Sequence
atgc intronic sequence ATGC exonic sequence...atttattgtttttatcttgtgttgctatatatgctttagttgcttacataaaattgattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
Basic information
species | Oryza sativa |
transcript | 13113.m00244 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 3
-----atttattgtttttatcttgtgttgctatatatgctttagttgcttacataaaattgattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
|| || || | || ||| |||| ||||| | ||| | || | || | | | | | ||| | |||| || ||| | ||||| |||||||||||||||||||||||||||||||| ||||| || |||||||| ||||| ||||| || ||||||| || ||||||||||||||||| |
cttggatgaatagtgcgctttttagtctgccatatttgcttaatttgaatgcaactactttgtctctactgt-taaaactgggatgtacactat----ttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC
upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G10470.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------------------------atttattgtttttatcttgtgttgctatatatgctttagttgctta--cataaaattgat-tgccattttctaattttaatatgtgcaatatgaactgat-cagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
| | |||| | | | || | || | | ||| | ||||| | || || || || || ||| | | || | |||| || ||| | |||||||| ||||| |||||||| || || || || || |||||||||||||| ||| |||| |||||||| || || || || || |
gtaatctatgatggatacattatatagggtctatagttgcatcttttaagggcataatgtgtattcagtttactagtctaaggtgcaagattttgttgtccatggcctctcaattttctgctacttgattgtgaaatttgtgctttggattttacttctataattagcatccttatgtgttgtagGTGGAGCAGCTACACAAGATATTCAAACTATGTGGTTCTCCTTCTGATGAATATTGGAAAAAGTCAAAGTTGCCTCATGCTACCATTTTTAAGCCCCAAC
upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------------------atttattgtttttatcttgtgttgctatatatgctttagttgctta--cataaaatt---gattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
| | ||||| | | | | ||| | || | | ||| | ||||| | || ||||| | |||| | | | ||||||| ||| | |||||||| ||||| |||||||| || || || || || |||||||||||||| ||| ||||||||||||| || || || || || |
gtaatctctatgatggatacactatatagggcttaatgtctatagttgcatcttttaagggcttaatgtgtattcagtttactagtctaaggtgcaaggttttgttgtcg-atggcttctcaattttctgctacttgattgtgaaatttgtgcttcagattttactgctataattagcatcctttatgtgttatagGTAGAGCAGCTACACAAGATATTCAAACTATGTGGTTCTCCTTCTGACGAATATTGGAAAAAGTCAAAGTTGCCACATGCTACCATTTTTAAGCCCCAAC
upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G40330.1 (Glycine max), 3'ss of exon 3
atttattgtttttatcttgtgttgctatatatgctttagttgcttacataaaattgat-tgccattttctaattttaatatgtgcaa--tatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
||| | || ||| || | |||| | | |||| | || || | | | |||| | | | | || | | | |||| ||||| ||||||||||| | ||| |||||||| || || ||||| ||||||||||| ||||| ||| |||| ||||||| || ||||| |
-tttgcatggtatagtttgaatt-taagatata-tcaaattgcatttatttgatgattataagaaaacacaattagattttttctaagtcttcactcgcatagGTGGAACAATTGCACAAGATATACAAACTATGTGGTTCACCTTCAGATGAGTATTGGAAGAAGTCAAAGTTGCCTAATGCTACCTCGTTTAAACCACGAG
upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S89_168V6.1 (Physcomitrella patens), 3'ss of exon 4
atttattgtttttatcttgtgttgctatatatgcttta-gttgctta---cataaaattga--ttgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
|||| | | || | || | ||| || | | |||| | ||| ||| | | | | ||| | |||| ||||| ||||||||||| || ||| | || || ||||| || |||||||||||||| ||||| || |||| ||||| || |||||||| ||||| |
-tttacctccggcgtttggtaacagattgtagggtttgtagggcccaagttgtggggttgaggccgtaattggaggggtttggcacattct-tgtgatgt----agGTGGAACAATTGCACAAGATCTTTAAGTTGTGCGGTTCCCCATCCGAGGAGTATTGGAAGAAGTCGAAATTGCCGCATGCGACGATATTCAAGCCTCAAC
upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S271_84V6.1 (Physcomitrella patens), 3'ss of exon 3
atttattgtttttatcttgtgttgctatatatgctttagttgcttacataaaattgattgccattttctaattttaatatgtgcaatatgaac---tgat--cagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
| | | |||| || || | | || | || ||| | | | | | | || ||| || | ||||| |||||| ||||||||||||||||| | || || || || || |||||||||||||| ||||| |||||||| || || || |||||||| |||||||
--cagtcgcggcgagtgtgtggtgagtgatggggggggggtgtgtg---gaatgtgaggcgcgtgctgaagtggggttggttgtggcatgggtgtgtggtggcagGTGGAACAGCTGCACAAGATTTTCAAGTTGTGCGGTTCGCCGTCGGAGGAGTATTGGAAGAAGTCGAAGCTGCCGCACGCGACGATATTCAAGCCTCAGC
upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S428_20V6.1 (Physcomitrella patens), 3'ss of exon 3
----atttattgtttttatcttgtgttgctatatatgc-tttagttgcttacataaaattgattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
| ||| | ||| || |||| ||| | | | | || ||| | | | ||| || | | |||||| || ||||| ||||| | || ||||| |||||| |||| || || || || |||||||||||||||||||| || |||| || ||||| |||||||| ||||| |
ttttccctcttgcggtggctacagattggagtagatgcgtttgggttgtaagatggtatttaat-ttagagaacgggtttggtacg-ggaatatgg--tgg-cagGTGGAACAACTTCATAAGATCTTCAAGTTATGCGGTTCTCCGTCCGAGGAGTATTGGAAAAAGTCAAAATTGCCGCACGCTACGATATTCAAGCCTCAAC
upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ35595 (Selaginella moellendorffii), 3'ss of exon 2
atttattgtttttatcttgtgttgctatatatgctttagttgcttacataaaattgattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
||| | || ||| || | | || || | || ||| | | ||| | || ||||| || || || ||||||||||| |||||||||||||| || || || |||||||||||||| ||||| || || || ||||| || || || || ||||
--------------------------gtatgctcgttggtt-tttgttttacgatgtttagtaacgcctgcctttcttct------tattgatcgaacagGTGGAGCAATTACACAAGATTTTTAAGCTATGTGGCTCGCCATCGGAAGAGTATTGGAAAAAATCCAAACTTCCTCACGCTACGATTTTTAAGCCGCAGC
upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ24328 (Selaginella moellendorffii), 3'ss of exon 4
atttattgtttttatcttgtgttgctatatatgctttagttgcttacataaaattgattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
||| | || ||| ||| | | || || | || ||| | || | || ||||| || || || ||||||||||| |||||||||||||| || || || |||||||||||||| ||||| || || || ||||| || || || || ||||
--------------------------gtatgctccttggtt-tttattttacgatgtttagtaacgcctgcctttctt---------attgatcgaacagGTGGAGCAATTACACAAGATTTTTAAGCTATGTGGCTCGCCATCGGAAGAGTATTGGAAAAAATCCAAACTTCCTCACGCTACGATTTTTAAGCCGCAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acataaaattgattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
attttctaattttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttattgtttttatcttgtgttgctatatatgctttagttgcttacataaaattgattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC