Sequence
atgc intronic sequence ATGC exonic sequencegtaagctactacccggacggccaggctccttggaaacgtacctagctacaaattaacttctcttttactgttagatcagatcagacaacttaagttggttaattaagtgctaattgctgctcttcacctttttttaatttaaaccagAGGGTATCTGGCAGACAGGAACAAACCAATCATCTTCTCGATGGCAAGGCTTGATAAGGTAAAAAACATAACTGGGCTTGTGGAGTGGTATGGCCAGAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os04g17650.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g17650.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G060659_T02 (Zea mays), 3'ss of exon 10
gtaagctactacccggacggccaggctccttggaaacgtacctagctacaaattaacttctcttttactgttagatcagatcagacaacttaagttggttaattaagtgctaattgctgctcttcacctttttttaatttaaaccagAGGGTATCTGGCAGACAGGAACAAACCAATCATCTTCTCGATGGCAAGGCTTGATAAGGTAAAAAACATAACTGGGCTTGTGGAGTGGTATGGCCAGAAC
| | |||| |||| || || | | |||| | || || | | | || |||| | | || | || ||||||||||||||||||| ||||| ||||| || ||||||||||||||||||||||| || ||||| || || || || ||||| ||||||||||| |||||||||
---------------------------------------------------gtaagtttcttttttttcctt---tcctttttcatggcttacgca---taggtagg-acaagtt--tgctaaccgctttgatgccatc-aaaccagAGGGTATCTGGCGGACAGAAACAAGCCTATCATCTTCTCGATGGCAAGGCTGGACAAGGTGAAGAATATCACCGGGCTAGTGGAGTGGTACGGCCAGAAC
upper sequence: LOC_Os04g17650.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA09G29710.1 (Glycine max), 3'ss of exon 11
gtaagctactacccggacggccaggctccttggaaacgtacctagctacaaattaacttctcttttactgttagatcagatcagacaacttaagttggttaattaagtgctaattgctgctcttcacctttttttaatttaaac-cagAGGGTATCTGGCAGACAGGAACAAACCAATCATCTTCTCGATGGCAAGGCTTGATAAGGTAAAAAACATAACTGGGCTTGTGGAGTGGTATGGCCAGAAC
| | | || || || | | | | | || || |||| || | || | ||| | || | || | | | ||| || |||||| | | ||| ||||| ||| ||||||||||||||||| ||||| |||||||| || || || ||| | | ||| || || |||||||||| |||
-----------------------------------gtgagtttcattgcactttgctcaatcatcaatttgttttttag------taatgaaagtgtgtcatttcattgcgatggcctaattcaaactataatgtgttttggactcagAGGATTTTTGGAAGACATGAAGAAACCAATCATCTTCTCCATGGCTAGGCTTGACAAAGTGAAGAACCTTAGTGGCCTAGTTGAGTGGTATGCAAGAAAC
upper sequence: LOC_Os04g17650.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA16G34290.1 (Glycine max), 3'ss of exon 11
gtaagctactacccggacggccaggctccttggaaacgtacctagctacaaattaacttctcttttactgttagatcagatcagacaacttaagttggttaattaagtgctaattgctgctcttcacctttttttaattta-aaccagAGGGTATCTGGCAGACAGGAACAAACCAATCATCTTCTCGATGGCAAGGCTTGATAAGGTAAAAAACATAACTGGGCTTGTGGAGTGGTATGGCCAGAAC
| | | | |||| ||| | | | || || || |||| || | || | ||| | || | || | | | ||| || |||||| | ||| ||||| ||| ||||||||||||||||| ||||| |||||||| || || || ||| | | ||| || || |||||||||| |||
-----------------------------------------gtgagtttcattccacttttctctcgttaatttattttattga--aatggaagtgtgtcatttcattgcaatggcctaattcaaactatgatgtgttttctaatcagAGGACTTTTGGAAGACATGAAGAAACCAATCATCTTCTCCATGGCTAGGCTTGACAAAGTGAAGAACCTTAGTGGCCTAGTTGAGTGGTATGCAAGAAAC
upper sequence: LOC_Os04g17650.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA02G40740.1 (Glycine max), 3'ss of exon 10
gtaagctactacccggacggccaggctccttggaaacgtacctagctacaaattaacttctcttttactgttagatcagatcagacaacttaagttggttaattaagtgctaattgc-tgctcttcacctttt---tttaatttaaaccagAGGGTATCTGGCAGACAGGAACAAACCAATCATCTTCTCGATGGCAAGGCTTGATAAGGTAAAAAACATAACTGGGCTTGTGGAGTGGTATGGCCAGAAC
|| | | ||| | | |||||| || | || | | | || ||| | | ||||| || ||||| ||| || | || ||| || ||||| || || |||| || |||||||||||||| ||||||||||||||| || || ||| | | ||| | || || ||||||||| |||||
-----------------------------------------------gtaagtgaccttgt--tgcactgttgcatagtaacattta---tgaattaccacattc--ttccaattgaatgactttcacttttcgaattgttatggaaacagTGGATATCTAGCTGATAGGAGGAAGCCAATCATCTTCTCAATGGCAAGGCTTGATGTTGTGAAGAACTTGAGCGGGTTAGTTGAATGGTATGGCAAGAAC
upper sequence: LOC_Os04g17650.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA14G39070.1 (Glycine max), 3'ss of exon 11
gtaagctactacccggacggccaggctccttggaaacgtacctagctacaaattaacttctcttttactgttagatcagatca-gacaacttaagttggttaattaagtgctaattgctgc----tcttcaccttt----ttttaatttaaaccagAGGGTATCTGGCAGACAGGAACAAACCAATCATCTTCTCGATGGCAAGGCTTGATAAGGTAAAAAACATAACTGGGCTTGTGGAGTGGTATGGCCAGAAC
| || | || | | | || ||||| | || | || | | || | | || || || ||| | ||||| || ||||| | | || | || ||||| || || ||||| || || |||| || |||||||||||||| ||||||||||||||| || || ||| |||| ||| | || || ||||||||| |||||
-------------------------------gtaagtg-actttgttgca---------ctcttgcatggtaacattcagttatgatatcctacattcttt--ctaaatcctaatgaatgaatgactttcacttctgaaattgttatgtaaac-agTGGATATCTAGCTGATAGGAGGAAGCCAATCATCTTCTCAATGGCAAGGCTTGATGTTGTGAAGAACTTAACCGGGTTAGTTGAATGGTATGGCAAGAAC
upper sequence: LOC_Os04g17650.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv17s0053g00700.t01 (Vitis vinifera), 3'ss of exon 11
gtaagctactacccggacggccaggctccttggaaacgtacctagctacaaattaacttctcttttactgttagatcagatcagacaacttaagttg-gttaattaagtgctaattgctgctcttcacctttttttaatttaaaccagAGGGTATCTGGCAGACAGGAACAAACCAATCATCTTCTCGATGGCAAGGCTTGATAAGGTAAAAAACATAACTGGGCTTGTGGAGTGGTATGGCCAGAAC
| | | | ||| ||| || ||| |||| | | ||||| | || | | ||| | | ||| |||||||| ||||||| || || |||||||||||||| ||||||||||| |||| ||||||||||| || || || || |||||||| |||||
---------------------------------------------------------------gtaagtatgagagtt--tcattcattccgtgttctaacaattgcatac-aattgaatccctcaaaaatgttt----gtggaacagTGGGTATCTATCAGACAGAAAGAAGCCAATCATCTTCTCCATGGCAAGGCTAGATACAGTAAAAAACATTACAGGACTAACTGAATGGTATGGGAAGAAC
upper sequence: LOC_Os04g17650.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv04s0079g00230.t01 (Vitis vinifera), 3'ss of exon 10
gtaagctactacccggacggccaggctccttggaaacgtacctagctacaaattaacttctcttttactgttagatcagatcagacaacttaagttggttaattaagtgctaattgctgctcttcacctttttttaatttaaaccagAGGGTATCTGGCAGACAGGAACAAACCAATCATCTTCTCGATGGCAAGGCTTGATAAGGTAAAAAACATAACTGGGCTTGTGGAGTGGTATGGCCAGAAC
||| | ||| || | | | | | | | || | | | ||| ||| | || | ||| || | || | |||| ||| ||| ||||| ||| ||| || | ||| |||||||| || ||||| ||||||||||| ||||||||||| || | || || ||||| || ||| | ||||||| || | |||
--------------------gtaggtt--ttgaaagggaaatcatttgttcaattatttatttataactaccttg-cagtttgga-attttatgtctg------aattactaacatctggtctgaacctt--------gaaaaacagTGGATTTCTAGCAGACAGAAAGAAACCTATCATCTTCTCAATGGCAAGGCTGGACATAGTGAAGAACATTACGGGGTTAACTGAGTGGTTCGGGAACAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttggttaattaagtgctaattgctgctcttcacctttttttaatttaaaccagAGGGTATCTGGCAGACAGGAACAAACCAATCATCTTCTCGATGGCAAGGCTTGATAAGGTAAAAAACATAACTGGGCTTGTGGAGTGGTATGGCCAGAAC
ctcttcaccttttttt CT-rich tract
ttcacctttttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctactacccggacggccaggctccttggaaacgtacctagctacaaattaacttctcttttactgttagatcagatcagacaacttaagttggttaattaagtgctaattgctgctcttcacctttttttaatttaaaccagAGGGTATCTGGCAGACAGGAACAAACCAATCATCTTCTCGATGGCAAGGCTTGATAAGGTAAAAAACATAACTGGGCTTGTGGAGTGGTATGGCCAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG