Sequence
atgc intronic sequence ATGC exonic sequence...aaattttggcccatggtattgatttcaacatagatcctgtttcttgacactcctttcatatctctgcgctgcattcttacgagaaaccttattgcaccagGGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGTTACTTGTTTTCATCCC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g37832.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g37832.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G090647_T04 (Zea mays), 3'ss of exon 2
-aaattttggcccatggtattgatttcaacatagatcctgtttcttgacactcctttcatatctctgcgctgcattcttacgagaaaccttattgcaccagGGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGTTACTTGTTTTCATCCC--------------------------------------------------
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tgtatttatataattagtgatt-ttttagctcagatcctgttctttaagttcctcatcattggtaaaatctgcattctcatgagcatttttgctgcaccagGGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTCATCCCGTAAGTAGCTGAAGTCACTTGCTCGTTTAATGTATATTCATGTGCTCCCC
upper sequence: LOC_Os01g37832.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G090647_T05 (Zea mays), 3'ss of exon 2
-aaattttggcccatggtattgatttcaacatagatcctgtttcttgacactcctttcatatctctgcgctgcattcttacgagaaaccttattgcaccagGGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGTTACTTGTTTTCATCCC
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tgtatttatataattagtgatt-ttttagctcagatcctgttctttaagttcctcatcattggtaaaatctgcattctcatgagcatttttgctgcaccagGGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTCATCCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacactcctttcatatctctgcgctgcattcttacgagaaaccttattgcaccagGGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGTTACTTGTTTTCATCCC
ttcttac putative branch site (score: 2)
ccttatt putative PPT
tttcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaattttggcccatggtattgatttcaacatagatcctgtttcttgacactcctttcatatctctgcgctgcattcttacgagaaaccttattgcaccagGGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGTTACTTGTTTTCATCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA