Sequence
atgc intronic sequence ATGC exonic sequence...gtgtggctttctttgttgttactatatgttgtcattttcaatatgcatattacatatgttctgaagggaccttgaggatgcaaattctgttgtaatgcagGTATGGATGCTCAAGTGGCGTATGGATTTCACCATCTACGGGATGAAAAGCCATTCCTTGCTAGTGGTCCTTTATCTAATAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g15090.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g15090.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G01360.1 (Glycine max), 3'ss of exon 7
gtgtggctttctttgttgttactat----atgttgtcattt---tcaatatgcatattacatatgttctgaagggaccttgaggatgcaaattctgttgtaat--gcagGTATGGATGCTCAAGTGGCGTATGGATTTCACCATCTACGGGATGAAAAGCCATTCCTTGCTAGTGGTCCTTTATCTAATAAG
|||| || || || || ||||| ||| | ||||| || || | || ||| | | | || | || ||||| || | |||| |||||||| |||||||| ||||| || || |||||||| ||||||| || | ||||||||||||||| | || ||||||
-----gcttagggtgatggtaggatggaaatgttttcagatagctcaat-tgaatctctaatctgtatatctgagcattcacaga---atatcctgttatattttacagGAATGGATGCCCAAGTGGCTTATGGCTTCCATCATCTACGCAATGAAAAACCTTACCTTGCTAGTGGTCCAATTTCAAATAAG
upper sequence: LOC_Os08g15090.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S213_133V6.3 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------------------------------------------gtgtggctttctttgttgtta------ctatatgttgtcattttcaatatgcatat-tacatatgttctgaagggaccttgaggatgcaaattctgttg--taatgcagGTATGGATGCTCAAGTGGCGTATGGATTTCACCATCTACGGGATGAAAAGCCATTCCTTGCTAGTGGTCCTTTATCTAATAAG
| || | | || | |||| ||| | | || || | || || | | | | || | | || | | || | |||||| ||||||||||||||||||||||| ||||||||||| || ||| |||| || | |||||| | |||| | | ||| |
gtgagatcaatatgtcaatatccatccttctgtggaataaatggctttttaaaaaagaatcttgcactgatatatcagcaaaaggcattgcctgaacgtttggaccgtaaaagacctaatatagtgtagtactgaactgacacacatatgaatttattaatttaaactgatgaaaccatgctttattacttggtgcagGAATGGATGCTCAAGTGGCGTATGGCTTTCACCATCTGCGAGATAAAAAACCCTGGCTTGCTCGAGGTCGCACAGCCAATCAA
upper sequence: LOC_Os08g15090.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S99_240V6.1 (Physcomitrella patens), 3'ss of exon 10
------gtgtggctttctttgttgttactatatg----ttgtcattttcaatatgcatattacatatg----ttctgaagggaccttgaggatgcaaattctgttg--taatgcagGTATGGATGCTCAAGTGGCGTATGGATTTCACCATCTACGGGATGAAAAGCCATTCCTTGCTAGTGGTCCTTTATCTAATAAG
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gtaagctcaacacttccatcagcattcttctacggaatttatgggtgttaagagaatcattcattatgaagcttcgaacttaaactgaagaagtcatgctgtgttgcttggtgtagGAATGGATGCGCAAGTGGCATATGACTTTCACCATCTGCGGGATGAAAAACCCTGGCTCGCTCGCACTCGTGCAGCCAATAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catattacatatgttctgaagggaccttgaggatgcaaattctgttgtaatgcagGTATGGATGCTCAAGTGGCGTATGGATTTCACCATCTACGGGATGAAAAGCCATTCCTTGCTAGTGGTCCTTTATCTAATAAG
ttctgtt CT-rich tract
tacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtggctttctttgttgttactatatgttgtcattttcaatatgcatattacatatgttctgaagggaccttgaggatgcaaattctgttgtaatgcagGTATGGATGCTCAAGTGGCGTATGGATTTCACCATCTACGGGATGAAAAGCCATTCCTTGCTAGTGGTCCTTTATCTAATAAG
- - - - - - ttgttgt
- - - - - - - - - - - - -atgttgt
- - - - - - - - - - - - - - - - - - - - - atgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatgca