Sequence
atgc intronic sequence ATGC exonic sequence...tttcctactggattttcttaactgaaagggaaaaacttgctaactgatcatacttctctttagtttttctattcataattttttggtttttttttttcagGTGGGAAAATTAGCTGACCTTGTTATTTGGAAACCTTCTTTCTTTGGAGCAAAACCAGAAATGGTTATAAAGGGTGGTGCTATTGCATGCGCTAATATGG
Basic information
species | Oryza sativa |
transcript | 13114.m00152 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: 13114.m00152 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G461569_T01 (Zea mays), 3'ss of exon 15
tttcctactggattttcttaactgaaagggaaaaacttgctaactgatcatacttctctttagtttttctattcataatttt-ttggtttt------tttttttcagGTGGGAAAATTAGCTGACCTTGTTATTTGGAAACCTTCTTTCTTTGGAGCAAAACCAGAAATGGTTATAAAGGGTGGTGCTATTGCATGCGCTAATATGG
| | || | | | | | | ||||| || | | | || || | || || || | | || | ||||| ||||||||||||||||||||||||||| |||||||||| |||||||| || || ||||||||| ||||| ||||||| ||||| |||||||| ||||| ||||
-------ccgtatgtcatgacattgacacccagtgattgctggctaagcgtttcctctattcgtatctcaatccaaggtctaactgaagctacacaatttttgacagGTGGGAAAATTAGCTGACCTTGTTCTTTGGAAACCATCTTTCTTCGGCGCTAAACCAGAACTGGTTGTAAAGGGAGGTGCAATTGCATGGGCTAACATGG
upper sequence: 13114.m00152 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 16
--tttcctactggattttcttaactgaaagggaaaaacttgctaactgatcatacttctctttagtttttctattcataattttttggtttttttttttcagGTGGGAAAATTAGCTGACCTTGTTATTTGGAAACCTTCTTTCTTTGGAGCAAAACCAGAAATGGTTATAAAGGGTGGTGCTATTGCATGCGCTAATATGG
| || | | || || | | | ||| ||| | |||||| | || | || | ||| | | ||| | | |||| |||| ||| || || ||||| ||||| | ||||| || || || ||||||||||||||||||||||| || || ||||||| |||||| ||||| ||||
ctccccataatcattaacctcaatttacatatcaaa--ttggcagctgatccttctaatattagtatcatcttgaccccctcatttagacctagttttgcagGCGGGTAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGCAAAACCAGAAATGGTGATCAAAGGTGGTGAGGTTGCATATGCTAACATGG
upper sequence: 13114.m00152 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 15
tttcctactggattttcttaactgaaagggaa----aaacttgctaactgatcatacttctctt-tagtttttctattcataattttttggttttttttttt-cagGTGGGAAAATTAGCTGACCTTGTTATTTGGAAACCTTCTTTCTTTGGAGCAAAACCAGAAATGGTTATAAAGGGTGGTGCTATTGCATGCGCTAATATGG
|| | | | || || || | | | | | | | | | |||| | | | || || | || | ||| |||||||| || | ||||| |||||| | ||||| || ||||||||||| ||||||||||||||||| ||||| ||||||| |||||||| ||||| ||||
------gcttgtgtgtgtttacagagatcatactctggttccacccttgagttacattaccaaaattgtttactcgtccttgatgttgtatcttgtgtttccacagGTGGGGAAGGTGGCTGATCTTGTTCTCTGGAATCCATCTTTCTTTGGGGCAAAACCAGAAATGGTGATAAAAGGTGGTGTAATTGCATGGGCTAACATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcatacttctctttagtttttctattcataattttttggtttttttttttcagGTGGGAAAATTAGCTGACCTTGTTATTTGGAAACCTTCTTTCTTTGGAGCAAAACCAGAAATGGTTATAAAGGGTGGTGCTATTGCATGCGCTAATATGG
aactgat putative branch site (score: 3)
ttttttggtttttttt putative PPT
tttagtttttctattc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcctactggattttcttaactgaaagggaaaaacttgctaactgatcatacttctctttagtttttctattcataattttttggtttttttttttcagGTGGGAAAATTAGCTGACCTTGTTATTTGGAAACCTTCTTTCTTTGGAGCAAAACCAGAAATGGTTATAAAGGGTGGTGCTATTGCATGCGCTAATATGG
- -cctactg
- - - - - - - - - - - - - -gggaaaaa
- - - - - - - - - - - - - - - - - -cttgcta