Sequence
atgc intronic sequence ATGC exonic sequence...gagaatgttaagatgttgccccattcaaggtcacatgtataagttgatttaatcatgtaatgtccatgtcacttaacatgttaggtattctcctctgtagGTTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGTGCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g32610.4 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G059671_T01 (Zea mays), 3'ss of exon 7
gagaatgttaagatgttgccccattcaaggtc-acatgtataagttgatttaatcatgtaatgtccat--gtcacttaacatgttaggtattctcctctgtagGTTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGTGCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAA
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---atacttaagatgttgcctcattgaagaactatatatatgcattgttgtagcattgtgatgttcatttatcatttactgtattgaggattcttctttgtagGTTGCAATTATGAGAAGTTTGCGACATCCGAACATTGTTCTTCTTATGGGTGCTGTCACTCAGCCACCTAACCTTTCAATTGTGACTGAATACCTATCAA
upper sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA13G21480.1 (Glycine max), 3'ss of exon 8
gagaatgttaagatgttgccccattcaaggtcacatgtataagttgatttaatcatgtaatgtccatgtcacttaacatgttaggtattctcctctg-tagGTTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGTGCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAA
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--gtatgcttgaaagttgaaa-gtcctaaccctgctttatttgctt-tttagatattttcttgctgt-ttatttgatctgtgttttcccttctcttggtagGTTGCAATAATGAAACGTTTACGGCATCCAAACATTGTTTTGTTTATGGGGGCAGTCACTCAGCCTCCTAACTTATCAATTGTCACGGAATATTTATCTA
upper sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA10G07610.1 (Glycine max), 3'ss of exon 10
gagaatgttaagatgttgccccattcaaggtcacatgtataagttgatttaatcatgtaatgtccatgtcacttaacatgttaggtattctcctctgtagGTTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGTGCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAA
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-----------------gtatgcttgaaagtccta-accctgctttatttgctttttagatatttgc-ttactgtttatttgatctgtgtttat---tagGTTGCAATAATGAAACGTTTACGGCATCCAAACATTGTTTTGTTTATGGGGGCAGTCACTCAGCCTCCTAACTTATCAATTGTCACAGAATATTTATCAA
upper sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv13s0074g00430.t01 (Vitis vinifera), 3'ss of exon 8
---------------------------------------------------gagaatgttaagatg--ttgcccc--attcaaggtcacatg-tataagttgatttaatcat-gtaatgtccatgtcacttaacatgttaggtattctcctctgtagGTTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGTGCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAA
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gtacttagctacttcctgctatttccaaataaatcctcttttaatgcatgaataaatgtctagttgaactgtttttgggttgggaaaatattctgtgtctcatcttttttattatcattttaagtctgcagttcatctcatgtatt-ttattggcagGTTGCAATCATGAAACGCTTGAGGCATCCAAACATTGTTCTCTTTATGGGTGCTGTTACTCAGCCTCCACATCTGTCCATAGTTACAGAATACTTATCAAMapped 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|29665412|gb|CB661687.1|CB661687EST: TGATGGAGCAAGACTTCCACCCAGAGCGTCTCAAAGAATTTCTTAGGGAG GTTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGT
genomic: TGATGGAGCAAGACTTCCACCCAGAGCGTCTCAAAGAATTTCTTAGGGAGgtataacatc ... tcctctgtagGTTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGT
EST:
gi|29664339|gb|CB660614.1|CB660614EST: TGATGGAGCAAGACTTCCACCCAGAGCGTCTCAAAGAATTTCTTAGGGAG GTTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGT
genomic: TGATGGAGCAAGACTTCCACCCAGAGCGTCTCAAAGAATTTCTTAGGGAGgtataacatc ... tcctctgtagGTTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttaatcatgtaatgtccatgtcacttaacatgttaggtattctcctctgtagGTTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGTGCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAA
acttaac putative branch site (score: 3)
tattctcctct putative PPT
atgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gagaatgttaagatgttgccccattcaaggtcacatgtataagttgatttaatcatgtaatgtccatgtcacttaacatgttaggtattctcctctgtagGTTGCAATTATGAAAAGTCTGCGCCATCCAAACATTGTCCTTTTTATGGGTGCTGTTACTCAGCCACCAAAACTTTCGATTGTGACAGAATATCTATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT