Sequence
atgc intronic sequence ATGC exonic sequence...gcatcaggctaacaaaacacttctgtggaatgtggattacggtatgaaacgtggagtagctgggatggggttttacagtggcatcctgcgttccgtgcagGTATTTCAATTCGTTGCAGAGCGAGTGCTTCCCTGCATGCTTCCTCTCGGATGTAAACATGGTTATCTCTGCGCCTACTGGGAGTGGCAAAACCGTGCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g40450.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g40450.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G346278_T01 (Zea mays), 3'ss of exon 1
gcatcaggctaacaaaac----acttctgtggaatgtggattacggtatgaaacgtggagtagctgggatggggttt--tacagtggcatcctgcgttccgtgcagGTATTTCAATTCGTTGCAGAGCGAGTGCTTCCCTGCATGCTTCCTCTCGGATGTAAACATGGTTATCTCTGCGCCTACTGGGAGTGGCAAAACCGTGCTG
| ||| ||| ||| | || || || || |||| || | | ||| || | | |||| ||| | ||| | || ||| ||||| || |||||||| |||||||| |||||||||| || ||| ||| |||||||||| |||||||||||||| || ||||| |||||||| || ||||| ||
---ttaggttaatgaaatttagaattatgggggatatggagtaatatcgagagactggtgtgg---aggtgggatttagtgaagtaatgttttggtttctctgcagATACTTCAATTCCTTGCAGAGTGAGTGCTTCCATGTATGTTTCTTCTCGGATGTGAACATGGTTATCTCGGCACCTACGGGGAGTGGGAAGACCGTACTA
upper sequence: LOC_Os02g40450.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G07850.1 (Glycine max), 3'ss of exon 1
gcatcaggctaacaaaacacttctgtgg--aatgtggattacggtatgaaacgtggagtagctgggatggggttttacagtggcatcctgcgttcc-----gtgcagGTATTTCAATTCGTTGCAGAGCGAGTGCTTCCCTGCATGCTTCCTCTCGGATGTAAACATGGTTATCTCTGCGCCTACTGGGAGTGGCAAAACCGTGCTG
| || |||| | || | | || | | || | || | | | ||||| | | | |||| || | | | ||| ||||| ||||| | ||||| || ||||| ||| || |||| ||| |||||||||||||| |||||||| || ||||||||||| ||||| || ||
------gcctttcaaacctctgattgaatcggttcagaaaatattctgcatt-tgaattggtctcacaagggttcttgatttacatcatgagctttcgattatacagATATTTTAATTCACTTCAGAGTGAATGCTTTCCTATCTGTTTCCACTCTGATGTAAACATGGTCATCTCTGCACCAACTGGGAGTGGTAAAACTGTACTC
upper sequence: LOC_Os02g40450.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv14s0066g00880.t01 (Vitis vinifera), 3'ss of exon 1
gcatcaggctaacaaaac--acttctgtggaatgtggattacggtatgaaacgtggagtagctgggatggggttttacagtggcatcctgcgttc-cgtgcagGTATTTCAATTCGTTGCAGAGCGAGTGCTTCCCTGCATGCTTCCTCTCGGATGTAAACATGGTTATCTCTGCGCCTACTGGGAGTGGCAAAACCGTGCTG
| | | ||| ||| | || |||||| ||| ||| ||| | | || || |||| || || | | | | ||||||||||| |||||| ||||||| || |||||| |||| || || ||||| ||||||||||||||||| || || || ||||| ||||| ||||| |||||
acctgaatctacaaaatttaaatttattggaattgaaattct--tattcaactcatcacaatcag-ataaggccttactatgtttcactccttccgcatgcagGTATTTTAATTCGCTGCAGAGTGAATGCTTCTCTGCCTGTTTTCTCTCCGATGTAAACATGGTTATTTCAGCACCAACTGGAAGTGGTAAAACAGTGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaacgtggagtagctgggatggggttttacagtggcatcctgcgttccgtgcagGTATTTCAATTCGTTGCAGAGCGAGTGCTTCCCTGCATGCTTCCTCTCGGATGTAAACATGGTTATCTCTGCGCCTACTGGGAGTGGCAAAACCGTGCTG
ttttaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatcaggctaacaaaacacttctgtggaatgtggattacggtatgaaacgtggagtagctgggatggggttttacagtggcatcctgcgttccgtgcagGTATTTCAATTCGTTGCAGAGCGAGTGCTTCCCTGCATGCTTCCTCTCGGATGTAAACATGGTTATCTCTGCGCCTACTGGGAGTGGCAAAACCGTGCTG
gcatcag
- - - - -taacaaa
- - - - - - - - - acttctg
- - - - - - - - - - - - - -gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gtagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcatcc