Sequence
atgc intronic sequence ATGC exonic sequence...gtcggcacccgtggtttttttccgcaaggattctccatgtaaaattttatgtctctgttgtgcatctattttcataacattgatgtaactttttcatcagGTGGAAGTGTGCCTTCAGACATTTGGTCCAGGCCAAAGGACACCCATCCACAGGCACTCATGTGAGGAAGTTTTTGTTGTGTTGAAAGGGAAAGGCACAC
Basic information
species | Oryza sativa |
transcript | LOC_Os12g34450.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g34450.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G078508_T01 (Zea mays), 3'ss of exon 2
gtcggcacccgtggtttttttccgcaa---ggattctccatgtaaaattttatgtctctgttgtgcatctattttcataacattgatgtaactttttcatcagGTGGAAGTGTGCCTTCAGACATTTGGTCCAGGCCAAAGGACACCCATCCACAGGCACTCATGTGAGGAAGTTTTTGTTGTGTTGAAAGGGAAAGGCACAC
| |||| | | || | | || || ||||| | | | ||| || || || | | || | |||| | |||||||||||||| || || |||||||||||||| |||||||| || ||||||||||| || ||||| || ||||| |||| | || ||||||||||| |
gatatgtttggtggctcatgtctcatattcgaataatctatgtacggtgta--gatgtggttatg-attccttcttgcttctttatcaaatgttttcctgcagGTGGAAGTGTGGCTACAAACATTTGGTCCAGGTCAAAGGACCCCAATCCACAGGCATTCTTGTGAAGAGGTTTTCATTGTCCTCAAGGGGAAAGGCACGC
upper sequence: LOC_Os12g34450.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G116204_T01 (Zea mays), 3'ss of exon 2
---gtcggcacccgtggtttttttccgcaaggattctccatgtaaaattttatgtctctgttgtgcatctattttcataacattgatgtaactttttcat-cagGTGGAAGTGTGCCTTCAGACATTTGGTCCAGGCCAAAGGACACCCATCCACAGGCACTCATGTGAGGAAGTTTTTGTTGTGTTGAAAGGGAAAGGCACAC
|| | | || | | || || || | | | | || | ||||| ||| || || | | | ||| || ||||| | |||||||||||||| ||||||||| | ||||||| |||||||| || ||||||||||| || ||||| |||||||| ||| | |||||||| || || |
tgtgtagatatgtttgatagagtcatattcaaatagtctat-tgacagtgta-gatactgttatgcttcc-ttcttgcttcgtc-atgaaatgttttcctgcagGTGGAAGTGTGGCTTCAGACAATAAGTCCAGGTCAAAGGACGCCAATCCACAGGCATTCCTGTGAAGAAGTTTTCACTGTCCTCAAAGGGAAGGGTACGC
upper sequence: LOC_Os12g34450.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064371_T03 (Zea mays), 3'ss of exon 2
---gtcggca-cccgtggtttttttccgcaaggattctccatgtaaaattt---tatgtctctgttgtgcatctattttcataacattgatgtaactttttcatcagGTGGAAGTGTGCCTTCAGACATTTGGTCCAGGCCAAAGGACACCCATCCACAGGCACTCATGTGAGGAAGTTTTTGTTGTGTTGAAAGGGAAAGGCACAC
| || | | || | | | || || || ||||| | | | | | || | | || || || |||| |||| | |||||||||||||| || || |||||||||||||| |||||||| || ||||||||||| || ||||| || ||||| |||| | || ||||||||||| |
atgtttggtggctcatgtctcatattcg----aataatctatgtacggtgtagatgcggttatgattccttcttgcttctttatca--aatgtt-tttttcctgcagGTGGAAGTGTGGCTACAAACATTTGGTCCAGGTCAAAGGACCCCAATCCACAGGCATTCTTGTGAAGAGGTTTTCATTGTCCTCAAGGGGAAAGGCACGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatgtctctgttgtgcatctattttcataacattgatgtaactttttcatcagGTGGAAGTGTGCCTTCAGACATTTGGTCCAGGCCAAAGGACACCCATCCACAGGCACTCATGTGAGGAAGTTTTTGTTGTGTTGAAAGGGAAAGGCACAC
ctttttcatc CT-rich tract
tattttcataacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcggcacccgtggtttttttccgcaaggattctccatgtaaaattttatgtctctgttgtgcatctattttcataacattgatgtaactttttcatcagGTGGAAGTGTGCCTTCAGACATTTGGTCCAGGCCAAAGGACACCCATCCACAGGCACTCATGTGAGGAAGTTTTTGTTGTGTTGAAAGGGAAAGGCACAC
- cggcacc
- - - - - - - - - - - - - - - - ctccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgatgt