Sequence
atgc intronic sequence ATGC exonic sequence...aagtcatgctcttctggcattgtttttcctactttgttgatgagattcttgtatatcgttaaaaatccaagctttgacagagatccttctaattttccagCGGAATGTTTTCCGGATAGAACCGATGTACAATGCTTGCACAGGTGGCAAAAGGTTCTAAACCCTGAATTGGTCAAAGGGCCATGGTCCAAAGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os12g13570.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G470307_T01 (Zea mays), 3'ss of exon 1
aagtcatgctcttctggcattgtttttcctactttgttgatgagattcttgtatatcgttaaaaatccaagctttgacagagatccttctaattttccagCGGAATGTTTTCCGGATAGAACCGATGTACAATGCTTGCACAGGTGGCAAAAGGTTCTAAACCCTGAATTGGTCAAAGGGCCATGGTCCAAAGAA
| || | | | || ||||| | |||||| | | ||||| |||| |||||||| ||||||| || ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-------------------------------------------aagctctgcctcttgccttaagtccaaaccttgacaaaatgcgttctactttttcagcggaaagttttccagacagaaccgatgtacaatgtttgcacagGTGGCAAAAGGTTCTAAACCCTGAATTGGTCAAAGGGCCATGGTCCAAAGAA
upper sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G08660.1 (Glycine max), 3'ss of exon 4
--------aagtcatgctcttctggcattgtttttcctactttgttgatgagattcttgtatatcgttaaaaatccaagctttgacagagatccttctaattttccagCGGAATGTTTTCCGGATAGAACCGATGTACAATGCTTGCACAGGTGGCAAAAGGTTCTAAACCCTGAATTGGTCAAAGGGCCATGGTCCAAAGAA
| | | | ||| | || | | | || | | ||| | |||| || | | ||| | || || | ||| || ||||| ||||||||| ||||||||||||||||| |||||||| || || |||| || ||| | |||||||| |||||||| |||||
cacatacacacagagacatattaagcacttttaatttacccaaactaatta---tgcaatattttgttatgtgacct-gttctgattgccgaatttgta----tgtagCTGAGTGTTTCAAGGATAGAACTGATGTACAATGCTTGCATAGGTGGCAGAAAGTCTTAAATCCAGAACTTGTCAAAGGTCCATGGTCTAAAGAG
upper sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G08550.1 (Glycine max), 3'ss of exon 4
--aagtcatgctcttctggcattgtttttcctactttgttgatgagattcttgtatatcgttaaaaatccaagctttgacagagatccttctaattttccagCGGAATGTTTTCCGGATAGAACCGATGTACAATGCTTGCACAGGTGGCAAAAGGTTCTAAACCCTGAATTGGTCAAAGGGCCATGGTCCAAAGAA
| || | | | | | || ||| | | | || | | || | | | || || | ||| |||||| ||||| ||||||||| ||||||||||||||||| |||||||| || || |||| || ||| | |||||||| |||||||| |||||
tacacacacacacagatacattaagcacttttaatttac--acaaattaattatgcaatattttgttatgtgacctgttctgattgccaaatttgtttgtagCGGAGTGTTTCAAGGATAGAACTGATGTACAATGCTTGCATAGGTGGCAGAAAGTCTTAAATCCAGAACTCGTCAAAGGTCCATGGTCTAAAGAG
upper sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0008g03780.t01 (Vitis vinifera), 3'ss of exon 3
aagtcatgctcttctggcattgtttttcctactttgttgatgagattcttg--tatatcgttaaaaatccaagctt-tgacagagatccttctaattttccagCGGAATGTTTTCCGGATAGAACCGATGTACAATGCTTGCACAGGTGGCAAAAGGTTCTAAACCCTGAATTGGTCAAAGGGCCATGGTCCAAAGAA
|| || || | | | | || | | ||| | | | | | |||| | | | || | | || | ||| | |||| |||||||||||| |||| | || ||||| |||||||||||||||||||| ||||| | || || ||| | |||||||| |||||||| |||||
aatccacaacattttaa-gcttctcctattattgtattgcctaaaatttgaaatgtatctctgttgacggatatttctaatagtaaaacttgt--ttttttagCGGAATGTTTCAAGGATCGGACAGATGTGCAATGCTTGCACAGGTGGCAGAAGGTCTTGAATCCAGAACTTGTCAAAGGTCCATGGTCAAAAGAG
upper sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S36_43V6.1 (Physcomitrella patens), 3'ss of exon 3
-------aagtcatgctc-ttctggcattgtttttcctactttgttgatgagattcttgtatatcgttaaaaatccaagctt-tgacaga-----------gatccttc-taattttccagCGGAATGTTTTCCGGATAGAACCGATGTACAATGCTTGCACAGGTGGCAAAAGGTTCTAAACCCTGAATTGGTCAAAGGGCCATGGTCCAAAGAA-----
|| ||| || ||| | | | || ||||| | |||| | | | || | ||||| || | | | | ||||| ||| || |||||| ||||||| | || ||||| |||| ||||| |||||||||||||| |||||||||||||| ||||| || ||||||| || ||||| |||||||
gtgagtgaattcaagcaaattccagtact-ttgaatctactcttttgagaaattgcgagtccaa-gttaattctctactcgtgtcacagatcacatatctggattttttacaattttgcagCGGAGTTCTTCACGGATCGAACAGATGTGCAATGCTTGCACAGATGGCAAAAGGTTCTCAACCCAGATCTGGTCAAGGGTGCATGGACCAAAGAGGAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttgtatatcgttaaaaatccaagctttgacagagatccttctaattttccagCGGAATGTTTTCCGGATAGAACCGATGTACAATGCTTGCACAGGTGGCAAAAGGTTCTAAACCCTGAATTGGTCAAAGGGCCATGGTCCAAAGAA
ttctaat putative branch site (score: 2)
tccttctaattttcc CT-rich tract
tatatcgttaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagtcatgctcttctggcattgtttttcctactttgttgatgagattcttgtatatcgttaaaaatccaagctttgacagagatccttctaattttccagCGGAATGTTTTCCGGATAGAACCGATGTACAATGCTTGCACAGGTGGCAAAAGGTTCTAAACCCTGAATTGGTCAAAGGGCCATGGTCCAAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - catgctc
- - - - - -ttctggc
- - - - - - - - - - - - - - - - - -gttgatg
- - - - - - - - - - - - - - - - - - - - - - attcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccaagc