Sequence
atgc intronic sequence ATGC exonic sequencegttaccttgagattcaactcaagctttctccataatatgaaatcttttgacactattgtaaccttgcaacatccatatctctagATTACCCCAGCAAAGGATGGTAAACCCGTGTTGATTGAGTTAATTGATGCTAAGACAAAGGAACACAAGGAAACACTTGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g23610.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 5
gttaccttgagattcaactcaagctttctccataatatgaaatcttttgacactattgta-------accttgcaacatccatatctctagATTACCCCAGCAAAGGATGGTAAACCCGTGTTGATTGAGTTAATTGATGCTAAGACAAAGGAACACAAGGAAACACTTGAG
|| | || || ||||||||| |||| | || || || |||||| || |||||| |||| | || ||| |||||||||||||||||||||||||||||| || || ||||||||| | ||||||||||| ||||| ||||||||||| |||||||||
gtaaagttaag-ctcaactcaatcttttta-atgatgtgtaatcttccagcatgattgtataattatacctcaaagtattcatgtctctagATTACCCCAGCAAAGGATGGTAAGCCTGTTTTGATTGAGCTGATTGATGCTAAAACAAAAGAACACAAGGAGACACTTGAG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 6
gttaccttgagattcaactcaagctttctccataatatgaaatcttttgacacta---ttgtaaccttgcaacatccatatctct----agATTACCCCAGCAAAGGATGGTAAACCCGTGTTGATTGAGTTAATTGATGCTAAGACAAAGGAACACAAGGAAACACTTGAG
|| | | | || |||| || || | || | || || || ||| | || | || | | ||| |||| || |||||||||||||| ||||| ||| ||||||| |||||||||| || || ||||||| |||||| || | |||
gtaagcctt---tttgtctcatgcattttaaattagatatcttccttacacagtgggtttacgaattttttttgttaacgcttctttacagATCACTCCAGCAAAGGATGGGAAACCAGTGCTGATTGAACTAATTGATGCCAAAACCAAGGAACCCAAGGATACTTTGGAG
upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 6
gttaccttgagattca--actcaagctttctccataatat--gaaatcttttgacactattgtaaccttgcaacatccatatctctagATTACCCCAGCAAAGGATGGTAAACCCGTGTTGATTGAGTTAATTGATGCTAAGACAAAGGAACACAAGGAAACACTTGAG
| | | ||| ||| || ||| || | ||| | | ||| | | | || || | | | | ||||||| ||||| |||||||| ||||| || ||||||| | |||||||| ||||||||||||| ||||| || | |||
-gtgtttgatggctcacagctcttctttcaattgtaaaattaggaatagtataacagttaaatttctttctttaatgcttgt-tacagATTACTCCAGCTAAGGATGGAAAACCTGTTATGATTGACCTCATTGATGCAAAGACAAAGGAACCAAAGGATACTTTAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccataatatgaaatcttttgacactattgtaaccttgcaacatccatatctctagATTACCCCAGCAAAGGATGGTAAACCCGTGTTGATTGAGTTAATTGATGCTAAGACAAAGGAACACAAGGAAACACTTGAG
ttgtaac putative branch site (score: 2)
tatctct putative PPT
atatgaaatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaccttgagattcaactcaagctttctccataatatgaaatcttttgacactattgtaaccttgcaacatccatatctctagATTACCCCAGCAAAGGATGGTAAACCCGTGTTGATTGAGTTAATTGATGCTAAGACAAAGGAACACAAGGAAACACTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA