=15, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=7, recurrence=15, mappability=10 UCSC ↗ IGV*
chr6:36089785-36090942+GT-AGU2-type77Probable Twintron15 (9,6) / 0 (0,0)441 / 540.033 / 0.000NoNovelmotif_strength=7, inner_reads=15, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=0, recurrence=15, mappability=10 UCSC ↗ IGV*
chr6:36077865-36083030+GT-AGU2-type75Probable Twintron8 (4,4) / 0 (0,0)441 / 540.018 / 0.000NoNovelmotif_strength=10, inner_reads=10, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=0, recurrence=15, mappability=10 UCSC ↗ IGV*
chr6:36091044-36091452+GT-AGU2-type59Possible Twintron4 (4,0) / 0 (0,0)441 / 540.009 / 0.000NoNovelmotif_strength=6, inner_reads=5, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=0, recurrence=8, mappability=10 UCSC ↗ IGV*
MAPK14;Homo_sapiens_6_36076609_36100187_F — 1 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr6:36095867-36095986+GT-AGU2-type79Probable Twintron15 (10,5) / 0 (0,0)261 / 170.054 / 0.000NoNovelmotif_strength=6, inner_reads=15, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=3, recurrence=15, mappability=10 UCSC ↗ IGV*
MCTS1 — 1 candidate(s) across 1 U12 intron(s)
MCTS1;Homo_sapiens_X_120608359_120611010_F — 1 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chrX:120608464-120609613+GT-AGU2-type52Possible Twintron3 (1,2) / 0 (0,0)248 / 980.012 / 0.000NoNovelmotif_strength=7, inner_reads=5, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=0, recurrence=0, mappability=10 UCSC ↗ IGV*
NAA20 — 1 candidate(s) across 1 U12 intron(s)
NAA20;Homo_sapiens_20_20022481_20025676_F — 1 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr20:20024636-20025668+GT-AGU2-type68Possible Twintron6 (6,0) / 0 (0,0)788 / 1940.008 / 0.000NoNovelmotif_strength=10, inner_reads=10, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=0, recurrence=8, mappability=10 UCSC ↗ IGV*
PTEN — 2 candidate(s) across 1 U12 intron(s)
PTEN;Homo_sapiens_10_87864549_87894024_F — 2 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr10:87879024-87880299+GT-AGU2-type65Possible Twintron6 (3,3) / 0 (0,0)193 / 00.030 / 0.000NoAnnotatedmotif_strength=10, inner_reads=10, outer_validated=10, cross_validation=10, novelty=0, inner_fraction=0, recurrence=15, mappability=10 UCSC ↗ IGV*
chr10:87864625-87875404+GT-AGU2-type52Possible Twintron3 (2,1) / 0 (0,0)193 / 00.015 / 0.000NoNovelmotif_strength=7, inner_reads=5, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=0, recurrence=0, mappability=10 UCSC ↗ IGV*
SLC35B4 — 3 candidate(s) across 1 U12 intron(s)
SLC35B4;Homo_sapiens_7_134295080_134296390_R — 3 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr7:134295176-134295395-GT-AGU2-type61Possible Twintron4 (4,0) / 0 (0,0)167 / 140.023 / 0.000NoNovelmotif_strength=8, inner_reads=5, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=0, recurrence=8, mappability=10 UCSC ↗ IGV*
chr7:134295231-134295395-GT-AGU2-type59Possible Twintron3 (3,0) / 0 (0,0)167 / 140.018 / 0.000NoNovelmotif_strength=6, inner_reads=5, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=0, recurrence=8, mappability=10 UCSC ↗ IGV*
chr7:134295231-134296267-GT-AGU2-type59Possible Twintron4 (3,1) / 0 (0,0)167 / 140.023 / 0.000NoNovelmotif_strength=6, inner_reads=5, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=0, recurrence=8, mappability=10 UCSC ↗ IGV*
SNRPE — 1 candidate(s) across 1 U12 intron(s)
SNRPE;Homo_sapiens_1_203861714_203862195_F — 1 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr1:203861744-203862181+GT-AGU2-type70Probable Twintron12 (9,3) / 0 (0,0)141 / 00.078 / 0.000NoAnnotatedmotif_strength=7, inner_reads=15, outer_validated=10, cross_validation=10, novelty=0, inner_fraction=3, recurrence=15, mappability=10 UCSC ↗ IGV*
SRSF10 — 1 candidate(s) across 1 U12 intron(s)
SRSF10;Homo_sapiens_1_23975081_23977910_R — 1 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr1:23975269-23977316-GT-AGU2-type79Probable Twintron15 (7,8) / 0 (0,0)142 / 80.096 / 0.000NoNovelmotif_strength=6, inner_reads=15, outer_validated=10, cross_validation=10, novelty=10, inner_fraction=3, recurrence=15, mappability=10 UCSC ↗ IGV*
TMEM258 — 2 candidate(s) across 1 U12 intron(s)
TMEM258;Homo_sapiens_11_61789922_61790492_R — 2 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr11:61789991-61790422-GT-AGU2-type67Possible Twintron18 (4,14) / 0 (0,0)989 / 3100.018 / 0.000NoAnnotatedmotif_strength=7, inner_reads=15, outer_validated=10, cross_validation=10, novelty=0, inner_fraction=0, recurrence=15, mappability=10 UCSC ↗ IGV*
chr11:61789991-61790374-GT-AGU2-type66Possible Twintron9 (9,0) / 0 (0,0)989 / 3100.009 / 0.000NoAnnotatedmotif_strength=18, inner_reads=10, outer_validated=10, cross_validation=10, novelty=0, inner_fraction=0, recurrence=8, mappability=10 UCSC ↗ IGV*
TRAPPC2L — 1 candidate(s) across 1 U12 intron(s)
TRAPPC2L;Homo_sapiens_16_88858792_88859662_F — 1 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr16:88859444-88859572+GT-AGU2-type50Possible Twintron3 (0,3) / 0 (0,0)398 / 860.007 / 0.000NoAnnotatedmotif_strength=7, inner_reads=5, outer_validated=10, cross_validation=10, novelty=0, inner_fraction=0, recurrence=8, mappability=10 UCSC ↗ IGV*
ZDHHC16 — 3 candidate(s) across 1 U12 intron(s)
ZDHHC16;Homo_sapiens_10_97452924_97455601_F — 3 candidate(s)
CoordinatesStrandMotifClassEvidence ScoreTierInner reads (case/ctrl, per-rep)Outer reads (case/ctrl)Inner fraction (case/ctrl)Differential?AnnotationScore breakdownLinks
chr10:97453664-97454713+GT-AGU2-type80Probable Twintron287 (150,137) / 28 (14,14)53 / 80.844 / 0.778NoAnnotatedmotif_strength=10, inner_reads=15, outer_validated=10, cross_validation=10, novelty=0, inner_fraction=10, recurrence=15, mappability=10 UCSC ↗ IGV*
chr10:97453664-97453798+GT-AGU2-type79Probable Twintron1467 (827,640) / 12 (0,12)53 / 80.965 / 0.600YesAnnotatedmotif_strength=9, inner_reads=15, outer_validated=10, cross_validation=10, novelty=0, inner_fraction=10, recurrence=15, mappability=10 UCSC ↗ IGV*
chr10:97453847-97454713+GT-AGU2-type78Probable Twintron1111 (641,470) / 22 (14,8)53 / 80.954 / 0.733YesAnnotatedmotif_strength=8, inner_reads=15, outer_validated=10, cross_validation=10, novelty=0, inner_fraction=10, recurrence=15, mappability=10 UCSC ↗ IGV*