Sequence
atgc intronic sequence ATGC exonic sequence...ctaattaaacaacctacatatatatcataagatatacaaatatgtgtatgttttcataattagcttatgtatgtttaatcatagatatatgtatatgcagCTATGGCGGCGATAGGAGAGAAAGAGTGGTACTTCTATGTGCCAAGAGATCGGAAATATAGAAATGGAGATAGACCGAACCGAGTAACGACTTCAGGATA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G02450.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G02450.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g66490.1 (Oryza sativa), 3'ss of exon 1
ctaattaaacaacctacatatatatcataagatatacaaatatgtgtatgttttcataattagcttatgtatgtttaatcatagatatatgtatatgcagCTATGGCGGCGATAGGAGAGAAAGAGTGGTACTTCTATGTGCCAAGAGATCGGAAATATAGAAATGGAGATAGACCGAACCGAGTAACGACTTCAGGATA
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gtaattagttagttactctccgcctcg---atcatatcaatcgat---tgatttaggaattga---gcatctaattaacaa--gctcgatgggggtgcagCAATGGCGGCGATAGGGGAGAAGGAGTGGTTCTTCTACGTGCCTCGGGACAGGAAGTACAGGAACGGGGACCGGCCGAACCGGGTGACGGCGTCGGGGTA
upper sequence: AT2G02450.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G00650.1 (Glycine max), 3'ss of exon 1
ctaattaaacaacctacatatatatcataagatatacaaatatgtgtat-gttttcataattagcttatgtatgtttaatcatagatatatgt-atatgcagCTATGGCGGCGATAGGAGAGAAAGAGTGGTACTTCTATGTGCCAAGAGATCGGAAATATAGAAATGGAGATAGACCGAACCGAGTAACGACTTCAGGATA
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-ctcttacgcatac-atatagatatttttatttcaattgagatgtttattgtgcacacggattgttgaattttaatcaagtatgtgtgtgtgttatgagcagCCTTGGCAGCTATTGGTGAGAAGGAGTGGTACTTCTATGTGCCCAGAGATAGGAAGTATCGCAACGGTGATCGTCCCAATCGTGTTACTACCTCTGGGTA
upper sequence: AT2G02450.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G40140.1 (Glycine max), 3'ss of exon 1
---ctaattaaacaacctacatatatatcata-agatatacaaatatgtgtatgttttcataattagcttatgtatgtttaatcatagatatatgtatatgcagCTATGGCGGCGATAGGAGAGAAAGAGTGGTACTTCTATGTGCCAAGAGATCGGAAATATAGAAATGGAGATAGACCGAACCGAGTAACGACTTCAGGATA
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cgcatacatataaggtggtcatgtgcaatatatatatatatatatatattcatattttgtt--tcaattcacggattctatgtcttgaattt-tg-atgagcagCCTTGGCAGCTATTGGTGAGAAGGAGTGGTACTTCTATGTGCCCAGAGATAGGAAGTATCGCAACGGTGATCGTCCCAATCGCGTTACTACCTCTGGGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatgttttcataattagcttatgtatgtttaatcatagatatatgtatatgcagCTATGGCGGCGATAGGAGAGAAAGAGTGGTACTTCTATGTGCCAAGAGATCGGAAATATAGAAATGGAGATAGACCGAACCGAGTAACGACTTCAGGATA
gtttaat putative branch site (score: 4)
tatgtttaatcataga TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaattaaacaacctacatatatatcataagatatacaaatatgtgtatgttttcataattagcttatgtatgtttaatcatagatatatgtatatgcagCTATGGCGGCGATAGGAGAGAAAGAGTGGTACTTCTATGTGCCAAGAGATCGGAAATATAGAAATGGAGATAGACCGAACCGAGTAACGACTTCAGGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - aaacaac
- - - - - - - -acatata
- - - - - - - - - - - -atcataa
- - - - - - - - - - - - - - - - -atacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatcata