Sequence
atgc intronic sequence ATGC exonic sequencegtaaattcttacggttttgataaacattttggaattagttattacttgctcttcgggtttatcattcttctggcaaatgtcacacaggtggaattgaccctcacactcacctggagatggaattcatgggaactgtaaccattgatgatttctttagtggtcatgctgcagCATTGGCTGGTGGGACAACAATGCACATTGACTTCGTCATTCCAGTGAATGGCAATTTAACTGCAGGTTTGGAATCCTACAAACAGAAGGCAGAAAAATC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g59340.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 3
gtaaattcttacggttt------tgataaacattttgg-aattagtta------ttacttgctcttcgggtttatcattcttctggcaaatgtcacacaggtggaattgaccctcacactcacctggagatggaattcatgggaactgtaaccattgatgatttctttagtggtcatgctgcagCATTGGCTGGTGGGACAACAATGCACATTGACTTCGTCATTCCAGTGAATGGCAATTTAACTGCAGGTTTGGAATCCTACAAACAGAAGGCAGAAAAATC
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gtgaattcttactatcccccttgtggtgaatagttgaacaatctgctaagagcattacttgttgcacag-tttataagccttccggtgaatgttgca--gGTGGAATTGACCCTCACACGCACCTGGAGATGGAGTTCATGGGCACCGTGACCATAGATGACTTCTTCAGCGGCCATGCTGCGGCACTGGCGGGTGGGAC------------------------------------------------------------------------------------
upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA14G04030.1 (Glycine max), 3'ss of exon 3
---------gtaaatt--cttacggttttgataaacattttggaattagttattacttg-ctcttcgggtttatcattcttctggcaaatgtcaca-caggtggaattgaccctcacactcacctggagatggaattcatgggaactgtaaccattgatgatttctttagtggtcatgctgcagCATTGGCTGGTGGGACAACAATGCACATTGACTTCGTCATTCCAGTGAATGGCAATTTAACTGCAGGTTTGGAATCCTACAAACAGAAGGCAGAAAAATC
| ||||| ||| | | || | ||| | | | |||||| || || | | | ||| | | || | | | |||| || ||||| |||||||| || || || ||||| | |||| ||| ||||||| ||||| |||||||| || ||||||||||||||||||||
aaagtgcatgaaaattaatttatcatcgtcatcattattattgttgttattattatgtgtctgatagactctatgaatgctccttttgttaactgatcagGGGGCATTGATCCTCACACCCATCTAGATATGGATGTTGGTTTTACTGCAACGGTTGATGACTTCTTCAGTGGTCAGGCGGCAGCATTGGCTGGTGGGAC------------------------------------------------------------------------------------
upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 3
-gta-aattcttacg-gttttgataaacattttggaattagttattacttgctcttcgggtttat--------------cattcttctggcaaatgtcacacaggtggaattgaccctcacactcacctggagatggaattcatgggaactgtaaccattgatgatttctttagtggtcatgctgcagCATTGGCTGGTGGGACAACAATGCACATTGACTTCGTCATTCCAGTGAATGGCAATTTAACTGCAGGTTTGGAATCCTACAAACAGAAGGCAGAAAAATC
|| ||||| ||| || | | | | || | | | ||||||| | ||||| | | |||| || || || || |||| || |||||||||||||| ||||| ||| | || || |||| || | ||| | ||||| ||||| |||||||| ||||||||||| |||||||||||
ggtggaattcctactcgtgtcgttcactgttgttgtggttgttattatattatcttctacctgacagattccaggaatgcatttttttgttaactg----gcagGGGGCATTGACCCTCACACCCACCTAGAGTTTGAGTTTATGGATACGGAAACTGTAGATGACTTCTTCAGTGGTCAGGCTGCAGCATTAGCTGGTGGGAC------------------------------------------------------------------------------------
upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 3
--------gtaaattcttacggttttgataaacatt-ttggaatta--gttattacttgctcttcgggttt-----atcattcttctggcaaatgtcacacaggtggaattgaccctcacactcacctggagatggaattcatgggaactgtaaccattgatgatttctttagtggtcatgctgcagCATTGGCTGGTGGGACAACAATGCACATTGACTTCGTCATTCCAGTGAATGGCAATTTAACTGCAGGTTTGGAATCCTACAAACAGAAGGCAGAAAAATC
|||||| ||| || | | ||| || ||| ||||||| | | | || | || | ||| || || || | |||| || ||||| |||||||| || || || ||||| | |||| ||| ||||||| ||||| |||||||| || ||||||||||||||||||||
atgaaaaattaaattattatagtcctcgtcgtcatcattattattgttgttattatgttcccgaaggactctatgaatggtccttttgttaactgac---cagGGGGCATTGATCCTCACACCCATCTAGATATGGATGTTGGTTTTACTGCAACGGTTGATGACTTCTTCAGTGGTCAGGCAGCAGCATTGGCTGGTGGGAC------------------------------------------------------------------------------------
upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------gtaaattcttacggttttgat--aaacattt---tggaattagttattact-----tgctcttcgggtttatc--attcttctggcaaatgtcacacaggtggaattgaccctcacactcacctggagatggaattcatgggaactgtaaccattgatgatttctttagtggtcatgctgcagCATTGGCTGGTGGGACAACAATGCACATTGACTTCGTCATTCCAGTGAATGGCAATTTAACTGCAGGTTTGGAATCCTACAAACAGAAGGCAGAAAAATC
||| | ||| ||||| | || || | | | |||| | | | || | | || ||| | |||| | | |||| | | ||| ||||||||||| ||||| ||||| | |||||||| ||||| || | || |||||||||||||| |||||||| || || ||||| |||||||| ||
gttaatcaattcatactagttgatactttccaaaattttagccttttgttttgaatccttaactagtttcagttctaattaagaatggttagcattttcatcttactcttgtccctgatgt-aaatagGAGGAATTGACCCCCACACGCACCTCGCCATGGAATTTATGGGTACCGAGACTATTGATGATTTCTTCAGTGGTCAGGCAGCGGCATTAGCTGGTGGAAC------------------------------------------------------------------------------------
upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 3
---gtaaattcttacggttttg---ataaacattttggaat-tagttattacttgctcttcgggtttat-cattcttctggcaaatgtca-----cacaggtggaattgaccctcacactcacctggagatggaattcatgggaactgtaaccattgatgatttctttagtggtcatgctgcagCATTGGCTGGTGGGACAACAATGCACATTGACTTCGTCATTCCAGTGAATGGCAATTTAACTGCAGGTTTGGAATCCTACAAACAGAAGGCAGAAAAATC
| |||| | | || || ||||| | | || | ||| | || ||| ||| |||| | | |||||||||||||| |||||||| ||||| | ||||| || ||||| |||| ||||||||||| || || |||||||| ||||| ||| | || ||||| ||
aagtttaattagcatgtccatgtccatgtccatttccgtctctaagaactacatatatttgatccatatatattgcaacattaaattttaatgtttacagGTGGAATTGATCCTCACACACACCTAGCAATGGAGTTTATGGGTACTGAGACCATTGATGACTTTTTCAGTGGTCAAGCTGCTGCACTAGCAGGTGGAAC------------------------------------------------------------------------------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggaattcatgggaactgtaaccattgatgatttctttagtggtcatgctgcagCATTGGCTGGTGGGACAACAATGCACATTGACTTCGTCATTCCAGTGAATGGCAATTTAACTGCAGGTTTGGAATCCTACAAACAGAAGGCAGAAAAATC
atttcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattcttacggttttgataaacattttggaattagttattacttgctcttcgggtttatcattcttctggcaaatgtcacacaggtggaattgaccctcacactcacctggagatggaattcatgggaactgtaaccattgatgatttctttagtggtcatgctgcagCATTGGCTGGTGGGACAACAATGCACATTGACTTCGTCATTCCAGTGAATGGCAATTTAACTGCAGGTTTGGAATCCTACAAACAGAAGGCAGAAAAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG