Sequence
atgc intronic sequence ATGC exonic sequence...acagtcattttcaagatttacttgcttgaattctgcacggaattgaagactactgaaaatatattatactgatgcatttgttttttttttcctttttcagGAAACTTTAGGCTACATTGATATAAACCTCGCAGACGTGATCAGTAATAAGCGGATTAATGAAACGTACCATCTCATCGACTCAAAAACCGGTCAGATTC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g60350.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g60350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G050193_T02 (Zea mays), 3'ss of exon 12
-------------------------------------------------------------------------------------------acagtcatttt-caagatttacttgcttgaattctgcacggaattgaagactactgaaa-atatattatac-tgatgcatt-tgtt--ttttttttcctttttcagGAAACTTTAGGCTACATTGATATAAACCTCGCAGACGTGATCAGTAATAAGCGGATTAATGAAACGTACCATCTCATCGACTCAAAAACCGGTCAGATTC
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gtagaacagaattcttgccctccatttaatttactaatctactgcatcagaatggttgatatttacgcccggcattacgacatcactagttgcattttttttgttatctccgctagcctgtagcatgtatagaaacagaatccgaagaggtaaatatcaaacgtcttgtatcctgatacctgtatttcttggttcagGAAACTTTGGGCTATATTGATATTAGCCTTGCAGACGTGATCAGCAACAAGCGGATTAATGAAAAGTACCATCTCATAGACTCGAAAAATGGTCAGATCC
upper sequence: LOC_Os01g60350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G098331_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------------------acagtcattttcaagatttacttgcttgaattctgcacggaattgaagactactgaaaatatattatactgatgcatttgttttttttttcctttttcagGAAACTTTAGGCTACATTGATATAAACCTCGCAGACGTGATCAGTAATAAGCGGATTAATGAAACGTACCATCTCATCGACTCAAAAACCGGTCAGATTC
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gtagaatgtaattctcgtctatttaataactaatctactgcacctggtgactgctaattgccttttttttggaactgccgccttgtatgtggactgaattctaa-cagtagatcatttgaaggcataaatatcaaatatcttttatcctaatgcctgtattttcttgatccagGAAACTTTGGGCTACATTGATGTCAACCTTGCAGACGTGATCAGTAACAAGAGAATTAATGAGAAGTACCATCTCATAGACTCAAAAAATGGTCAGATCC
upper sequence: LOC_Os01g60350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G111737_T01 (Zea mays), 3'ss of exon 10
acagtcattttcaagatttacttgcttgaattctgcacggaattgaagactactgaaaatatattata-ctgatgcatttgttttttttttccttt-ttcagGAAACTTTAGGCTACATTGATATAAACCTCGCAGACGTGATCAGTAATAAGCGGATTAATGAAACGTACCATCTCATCGACTCAAAAACCGGTCAGATTC
| |||| | |||| | | ||| | | ||| | | ||| | | || || || | | | | || ||| | ||||||||||| |||||||||||||| | |||||||||||||||||| || |||||||||||||||| |||||||||||| |||||||||| |||||||| |
-tttttttttttttggagcctctgctagcttgtagcatgtagaaacagaat-ccgaagaggtcaaatgtcttgtgtcctgatacctgtatttcttggtccagGAAACTTTGGGCTACATTGATATTAGCCTCGCAGACGTGATCAGCAACAAGCGGATTAATGAAAAGTACCATCTCATAGACTCAAAAAATGGTCAGATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagactactgaaaatatattatactgatgcatttgttttttttttcctttttcagGAAACTTTAGGCTACATTGATATAAACCTCGCAGACGTGATCAGTAATAAGCGGATTAATGAAACGTACCATCTCATCGACTCAAAAACCGGTCAGATTC
tactgat putative branch site (score: 2)
tgcatttgtttttttt CT-rich tract
aaaatatattatactg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acagtcattttcaagatttacttgcttgaattctgcacggaattgaagactactgaaaatatattatactgatgcatttgttttttttttcctttttcagGAAACTTTAGGCTACATTGATATAAACCTCGCAGACGTGATCAGTAATAAGCGGATTAATGAAACGTACCATCTCATCGACTCAAAAACCGGTCAGATTC
- - - - - - - - - - -ttgcttg
- - - - - - - - - - - - - - - ttctgca
- - - - - - - - - - - - - - - - - - - - - - - - actactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgatg