Sequence
atgc intronic sequence ATGC exonic sequencegtatactttgatcacctcatgcaaatgtttgttccaaagcatccgcaattgtatctaattcggtttcttgtgatttgcagGTTTAGGTCCAGGTACCCTTGTGGGTTCTGCTGCATTTGATCTGTTCCCCATACATGCTGTTTGTGTGGTTATGCCAAGGGCAGGCTCTAAGAAAAAGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os11g43860.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g43860.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G126601_T01 (Zea mays), 3'ss of exon 2
-----gtatactttgatcacctcatgcaaatgtttgttccaaagcatccgcaa--ttgtatctaattcggtt-----tcttgtgatttgcagGTTTAGGTCCAGGTACCCTTGTGGGTTCTGCTGCATTTGATCTGTTCCCCATACATGCTGTTTGTGTGGTTATGCCAAGGGCAGGCTCTAAGAAAAAGAT
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gtagtacaagtgtggttttccttttttcaatatatatactatgtaattggctagcttggtgcacgcacgataggtaatttggagctttgcagGTCTAGGTCCAGGCACACTTGTCGGCTCTGCGGCGTTTGATCTGTTTCCGATCCACGCTGTCTGTGTGCTTATGCCAAGGGCGGGATCAAAGAAGAAGAT
upper sequence: LOC_Os11g43860.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G02250.1 (Glycine max), 3'ss of exon 1
------------------gtatactttgatcacctcatgcaaatgttt----gttccaaagcatccgcaattgtatctaattcggtttcttgtgatttgcagGTTTAGGTCCAGGTACCCTTGTGGGTTCTGCTGCATTTGATCTGTTCCCCATACATGCTGTTTGTGTGGTTATGCCAAGGGCAGGCTCTAAGAAAAAGAT
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gctgtagtatttgttttattgtgatcttaattctttctggaattgttgaggggcattagattgttaagcaatgtaataactataactgctga--atattcagGTTTGGGACCCGGAACACTTGTTGGTTCTGCAGCATTTGACCTGTTCCCCATCCACGCTGTTTGTGTAGTAGTTCCAAAAGCAGGAGAGCTGAAGAAGAT
upper sequence: LOC_Os11g43860.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G47600.1 (Arabidopsis thaliana), 3'ss of exon 2
-------gtatactttgatcacctcatgcaaatgtttgttccaaagcatccgcaattgtat-ctaattcggtttcttgtgatttgcagGTTTAGGTCCAGGTACCCTTGTGGGTTCTGCTGCATTTGATCTGTTCCCCATACATGCTGTTTGTGTGGTTATGCCAAGGGCAGGCTCTAAGAAAAAGAT
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gtctggtggttgttcctttcttccttccaaaactctagtttttacttttaagttcatgaattcttatatcatgttttgtca--tatagGTCTTGGTCCTGGAACACTTGTTGGCTCAGCTGCATTTGATCTTTTCCCCATCCACGCTGTTTGTGTCGTTGTGCCAAAAGCTGGAGAACTGAAAAAGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttgttccaaagcatccgcaattgtatctaattcggtttcttgtgatttgcagGTTTAGGTCCAGGTACCCTTGTGGGTTCTGCTGCATTTGATCTGTTCCCCATACATGCTGTTTGTGTGGTTATGCCAAGGGCAGGCTCTAAGAAAAAGAT
atctaat putative branch site (score: 3)
tttcttgt putative PPT
aattgtatctaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatactttgatcacctcatgcaaatgtttgttccaaagcatccgcaattgtatctaattcggtttcttgtgatttgcagGTTTAGGTCCAGGTACCCTTGTGGGTTCTGCTGCATTTGATCTGTTCCCCATACATGCTGTTTGTGTGGTTATGCCAAGGGCAGGCTCTAAGAAAAAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA