Sequence
atgc intronic sequence ATGC exonic sequencegcatgtggttgctcttgcatttagttgtgaattaaattctgtatcacttaattttccaagtgggtatctaaccattttcgtatgcccatttatcagACAGCCCTTGTCGTTCCACATCTCTGCGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTACTTTTTCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G01270.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G01270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G42790.1 (Glycine max), 3'ss of exon 4
gcatgtggttgctcttgcatttagttgtgaattaaattctgtatcacttaattttccaagtgggtatctaaccattttcgtatgcccatttatcagACAGCCCTTGTCGTTCCACATCTCTGCGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTACTTTTTCAA-
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---tgtgg--gtttatgtatattactgcattttttaatttttttttctaaatattcatgatagagacactaatatattcttttc----tttattagaCGGCCAATGCTGTCCCAGTCCTATGTGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTGTTTTTTCAAG
upper sequence: AT5G01270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G17940.1 (Glycine max), 3'ss of exon 4
gcatgtggttgctcttgcatttagttgtgaattaaattctgtatcacttaattttccaagtgggtatctaaccattttcgtatgcccatttatcagACAGCCCTTGTCGTTCCACATCTCTGCGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTACTTTTTCAA
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gtttatgtatattattgcaatt--tttttaattttattttcta------aatattcttgatagagactttagtatattcttttc----tttattagACAGCCAATGCTGTCCCAGTCCTATGTGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTGTTTTTTCAA
upper sequence: AT5G01270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g02130.t01 (Vitis vinifera), 3'ss of exon 4
gcatgtggttgctct-tgcatttagttgtgaattaaattctgtatcacttaattttccaagtgggtatctaaccattttcgtatgcccattt-atcagACAGCCCTTGTCGTTCCACATCTCTGCGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTACTTTTTCAA
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gtaataaattatgctgtctataagattgataattgaaaattgttaca-ttatttcatcaagactggcactaatgtgatacatatatatttttgaatagACAACAAATCCTGTTCCAATCCTATGTGTAGCAAGAAATGTTGCGTGCAATGTCAGGGCGGGTTTTTTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcacttaattttccaagtgggtatctaaccattttcgtatgcccatttatcagACAGCCCTTGTCGTTCCACATCTCTGCGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTACTTTTTCAA
atctaac putative branch site (score: 2)
cccattt putative PPT
ttaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatgtggttgctcttgcatttagttgtgaattaaattctgtatcacttaattttccaagtgggtatctaaccattttcgtatgcccatttatcagACAGCCCTTGTCGTTCCACATCTCTGCGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTACTTTTTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA