Sequence
atgc intronic sequence ATGC exonic sequence...ttctctttcttttctttgctgctactgctagtactagtgcagtatgctttgttctttgtttctgtttcatgttatgttaacgattttggttttcttgcagCATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAAAGTGAGAAACTAGTTGCTAATCTTTTCCAGATGGCCCGTGAAAATGCTCCCTCCATTATC
Basic information
| species | Oryza sativa |
| transcript | LOC_Os01g04840.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g04840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G19120.1 (Glycine max), 3'ss of exon 2
---ttctctttcttttctttgctgctactgctagtactagtgcagtatgctttgttctttgtttctgtttcatgttatgttaacgattttggttttcttgcagCATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAAAGTGAGAAACTAGTTGCTAATCTTTTCCAGATGGCCCGTGAAAATGCTCCCTCCATTATC
| | |||| |||| | | | || | ||||||| | ||| | || || | | ||||| ||| || | ||| | |||||||||||||| |||||||| ||||||||||||||||| || || || | ||||||||||| ||||| || |||| ||| || || || ||
ccttgacagtgattttgtttgaaataaaaaaggttgtgaatgt-gagtgctttggtgggcattt-tcttgcagcatgttttaact-tttgaattcttcaccagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCTGGTCTCAAATCTTTTCCAAATGGCTCGCGAAAGTGCACCTTCTATAATA
upper sequence: LOC_Os01g04840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G09300.1 (Glycine max), 3'ss of exon 2
ttctctttcttttctttgc----tgctactgctagtactagtgcagtatgctttgttctt-tgtttctgtttcatgttatgttaacgattttggttttcttgcagCATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAAAGTGAGAAACTAGTTGCTAATCTTTTCCAGATGGCCCGTGAAAATGCTCCCTCCATTATC
| | |||| |||| | || | | ||||| || | | || | ||| || | |||||| ||||| |||| || | ||| | ||||| |||||||| |||||||| ||||||||||||||||| || || || | ||||||||||| ||||| || |||| ||| || || || ||
tgtcagtgattttgtttgaaaaataaggtcgcaaatgtaagtgct-taggttaggtgggcatttttttgctacatgtt---ttaact-ttttaattcttcaccagTGTTTCTTCGTCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCTGGTCTCAAATCTTTTCCAAATGGCACGCGAAAGTGCACCTTCTATCATA
upper sequence: LOC_Os01g04840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G39410.1 (Glycine max), 3'ss of exon 2
--ttctctttcttttctttgc-tgctactgctagtactagtgcagtatgctttgttctttgtttctgtttcatgttatgttaacgattttggttttcttgcagCATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAAAGTGAGAAACTAGTTGCTAATCTTTTCCAGATGGCCCGTGAAAATGCTCCCTCCATTATC
|| | | || | | | | || | || || | | | | | | | || || | | ||||| ||| || | ||| | ||||||||||||||||||||||| |||||||| |||||||| || || ||| | || |||||| | ||||| || |||| ||| || || || ||
ccttaaatcaggtaaattcatattccataaatgttatgaatgtag-gtccataagtggacatgt-tcttgcaagcatttttaact-tttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
upper sequence: LOC_Os01g04840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 2
ttctctttcttttctttgctgctactgctagtactagtgcagtatgctttgttctttgtttctgtttcatgttatgttaacgattttggttttcttgcagCATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAAAGTGAGAAACTAGTTGCTAATCTTTTCCAGATGGCCCGTGAAAATGCTCCCTCCATTATC
| | ||| || | | || | || ||| | | | | || || || | ||| || | ||| | ||||||||||||||||||||||| |||||||| |||||||| || || ||| | || |||||| | ||||| || |||| ||| || || || ||
cttgatatctattaaaaaaggtcttttgtattgttatgaatgtaggtccataagtggacatgttcttgcaagcatttttaacttttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
upper sequence: LOC_Os01g04840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 3'ss of exon 2
ttctctttcttttctttgctgctactgctagtactagtgcagtatgctttgttctttgtttctgtttcatgttatgttaacgattttggttttct----tgcagCATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAAAGTGAGAAACTAGTTGCTAATCTTTTCCAGATGGCCCGTGAAAATGCTCCCTCCATTATC
| || |||||| || | || | ||| |||| ||| ||| | |||| | || | | | |||| || | | |||| | ||||||||||||||||| || || |||||||| ||||||||||| ||||| | || |||||| ||||||||||||||| ||||||||| |||||
-ttggttgtttttctatgtcagt-ttgtttttac-agtgtt-tatacttggaaacatgttatagcttaagaaaagttgtttcctttttacttcccaaccttcagCGTGTCTTCATCAGACCTTGTCTCGAAGTGGATGGGTGAAAGTGAGAAGCTAGTATCAAACCTTTTCGAGATGGCCCGTGAAAGTGCTCCCTCGATTATT
upper sequence: LOC_Os01g04840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0106g00490.t01 (Vitis vinifera), 3'ss of exon 2
ttctctttcttttctttgctgctactgctagtactagtgcag-tatgctttgttctttgtttctgtttcatgttatgt-taacgattttggttttcttgcagCATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAAAGTGAGAAACTAGTTGCTAATCTTTTCCAGATGGCCCGTGAAAATGCTCCCTCCATTATC
| | | | | || | | ||| | | |||| | | | | || | | | | | | || || ||| | |||||||| || || ||||||||||||||||| |||||||| || ||||| | ||||| || || ||||| ||||||| |||||| ||||| ||
--tacaaacgaaagaagggttggcttaatatcatagatacaggtttattttgatagacttgagcctacaaagtcacaaatgccaaatattgtctttccacagTGTGTCTTCATCTGATCTAGTTTCAAAATGGATGGGTGAAAGTGAAAAGCTAGTCTCAAATCTGTTTCAAATGGCTCGTGAAAGTGCTCCTTCCATCATT
upper sequence: LOC_Os01g04840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S200_72V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------------ttctctttcttttctttgctgctactg---------ctagtactagtgcagtatgctttgttctttgtttctgtttcatgt----------tatgttaacgatttt----ggttttcttgcagCATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAAAGTGAGAAACTAGTTGCTAATCTTTTCCAGATGGCCCGTGAAAATGCTCCCTCCATTATC
|| || | ||| | | || || | |||| || | ||| | ||| | | ||| | || | |||||| ||| ||||| || || || || ||| | || ||||| ||||||||||| || |||||||| ||||| ||||| || || ||||||| |||| |||||| ||||||||
gtaactggagaagcatatatgcaaacaacaatgattttgttggatgcattttctttttgttttgttgcaataatcactattccagacttgggtcaaatgaagaataatctgagaagagtgggtaataaggtcttccaagcttcaggatgttgtgaatggtggctgcgtgactgattttttaaactttctctgcagTATTTCCTCTTCTGACTTGGTGTCAAAGTGGATGGGAGAGAGCGAGAAACTTGTTGCAAATCTGTTTCAAATGGCCCATGAAGCTGCTCCATCCATTATT
upper sequence: LOC_Os01g04840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S76_197V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------ttctctttcttttctttgct-------gctactgctagtactagtgcagtatgct-ttgtt----ctttgtttctgtttcat-----gttatgttaacgattttggttttctt--gcagCATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAAAGTGAGAAACTAGTTGCTAATCTTTTCCAGATGGCCCGTGAAAATGCTCCCTCCATTATC
|| | || | || ||| | | | || || | ||| ||||| |||| | || | ||| || | |||| | |||| | |||| || || || |||||| | || ||||| ||||||||||| |||||||| || ||||| ||||| || || |||||||||||| |||||| ||||| |||
gtaactgtcgaagcataatttggacacgatcatcttgtattaccaactttggctaaatgaagaattctccgggacgagcgagaaatgaggttgttaaacctttagtatacttggactggtggttctgggactgattattactttcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctttgttctttgtttctgtttcatgttatgttaacgattttggttttcttgcagCATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAAAGTGAGAAACTAGTTGCTAATCTTTTCCAGATGGCCCGTGAAAATGCTCCCTCCATTATC
tgttaac putative branch site (score: 2)
ttttcttgc putative PPT
ttatgttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctctttcttttctttgctgctactgctagtactagtgcagtatgctttgttctttgtttctgtttcatgttatgttaacgattttggttttcttgcagCATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAAAGTGAGAAACTAGTTGCTAATCTTTTCCAGATGGCCCGTGAAAATGCTCCCTCCATTATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - tgctgct
- - - - - - - - - - - - ctgctag
- - - - - - - - - - - - - - - - -ctagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttatg
