Sequence
atgc intronic sequence ATGC exonic sequencegtaagtagcattcttgctcaaccacatttttcacttatatactgtgacacatttctacataaccttttagtctgaatatgtttgactgatgctgatgtcattttcatgcagTGATGTCTTCGAATGACTCAATGGGTACAGTCTTTAAGTGTTTGTCAAAAGGAGCAGTTGACTTTCTAGTGAAGCCTATACGTAAGAATGAACTTAAGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g17570.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g17570.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G095727_T04 (Zea mays), 3'ss of exon 6
gtaagtagcattcttgctcaaccacatttttcacttatatactgtgacacatt-tctacataaccttttagtctgaatatgtttgactg--atgctgatgtcattttcatgcagTGATGTCTTCGAATGACTCAATGGGTACAGTCTTTAAGTGTTTGTCAAAAGGAGCAGTTGACTTTCTAGTGAAGCCTATACGTAAGAATGAACTTAAGAA
|||||||| ||| |||||| || || || || |||| | || ||| ||| || || | |||| ||| ||| | ||||||| ||| ||||||||||||||| ||||||| || ||| ||| || |||||||||||||| || ||||||||||| || | || || || ||||||||||||| ||||||||
gtaagtagatttc---ctcaactacc-------ctaatgcac-gtgaaattttatcttgttaattgttgggtttaaatacttttagctgctacactgatgtgttttgcatgcagTGATGTCTACGAATGATTCTATGAGTATGGTGTTTAAGTGTTTGTCGAAGGGAGCAGTTGATTTCTTGGTAAAACCACTACGTAAGAATGAGCTTAAGAA
upper sequence: LOC_Os03g17570.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G15580.1 (Glycine max), 3'ss of exon 3
gtaagtagcattcttgctcaaccacatttttcacttatatactgtgacacatttctacataaccttttagtctgaatatgtttgactgatgctgatgt-cattttcatgcagTGATGTCTTCGAATGACTCAATGGGTACAGTCTTTAAGTGTTTGTCAAAAGGAGCAGTTGACTTTCTAGTGAAGCCTATACGTAAGAATGAACTTAAGAA
|||||| || | | | | | |||| ||| | || | | |||| | || || || || |||| | ||| |||| || | |||||||||||||| || |||| || ||||||| |||||||||||||||||||||||| |||||||| ||| ||||||| || || || | |||||||||||| ||
gtaagtggcgtaccaa---agttatactttttactaa-atttaagtatatattttca-atgactattgctcatgtggtgttttgtttattgcacatgttcaaatgcatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGCGCAGTTGATTTTTTAGTGAAACCAATTCGGAGGAATGAACTTAAAAA
upper sequence: LOC_Os03g17570.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G19870.1 (Glycine max), 3'ss of exon 2
gtaagtagcattcttgctcaaccacatttttcacttatatactgtgacacatttctacataaccttttagtctgaatatgtttgactgatgctgatgtcattttcatgcagTGATGTCTTCGAATGACTCAATGGGTACAGTCTTTAAGTGTTTGTCAAAAGGAGCAGTTGACTTTCTAGTGAAGCCTATACGTAAGAATGAACTTAAGAA
|||||| |||| | | ||| | | | | | | ||| | | | | | | || | | | || ||| ||| |||||||||||| || |||| || |||||| ||||||||||||||||||||| || || |||||||||||||| || || ||||| |||||||| ||||| ||
gtaagttttccaagtgcttatatatgtttgtt-ttgaagcatttctttttctcatctcatgatgtaaaatagctactcttttgtatggcttctaatgggattggtctgcagTGATGTCATCTCATGATTCTATGGGTTTAGTCTTTAAGTGTTTGTCAAAGGGTGCTGTTGACTTTCTAGTTAAACCCATACGGAAGAATGAGCTTAAAAA
upper sequence: LOC_Os03g17570.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G07860.1 (Glycine max), 3'ss of exon 2
gtaagtagcattcttgctcaaccacatttttcacttatatactgtgacacatttctacataaccttttagtctgaatatgtttgactgatgctgatgt-cattttcatgcagTGATGTCTTCGAATGACTCAATGGGTACAGTCTTTAAGTGTTTGTCAAAAGGAGCAGTTGACTTTCTAGTGAAGCCTATACGTAAGAATGAACTTAAGAA
||||| |||| | | | | | | | | || | | |||| | || || || || |||| | ||| |||| || | |||||||||||||| || |||| || ||||||| |||||||||||||||||||||||| |||||||| ||| ||||||| ||||| || | |||||||||||| ||
gtaagcggcataccaa---agttatactctgttccaa-atttaagtatatattttca-atgactattgctcatgtggtgttttgtttattgcacatgttcaaatacatgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGTGCAGTTGATTTTTTAGTGAAACCTATTCGGAGGAATGAACTTAAAAA
upper sequence: LOC_Os03g17570.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G05520.1 (Glycine max), 3'ss of exon 2
gtaagtagcattcttgctcaaccacatttttcacttatatactgtgacacatttctacataaccttttagtctgaa----------tatgtttgactgatgctgatgtcattttcatgcagTGATGTCTTCGAATGACTCAATGGGTACAGTCTTTAAGTGTTTGTCAAAAGGAGCAGTTGACTTTCTAGTGAAGCCTATACGTAAGAATGAACTTAAGAA
| | || |||| | || | | | | | ||| ||||||| | | | | | ||| | | | || | | | || ||| ||| |||||||||||| || |||| || |||||| ||||||||||||||||||||| || || |||||||||||||| || || ||||| |||||||| ||||| ||
-------gtaagtttttccaactgc---ttatatatgtttggtttgaagcatttctttttctcatctcatgctgcaagagagctactcttttctatggcttctaatgggattggtctgcagTGATGTCATCTCATGATTCTATGGGTTTAGTCTTTAAGTGTTTGTCAAAGGGTGCTGTTGACTTTCTAGTTAAACCCATACGGAAGAATGAGCTTAAAAA
upper sequence: LOC_Os03g17570.4 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G02810.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------gtaagtagcattcttgc-tcaaccacatttttc---acttatatactgtgaca---catttctacataaccttttagtctgaatatgtttgactg-atgctgatgtcattttcatg---cagTGATGTCTTCGAATGACTCAATGGGTACAGTCTTTAAGTGTTTGTCAAAAGGAGCAGTTGACTTTCTAGTGAAGCCTATACGTAAGAATGAACTTAAGAA
| | | | || | | | | | || || | ||| | | || | | |||| | || | | || ||| ||| || | ||| | || || |||||||||| || ||||||||||||| ||||||||||| || || |||||||| ||||||||||| || ||||| ||| | || ||||| |||||||
gtgagttctttttccttggtcgttttacattgagctctttcttttgaagttacacgatttgttgagtcttctctagcgtatgttggaaagtagatgcttttaactacattcccctgtgagatttgtgttgcagTGATGTCATCTCATGACTCAATGGGGCTGGTCTTTAAGTGCTTATCGAAAGGAGCTGTTGACTTTCTTGTTAAGCCAATAAGAAAAAATGAGCTTAAGAT
upper sequence: LOC_Os03g17570.4 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv13s0067g03390.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtagcattcttgctcaaccacatttttcacttatatactgtgacacatttctacataaccttttagtc---tgaatatgtttgactgatgc---tgatgtcattttcatgcagTGATGTCTTCGAATGACTCAATGGGTACAGTCTTTAAGTGTTTGTCAAAAGGAGCAGTTGACTTTCTAGTGAAGCCTATACGTAAGAATGAACTTAAGAA
|| |||| |||| || | | || | || || | | | | | |||| || | |||| ||| | || | | ||||| ||| |||||||||||| || |||| || |||| | ||||||||| ||||||||||| || |||||||||||| | ||||||||||| || || ||||| ||||| ||
gtgagtattattcca----aaacgctttacatgcctaagtatttctctttttctgcaattgttatttttatcaaatcaatacttttaattgcttcacctgatgagttttgtgtgcagTGATGTCATCCCATGATTCTGTGGGCATAGTCTTTAAATGTTTGTCAAAGGGTGCAGTTGACTTTTTTGTGAAGCCTATTCGAAAAAATGAGCTTAAAAA
upper sequence: LOC_Os03g17570.4 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g03650.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtagcattcttgctcaaccacatttttcacttatatactgtgacacatttctacataaccttt-tagtctgaatatgtttgactg--atgctgatgtcattttcatgcagTGATGTCTTCGAATGACTCAATGGGTACAGTCTTTAAGTGTTTGTCAAAAGGAGCAGTTGACTTTCTAGTGAAGCCTATACGTAAGAATGAACTTAAGAA
||||||| |||| | | || |||||| | || | | | |||| || || || | | || || | | | |||| | |||| ||||||||||||| || |||| || ||||||| ||||||||||||| |||| || || |||||||| ||| | ||||| ||||| || |||||||||||||| ||
gtaagtatcattttagtgttttca---ttttcatagaaat-ttaaggcttattttcctatcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acataaccttttagtctgaatatgtttgactgatgctgatgtcattttcatgcagTGATGTCTTCGAATGACTCAATGGGTACAGTCTTTAAGTGTTTGTCAAAAGGAGCAGTTGACTTTCTAGTGAAGCCTATACGTAAGAATGAACTTAAGAA
tgctgat putative branch site (score: 3)
tcattttc CT-rich tract
aatatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtagcattcttgctcaaccacatttttcacttatatactgtgacacatttctacataaccttttagtctgaatatgtttgactgatgctgatgtcattttcatgcagTGATGTCTTCGAATGACTCAATGGGTACAGTCTTTAAGTGTTTGTCAAAAGGAGCAGTTGACTTTCTAGTGAAGCCTATACGTAAGAATGAACTTAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC