Sequence
atgc intronic sequence ATGC exonic sequence...atgatatatgcatttcaaataacgattttacttttaagcaaacttttgctactttcaacatagatctgactgttaacattttctttatttaatttaccagACTGTTATCATAAGCAAAATGCAAAAACTTACCAAGGAAGGGTTGCAAAGGACTGACAGGAGAATCAGTCTAATGAATGAAATATTAGCTGCAATGGATA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g52900.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 12
---atgatatatgcatttcaaataacgattttacttttaagcaaacttttgctactttcaacatagatctgactgttaacattttctttatttaatttaccagACTGTTATCATAAGCAAAATGCAAAAACTTACCAAGGAAGGGTTGCAAAGGACTGACAGGAGAATCAGTCTAATGAATGAAATATTAGCTGCAATGGATA
|| | || ||| | | |||| || | | |||| || | | || ||| | | | | | | ||||||| |||||||| ||||| |||||||||||||||||||| || || |||||||||||||| |||| | |||||||||| ||||||||| |||||||||| |||||||
gttgtggtttactggttt---gtgatttctttaagttgtggtttaattttaacacagatttcggttctttgcctggttaatctgtttgtgtttaattattcagACTGTAATCATCAGCAAAATGCAAAAACTTACTAAAGAGGGGTTGCAAAGGACCGACAAGCGAATCAGTCTCATGAATGAAGTATTAGCTGCTATGGATA
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 12
lower sequence: AT2G34660.1 (Arabidopsis thaliana), 3'ss of exon 12
-------------------------------------atgatatatgcatttcaaataacgattttacttttaagcaaacttttgctactttcaacatagatctgactgtt-aacattttctttatttaatttac-cagACTGTTATCATAAGCAAAATGCAAAAACTTACCAAGGAAGGGTTGCAAAGGACTGACAGGAGAATCAGTCTAATGAATGAAATATTAGCTGCAATGGATA
| ||| | || | || | | || | | ||| | | | | | | | || | ||| | |||| | ||| || | ||||||||||| |||||||||||||| || || || |||||||| |||| | ||||||| |||||| | || ||||||||| | ||||||||||||||||
gtacatgacttctaaatttcctcattttttttcctttgtagcttatttttctcta-tactgttcgcttgttcattcgtactcctaaaggctacttcttc--ttcgtctcctgaacttgttctctgttttcttaaaacagACTGTTATTATAAGCAAAATGCAGAAGCTGACAAAGGAAGGTCTGCAGCGTACTGACAAGAGAATTGGCCTTATGAATGAAGTTTTAGCTGCAATGGATA
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 12
lower sequence: AT1G30400.2 (Arabidopsis thaliana), 3'ss of exon 12
------------------------atgatatatgcatttcaaataacgattttacttttaa-gcaaacttttg--ctactttcaacatagatctgactgttaacattttctttatttaatttac-----cagACTGTTATCATAAGCAAAATGCAAAAACTTACCAAGGAAGGGTTGCAAAGGACTGACAGGAGAATCAGTCTAATGAATGAAATATTAGCTGCAATGGATA
|| | | ||| | | |||| ||| | || | || | | |||| ||| || | || | ||||||||| |||| ||| ||||||||||| |||||||||| ||| || | || || ||||||||||| | ||||||| |||||| | ||||||||||| | ||||| ||||||||||
gttcgtatatcttaataattccccattctctttgcgctgtcggttttttttttcttttgagtgcttatttctcatttgcttttcacaccaatgaaaatgatt-cattttcttcgtttattttgttgaaacagACTGTTATTATAAGCAAAACGCAGAAGTTAACAAAAGAAGGGTTGCAGCGTACTGACAAGAGAATTGGCCTAATGAATGAGGTTTTAGCGGCAATGGATA
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv10s0003g04470.t01 (Vitis vinifera), 3'ss of exon 13
---atgatatatgcatttcaaataacgattttacttttaagcaaacttttgctactttcaacatagatctgactgttaa--cattttctttatttaatttac-cagACTGTTATCATAAGCAAAATGCAAAAACTTACCAAGGAAGGGTTGCAAAGGACTGACAGGAGAATCAGTCTAATGAATGAAATATTAGCTGCAATGGATA
| || | | | || | ||||| ||||| | || | | ||| | || | | ||||| |||||| | | ||||| ||||||| |||||||||| |||| | |||||||||| |||||| | ||||||| |||| |||| || ||||||||||| || ||||| ||||| |
tgtttaatgtctatgatgaaagttgtgatttatctttttaa------ttgatcatctcttgtataatttcaccttctcatgcatttaaattattttgtcaaaacagACATTTATCATTAGCAAAATGCGAAAATTGTCCAAGGAAGGATTGCAACGAACTGACAAGAGAGTCAGCCTCATGAATGAAATTTTGGCTGCCATGGACA
upper sequence: LOC_Os04g52900.2 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv10s0003g04450.t01 (Vitis vinifera), 3'ss of exon 1
----atgatatatgcatttcaaataacgattttactt--ttaagcaaacttttgctactttcaacatagatctgactgttaacattttctttatttaatttaccagACTGTTATCATAAGCAAAATGCAAAAACTTACCAAGGAAGGGTTGCAAAGGACTGACAGGAGAATCAGTCTAATGAATGAAATATTAGCTGCAATGGATA
||| | | | || | | |||| | | || | || ||| || || || |||||| ||| | ||| | | ||||| || |||| ||||||||| | ||||| | |||||||| |||||| | ||||||| |||| |||| || ||||||||||| || ||||||||||||
ttatttgaattctatgatgaaatatatggttttttctcctcaactgatctcttgtataattttactccctcatgcatgttaa-attat-----tttgttagaacagACATTTGTCATTAGCAAAATGAAGAAACTGTCTAAGGAAGGATTGCAACGAACTGACAAGAGAGTCAGCCTCATGAATGAAATTTTGGCTGCAATGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgctactttcaacatagatctgactgttaacattttctttatttaatttaccagACTGTTATCATAAGCAAAATGCAAAAACTTACCAAGGAAGGGTTGCAAAGGACTGACAGGAGAATCAGTCTAATGAATGAAATATTAGCTGCAATGGATA
actgttaacattttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgatatatgcatttcaaataacgattttacttttaagcaaacttttgctactttcaacatagatctgactgttaacattttctttatttaatttaccagACTGTTATCATAAGCAAAATGCAAAAACTTACCAAGGAAGGGTTGCAAAGGACTGACAGGAGAATCAGTCTAATGAATGAAATATTAGCTGCAATGGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC