Sequence
atgc intronic sequence ATGC exonic sequencegtacacaccaatcatggatatcctacacatgatcagcttgagatagcatccaatgcatcctttgtcattgctcttgctaagttgctattgcatttcccttctttttctttttcttgaggaaatagtacattgattcatgttgcctaagagagaaaaaaaatgagtttaacaagaattgcgtcgttttcagGTCAAAAGTGAGCTGCCAAGTACTTTCAAAGCCTTTCGGTTTCAGCAGCACAGGTGGTCATGTGGGCCGGCAAACCTGTTCAGGAAGATGCTGATGGAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g09930.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g09930.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G105631_T05 (Zea mays), 3'ss of exon 1
gtacacaccaatcatggatatcctacacatgatcagcttgagatagcatccaatgcatcctttgtcattgctcttgctaagttgctattgcatttcccttctttttctttttcttgaggaaatagtacattga----ttcatgttgcctaagagagaaaaaaaatgagtttaacaagaat-tgcgt---cgtttt--------cagGTCAAAAGTGAGCTGCCAAGTACTTTCAAAGCCTTTCGGTTTCAGCAGCACAGGTGGTCATGTGGGCCGGCAAACCTGTTCAGGAAGATGCTGATGGAGA
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---------------------------------------------------------------------------------------------------------tttttttgttgagacgatggcgcattcagaatttcagactgcaca-gtgagaagaaagtgaaattcacccatgatgtgcctgcccgatttgattcctgcagGTGAAAAGCGAGCTGCCGAGTACCTTCAAGGCCTTCCGGTTCCAGCAGCACAGGTGGTCGTGCGGCCCGGCGAACCTGTTCAGGAAGATGCTCATGGAGA
upper sequence: LOC_Os02g09930.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G19490.1 (Glycine max), 3'ss of exon 5
gtacacaccaatcatggatatcctacacatgatcagcttgagatagcatccaatgcatcctttgtcattgctcttgctaagttgctattgcatttcccttctttttctttttcttgaggaaatagtacattgattcatgttgcctaagagagaaaaaaaatgagtttaacaagaattgcgtcgtttt-cagGTCAAAAGTGAGCTGCCAAGTACTTTCAAAGCCTTTCGGTTTCAGCAGCACAGGTGGTCATGTGGGCCGGCAAACCTGTTCAGGAAGATGCTGATGGAGA
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-------------------------------------gttaatcaatgctccatcta-cttacctattagtacttccaaagttaaca----attaacggagaatatgaatgacatatgattatgaattatcatttca-attttcttatactaagtaatggtgccttttttttaaatggtaactttatatagGCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCACAGATGGTCATGTGGTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGA
upper sequence: LOC_Os02g09930.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 5
gtacacaccaatcatggatatcctacacatgatcagcttgagatagcatccaatgcatcctttgtcattgctcttgctaagttgctattgcatttcccttctttttctttttcttgaggaaatagtacattgattcatgttgcctaagagagaaaaaaaatgagtttaacaagaattgcgtcgttttc-----agGTCAAAAGTGAGCTGCCAAGTACTTTCAAAGCCTTTCGGTTTCAGCAGCACAGGTGGTCATGTGGGCCGGCAAACCTGTTCAGGAAGATGCTGATGGAGA
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-----------------------------------------------------------------------------------------------tcattttacctttttaagaagtaaagatattttgttattacttgttgaaaaattggtatacatcataaatatatgagtcctttttactttctttgcatagGTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACATAGATGGTCTTGTGGACCTGCAAATCTCTTTAGGAAAATGGTTATGGAGA
upper sequence: LOC_Os02g09930.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 5
gtacacaccaatcatggatatcctacacatgatcagcttgagatagcatccaatgcatcctttgtcattgctcttgctaagttgctattgcatttcccttctttttctttttcttgaggaaatagtacattgattcatgttgcctaagagagaaaaaaaatgagtttaacaagaattgcgtcgttttcagGTCAAAAGTGAGCTGCCAAGTACTTTCAAAGCCTTTCGGTTTCAGCAGCACAGGTGGTCATGTGGGCCGGCAAACCTGTTCAGGAAGATGCTGATGGAGA
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---------------------------------------------------------------------------------------gtacatttaaataaatgtctttaagttggggaccatttcatttaaattgatagcttcttag------------ttgatttaacg------gcttcatcaatagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACACAGGTGGTCCTGTGGTCCAGCCAATTTGTTCAGAAAAATGGTGATGGAGA
upper sequence: LOC_Os02g09930.2 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ17366 (Selaginella moellendorffii), 3'ss of exon 5
gtacacaccaatcatggatatcctacacatgatcagcttgagatagcatccaatgcatcctttgtcattgctcttgctaagttgctattgcatttcccttctttttctttttcttgaggaaatagtacattgattcatgttgcctaagagagaaaaaaaatgagtttaacaagaattgcgtcgttttcagGTCAAAAGTGAGCTGCCAAGTACTTTCAAAGCCTTTCGGTTTCAGCAGCACAGGTGGTCATGTGGGCCGGCAAACCTGTTCAGGAAGATGCTGATGGAGA
|||| || | | || ||| ||| || ||| | | || | || |||||| || | ||||| || ||||| || || |||| ||| | |||||||||||| ||||||||||||||||| ||||| || |||||||| | || |
----------------------------------------------------------------------------------------------------------------------------gtacgtttagtaccttttccttgcttagagtaag--------taatatggtttctctgtttctcagGTGAAGAACGAGCTTCCCAGTACATTTAAGGCCTATCGTTATCAGCAGCACAGATGGTCATGTGGGCCGGCTAACCTCTTTCGGAAGATGATTCCGGGGG
upper sequence: LOC_Os02g09930.2 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ35401 (Selaginella moellendorffii), 3'ss of exon 5
gtacacaccaatcatggatatcctacacatgatcagcttgagatagcatccaatgcatcctttgtcattgctcttgctaagttgctattgcatttcccttctttttctttttcttgaggaaatagtacattgattcatgttgcctaagagagaaaaaaaatgagtttaacaagaattgcgtcgttttcagGTCAAAAGTGAGCTGCCAAGTACTTTCAAAGCCTTTCGGTTTCAGCAGCACAGGTGGTCATGTGGGCCGGCAAACCTGTTCAGGAAGATGCTGATGGAGA
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----------------------------------------------------------------------------------------------------------------------------gtacgtttggtaccttttccttgcttagagtaag--------taatatggtttctctgtttctcagGTGAAGAACGAGCTTCCCAGTACATTTAAGGCCTATCGTTATCAGCAGCACAGATGGTCATGTGGGCCGGCTAACCTCTTTCGGAAGATGATTCCGGGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgttgcctaagagagaaaaaaaatgagtttaacaagaattgcgtcgttttcagGTCAAAAGTGAGCTGCCAAGTACTTTCAAAGCCTTTCGGTTTCAGCAGCACAGGTGGTCATGTGGGCCGGCAAACCTGTTCAGGAAGATGCTGATGGAGA
gtttaac putative branch site (score: 3)
tcgttttc putative PPT
aaaaaaaatgagttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacacaccaatcatggatatcctacacatgatcagcttgagatagcatccaatgcatcctttgtcattgctcttgctaagttgctattgcatttcccttctttttctttttcttgaggaaatagtacattgattcatgttgcctaagagagaaaaaaaatgagtttaacaagaattgcgtcgttttcagGTCAAAAGTGAGCTGCCAAGTACTTTCAAAGCCTTTCGGTTTCAGCAGCACAGGTGGTCATGTGGGCCGGCAAACCTGTTCAGGAAGATGCTGATGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA