Sequence
atgc intronic sequence ATGC exonic sequencegtcagtcataccaccacatttctaaacttctggttgctaaagttctcagatggccttgtttggctcctgtagaagtagttaattaatggactgaatatgcttggtttgccattccagGTTTCAACTGAGGTGTTTGGCTCATTTGGATACAGTGCCCCGGAGTTTGCCATGTCAGGAATTTATACCGTAAAGAGTGATGTGTACAGTTTTGGAGTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g09740.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g09740.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G103070_T01 (Zea mays), 3'ss of exon 13
gtcagtcataccaccacatttctaaacttctggttgctaaagttctcagatggccttgtttggctcctgtagaagtagttaattaatggactgaatatgcttggtttgccattccagGTTTCAACTGAGGTGTTTGGCTCATTTGGATACAGTGCCCCGGAGTTTGCCATGTCAGGAATTTATACCGTAAAGAGTGATGTGTACAGTTTTGGAGTTG
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gcaagtaacac----acatctcttccactgaggtttcttt--tcttcaaatacccatttctggatagttt----ctacttattccatgtattaacta--attggcctgtcactgcagGTTTCAACTGAAGTATTTGGATCATTTGGCTATAGCGCCCCAGAGTTTGCAATGTCTGGCATTTATACTGTAAAGAGCGATGTATACAGTTTTGGAGTGG
upper sequence: LOC_Os02g09740.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT4G22130.2 (Arabidopsis thaliana), 3'ss of exon 8
gtcagtcataccaccacatttctaaacttctggttgctaaagttctcagatggccttgtttggctcctgtagaagtagttaattaatggactgaatatgcttggtttgccattccagGTTTCAACTGAGGTGTTTGGCTCATTTGGATACAGTGCCCCGGAGTTTGCCATGTCAGGAATTTATACCGTAAAGAGTGATGTGTACAGTTTTGGAGTTG
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-----------------------------------gtaataacaatggaaagaatcagatttaatctaattgaaacattttctgagtc--tttcatggtttatgcatgtcaa--cagGTTTCAACTCAAGTGGTAGGTTCATTTGGATACAGCGCTCCAGAGTTTGCACTGTCGGGAATTTACACAGTGAAAAGTGATGTATACACTTTTGGAGTAG
upper sequence: LOC_Os02g09740.2 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ34030 (Selaginella moellendorffii), 3'ss of exon 3
gtcagtcataccaccacatttctaaacttctggttgctaaagttctcaga--tggccttgtttggctcctgtagaagtagttaattaatggactgaatatgcttggtttgccattccagGTTTCAACTGAGGTGTTTGGCTCATTTGGATACAGTGCCCCGGAGTTTGCCATGTCAGGAATTTATACCGTAAAGAGTGATGTGTACAGTTTTGGAGTTG
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-----------------------------------------gtctgaagaactagcgct-tttaaattctcttttattcctttgctgatag---gaaaaaactgg-----------cagGTTGCGGCACAAATGCTGGGTTCCTTTGGCTACAGTGCTCCGGAGTTTGCAATGTCTGGTGTTTATACCGTTAAAAGCGATGTGTACAGTTTTGGAGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctcctgtagaagtagttaattaatggactgaatatgcttggtttgccattccagGTTTCAACTGAGGTGTTTGGCTCATTTGGATACAGTGCCCCGGAGTTTGCCATGTCAGGAATTTATACCGTAAAGAGTGATGTGTACAGTTTTGGAGTTG
aattaat putative branch site (score: 3)
ccattcc putative PPT
aagtagttaattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtcataccaccacatttctaaacttctggttgctaaagttctcagatggccttgtttggctcctgtagaagtagttaattaatggactgaatatgcttggtttgccattccagGTTTCAACTGAGGTGTTTGGCTCATTTGGATACAGTGCCCCGGAGTTTGCCATGTCAGGAATTTATACCGTAAAGAGTGATGTGTACAGTTTTGGAGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG