Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaaccctaataaaaaatacaccttctatttttgttgtctacaatccattcaggtctatgtgaaaaaccattcattaagtagatttttcatttgatttttatgatttgggtctgattagGTGGTCTCGGATTGCAAAATATTTACCGGGAAGAACAGACAACGAGATTAAGAACTATTGGCATTCCTATCTGAAGAAGAGATGGCTCAAATCTCAACCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G52260.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G52260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G38110.1 (Glycine max), 3'ss of exon 2
gtaagaaaccctaataaaaaatacaccttctatttttgttgtctacaatccattcaggtctatgtgaaaaaccattcattaagtagatttttcatttgatttttatgatttgggtctgattagGTGGTCTCGGATTGCAAAATATTTACCGGGAAGAACAGACAACGAGATTAAGAACTATTGGCATTCCTATCTGAAGAAGAGATGGCTCAAATCTCAACCA
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--------------cagaaattcaacactactttccagtaaaataaaatttg--cagtgtaatttcttcctcttttaattaag---actgctga---gagcaacttgaattatat-tggctagGTGGTCACAGATATCACAGCATTTGCCAGGAAGGACAGACAATGAGATTAAAAACTATTGGCATTCATATTTGAAAAAGAGAGTGGCCAAAGCTAAGGAA
upper sequence: AT5G52260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G29710.1 (Glycine max), 3'ss of exon 2
gtaagaaaccctaataaaaaatacaccttctatttttgttgtctacaatccattcaggtctatgtgaaaaaccattcattaagtagatttttcatttgatttttatgatttgggtctgattagGTGGTCTCGGATTGCAAAATATTTACCGGGAAGAACAGACAACGAGATTAAGAACTATTGGCATTCCTATCTGAAGAAGAGATGGCTCAAATCTCAACCA
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--actttccggtaaaataaaatattgcagtgtaatttctttcctataatttcttccacttttaattaaga-----ctgctgagagca------acttgaattatat----------tggctagGTGGTCACGGATATCACAGCATTTGCCTGGAAGGACAGACAATGAGATTAAAAACTATTGGCATTCATATTTGAAAAAGAGAGTGGCCAAAGCTAAGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaccattcattaagtagatttttcatttgatttttatgatttgggtctgattagGTGGTCTCGGATTGCAAAATATTTACCGGGAAGAACAGACAACGAGATTAAGAACTATTGGCATTCCTATCTGAAGAAGAGATGGCTCAAATCTCAACCA
atttgat putative branch site (score: 5)
attaagtagatttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaaccctaataaaaaatacaccttctatttttgttgtctacaatccattcaggtctatgtgaaaaaccattcattaagtagatttttcatttgatttttatgatttgggtctgattagGTGGTCTCGGATTGCAAAATATTTACCGGGAAGAACAGACAACGAGATTAAGAACTATTGGCATTCCTATCTGAAGAAGAGATGGCTCAAATCTCAACCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG