Sequence
atgc intronic sequence ATGC exonic sequence...attgtagttcagagcattttgtgattcaattataaaattatactatatggtttcctcttgcttctaacaatgcccctccccttatttgggtgatctacagATGTGTGGAAGGGCTGGGCGTCCACCATTTGATGATACTGGAACAATTATAATCATGACAAGAAGAGAGACA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g40450.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g40450.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G346278_T02 (Zea mays), 3'ss of exon 8
----attgtagttcagagcattttgtgattcaattataaaattatactatatggtt-tcctcttgcttctaacaatgcccctccccttatttgggtgatctacagATGTGTGGAAGGGCTGGGCGTCCACCATTTGATGATACTGGAACAATTATAATCATGACAAGAAGAGAGACA
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taacgtaacacatttaataatttcaattttcaaaaatataaaaatactatatgactatcctcttgtttttgagaaagtttctat-----ttcgggtgatccacagATGTGTGGGAGGGCTGGACGTCCACCATTCGATGATACTGGAACAATTATAATCATGACAAGAAAAGAAACG
upper sequence: LOC_Os02g40450.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA16G07850.1 (Glycine max), 3'ss of exon 11
attgtagttcagagcattttgtgattcaattataaaattatactatatggtttcctcttgcttcta-acaatgcccctccccttatttgggtgatcta-----cagATGTGTGGAAGGGCTGGGCGTCCACCATTTGATGATACTGGAACAATTATAATCATGACAAGAAGAGAGACA
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------aatcacactatgtctacctaatatagtaggggcagggaaaatcaatgcttgacttttccatgtaatgtatatcatttgaggtaaaacatttatggtacagATGTGTGGAAGGGCAGGCCGACCACCATTTGATGATACAGGCATGGTTATAATCATGACAAGGAGAGAAACG
upper sequence: LOC_Os02g40450.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv14s0066g00880.t01 (Vitis vinifera), 3'ss of exon 11
-----attgtagttcagagcattttgtgattcaattataaaattatactatatggtttcctct-tgctt--ctaacaatgcccctccccttatttgggtgatctacagATGTGTGGAAGGGCTGGGCGTCCACCATTTGATGATACTGGAACAATTATAATCATGACAAGAAGAGAGACA
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ctatgcctagggcccaaagaaaaaaattatcctagtataag--catgtt---tgttttcctcaatactttgcttatcatgtcattaagtttgtct---taaaatgcagATGTGTGGGAGGGCAGGTCGTCCACCATTTGAGGATACGGGAATGGCTATAATCATGACAAGACGAGAAACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatggtttcctcttgcttctaacaatgcccctccccttatttgggtgatctacagATGTGTGGAAGGGCTGGGCGTCCACCATTTGATGATACTGGAACAATTATAATCATGACAAGAAGAGAGACA
ttctaac putative branch site (score: 1)
ttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgtagttcagagcattttgtgattcaattataaaattatactatatggtttcctcttgcttctaacaatgcccctccccttatttgggtgatctacagATGTGTGGAAGGGCTGGGCGTCCACCATTTGATGATACTGGAACAATTATAATCATGACAAGAAGAGAGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - -tgattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttct