Sequence
atgc intronic sequence ATGC exonic sequence...actttcagacttcattgtcactgtgctctgctggttctatgtattttaatagtttttaaccatattttttcctaaacaaatgtttcatccttcttcatagGCATGTCTGGATTCAGGCTTCTTCTATGTGGTGGATCATGGAATAAGCCAGGAGTTAATGGATGATGTTTTTGCCCAGAGCAAGAAATTCTTTGACCTTC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g09300.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G147882_T01 (Zea mays), 3'ss of exon 1
--actttcagacttcattgtcactgtgctctgctggttctatgtattttaatagtttttaaccatattttttcctaaacaaatgtttcatccttcttcatagGCATGTCTGGATTCAGGCTTCTTCTATGTGGTGGATCATGGAATAAGCCAGGAGTTAATGGATGATGTTTTTGCCCAGAGCAAGAAATTCTTTGACCTTC
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gaagtttccatgtttgacagctcaaatctttgttggctctgttcgtaa-aaaagctctgtatcatactcttcttcctgaaaacaatgt-ttttatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAAGAGTTCATGGATGAAGTTTTTGCCCAGAGCAAGAAGTTCTTTGACCTTC
upper sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA01G01170.2 (Glycine max), 3'ss of exon 1
actttcagacttcattgtcac-tgtgctctgctggttctatgtattttaatagtttttaaccatattttttcctaaacaaatgtt-------tcatccttcttcatagGCATGTCTGGATTCAGGCTTCTTCTATGTGGTGGATCATGGAATAAGCCAGGAGTTAATGGATGATGTTTTTGCCCAGAGCAAGAAATTCTTTGACCTTC
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-gtttttgcttcctcttttacatgatttgtcacaattcactttgtttt--tagaccatgatctttttttatgtcatcttaatgttgttgtttttttgctttgttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAGGAATTCATGGACGAGGTTTTTGCGCAGAGCAAGAAGTTCTTCTCTCTTC
upper sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G08470.1 (Glycine max), 3'ss of exon 1
actttcagacttcattgtcactgtgctctgctggttctatgtattttaatagtttttaaccatattttttcctaaacaaatgtttcatccttcttcatagGCATGTCTGGATTCAGGCTTCTTCTATGTGGTGGATCATGGAATAAGCCAGGAGTTAATGGATGATGTTTTTGCCCAGAGCAAGAAATTCTTTGACCTTC
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-------gtttttgcttcctcaattcact--ttgttttttgaacc---atgattttttatcatgt-----catattaatgttttttgtttttgtttttagGCATGTTTGGATTCCGGTTTTTTCTACGTTGTCAATCATGGAATAAGCCAGGAATTCATGGAAGAGGTTTTTGCACAGAGCAAGAAATTCTTCTCTCTTC
upper sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 1
---------actttcagacttcattgtcactgtgctctgctggttctatgtatttt---aatagtttttaaccatattttttcctaaacaaatgtttcatccttcttcatagGCATGTCTGGATTCAGGCTTCTTCTATGTGGTGGATCATGGAATAAGCCAGGAGTTAATGGATGATGTTTTTGCCCAGAGCAAGAAATTCTTTGACCTTC
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gtgcgttttgtatccaagctcctccgtttggttgccgagaaaggagaaagaaggaagggaagggagaaagagaagaaaactttttaatcttagtttgtgctttgtggttcagGCATGTTTGGATTCTGGATTCTTCTATGTGATCAATCACGGAATCAGCCAGGAATTTATGGACGAGGTTTTCGCCCAAAGCAAAAGGTTTTTCACTTTGCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|29674320|gb|CB670595.1|CB670595EST: TCAGCCTGGGTGACCCGGACACCAAGAAATCGGTCGCGCTCCTCAAGCAG GCATGTCTGGATTCAGGCTTCTTCTATGTGGTGGATCATGGAATAAGCCAG
genomic: TCAGCCTGGGTGACCCGGACACCAAGAAATCGGTCGCGCTCCTCAAGCAGgtcttcttcc ... ttcttcatagGCATGTCTGGATTCAGGCTTCTTCTATGTGGTGGATCATGGAATAAGCCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatagtttttaaccatattttttcctaaacaaatgtttcatccttcttcatagGCATGTCTGGATTCAGGCTTCTTCTATGTGGTGGATCATGGAATAAGCCAGGAGTTAATGGATGATGTTTTTGCCCAGAGCAAGAAATTCTTTGACCTTC
tcctaaa putative branch site (score: 2)
tgtttcatccttcttc putative PPT
tttttaaccatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actttcagacttcattgtcactgtgctctgctggttctatgtattttaatagtttttaaccatattttttcctaaacaaatgtttcatccttcttcatagGCATGTCTGGATTCAGGCTTCTTCTATGTGGTGGATCATGGAATAAGCCAGGAGTTAATGGATGATGTTTTTGCCCAGAGCAAGAAATTCTTTGACCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA