Sequence
atgc intronic sequence ATGC exonic sequence...ttcctactgtctgtatttttgcattcaagtagtatattaaagaagttttgtactttgaataaggaaatcgtgtcgtcatgttatttattttccatttcagGCATTTGGTCGCACTCCTCTTACTGATATAAGCCCTAAGAAGACCTTGGAGGGTGCTTTAGCTGGTCTAACTGGCTGTGTACTGACCACTGTGCTTCTTT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g03460.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g03460.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G027043_T01 (Zea mays), 3'ss of exon 3
ttcctactgtctgtatttttgcattcaagtagtatattaaagaagttttgtactttgaataaggaaatcgtgtcgtca----tgttatttattttccatttcagGCATTTGGTCGCACTCCTCTTACTGATATAAGCCCTAAGAAGACCTTGGAGGGTGCTTTAGCTGGTCTAACTGGCTGTGTACTGACCACTGTGCTTCTTT
| | | ||| | | | || | || | || || ||| || || || | ||| | | ||||||||||| || ||||||||||||||||| || ||| | ||| | |||||||||||||| ||||||||||||||||||||||| ||| |||||||||| |||||||||||||| || |
----cagttaatctatctgtataatctggccagttaagtttgcagattagtagttgaaaggagtaccatgtgaccttgaccttgttatttattctctgtttcagGCATTTGGTCGTACCCCTTTGACTAACATAAGCCCTAAGAAAACCTTGGAGGGTGCTTTAGCTGGCCTAGCTGGCTGTGTGCTGACCACTGTGCTGCTGT
upper sequence: LOC_Os02g03460.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G053711_T05 (Zea mays), 3'ss of exon 3
-ttcctactgtctgtatttttgcattcaagt-agtatattaaagaagttttgtactttgaataaggaaatcgtgtcgtcatgttatttattttccatttcagGCATTTGGTCGCACTCCTCTTACTGATATAAGCCCTAAGAAGACCTTGGAGGGTGCTTTAGCTGGTCTAACTGGCTGTGTACTGACCACTGTGCTTCTTT
| | | | | ||| | | || ||| | | | | ||| ||| | || | | | ||| ||||||||| ||| || ||||||||||||||||| || ||| | ||| | |||||||||||||||||||||||||||||||||||||| ||| ||||||| ||||||||||||||||| || |
gtgctcagttaattcattggtataacatggtcagttaagtttacagatttagtagctgaaa--ggagtaccatgtgaccatgttattcattctctgtttcagGCATTTGGTCGTACCCCTTTGACTAACATAAGCCCTAAGAAGACCTTGGAGGGTGCTTTAGCTGGCCTAGCTGGCTGCGTACTGACCACTGTGCTGCTGT
upper sequence: LOC_Os02g03460.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G053711_T03 (Zea mays), 3'ss of exon 3
ttcctactgtctgtatttttgcattcaagtagtatattaaagaagttttgtactttgaataaggaaatcgtgtcgtcatgttatttattttccatttcagGCATTTGGTCGCACTCCTCTTACTGATATAAGCCCTAAGAAGACCTTGGAGGGTGCTTTAGCTGGTCTAACTGGCTGTGTACTGACCACTGTGCTTCTTT
| | ||| ||| | | | | ||| ||| | || | | | ||| ||||||||| ||| || ||||||||||||||||| || ||| | ||| | |||||||||||||||||||||||||||||||||||||| ||| ||||||| ||||||||||||||||| || |
---------------gtataacat--ggtcagttaagtttacagatttagtagctgaaa--ggagtaccatgtgaccatgttattcattctctgtttcagGCATTTGGTCGTACCCCTTTGACTAACATAAGCCCTAAGAAGACCTTGGAGGGTGCTTTAGCTGGCCTAGCTGGCTGCGTACTGACCACTGTGCTGCTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgtactttgaataaggaaatcgtgtcgtcatgttatttattttccatttcagGCATTTGGTCGCACTCCTCTTACTGATATAAGCCCTAAGAAGACCTTGGAGGGTGCTTTAGCTGGTCTAACTGGCTGTGTACTGACCACTGTGCTTCTTT
tttattttccatttc CT-rich tract
ttatttattttccatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcctactgtctgtatttttgcattcaagtagtatattaaagaagttttgtactttgaataaggaaatcgtgtcgtcatgttatttattttccatttcagGCATTTGGTCGCACTCCTCTTACTGATATAAGCCCTAAGAAGACCTTGGAGGGTGCTTTAGCTGGTCTAACTGGCTGTGTACTGACCACTGTGCTTCTTT
- cctactg
- - - - - - - - - -tgcattc
- - - - - - - - - - - - - - - - - - -taaagaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtt