Sequence
atgc intronic sequence ATGC exonic sequence...aattaaccaaaaccatttaaaaaatcgttaataaaagccttgtatttctctgccttttgtaattcttatttagctcttctattttaactcttattttcagGTTGAGAGTGAGTTTCAAAAAGCTTACGACAAAGGAATGCCAAAATCAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os11g33240.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 9
-----aattaaccaaaaccatttaaaaaatcgttaataaaagccttgtatttctctgccttttgtaattcttatttagctcttctattttaactcttattttcagGTTGAGAGTGAGTTTCAAAAAGCTTACGACAAAGGAATGCCAAAATCAAA
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gtggtacttaaattaa-tctcccattgtgtcgtggatgctgtttttaaattatgtagcc----gtgaaagtgacttagttttccatttttaaaccccattttcagGTTGAGAGCGAATTTCAAAAAGCTTATGACAATGGATTGCCAAAATCAAA
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G063909_T02 (Zea mays), 3'ss of exon 8
---aattaaccaaaaccatttaaaaaatcgttaataaaagccttgtatttctctgccttttgtaattcttatttagctcttctattttaactcttattttcagGTTGAGAGTGAGTTTCAAAAAGCTTACGACAAAGGAATGCC-AAAATCAAA
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aagtggtatttaaattaatcccccattgtgtcatggatgtatttgtaaattatgaagcctcgaaagtg--acttagttttccatttttaaatcccattt-cagGTTGAGAGCGAATTTCAAAAAGCTTACGGCAATGGATTGCCCAAAATCAAA
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 9
aatta-accaaaaccatttaaaaaatcgttaataaaagccttgtatttctctgccttttgtaattcttatttagctcttctattttaactcttattttcagGTTGAGAGTGAGTTTCAAAAAGCTTACGACAAAGGAATGCCAAAATCAAA
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agttgtatttaaattaatttcctattgtgtcatggatgctctttgtaaattctaaagcctaaaaaatgactta-cttttccattttcaaaccccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|38470398|gb|CF954529.1|CF954529EST: TAACTGCTCATCCAATGACACAGTTTACCACAGGGGTGATGGCACTTCAA GTTGAGAGTGAGTTTCAAAAAGCTTACGACAAAGGAATGCCAAAATCAAA
genomic: TAACTGCTCATCCAATGACACAGTTTACCACAGGGGTGATGGCACTTCAAgtaaacactt ... ttattttcagGTTGAGAGTGAGTTTCAAAAAGCTTACGACAAAGGAATGCCAAAATCAAA
EST:
gi|86904765|gb|CI310558.1|CI310558EST: TAACTGCTCATCCAATGACACAGTTTACCACAGGGGTGATGGCACTTCAA GTTGAGAGTGAGTTTCAAAAAGCT
genomic: TAACTGCTCATCCAATGACACAGTTTACCACAGGGGTGATGGCACTTCAAgtaaacactt ... ttattttcagGTTGAGAGTGAGTTTCAAAAAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctctgccttttgtaattcttatttagctcttctattttaactcttattttcagGTTGAGAGTGAGTTTCAAAAAGCTTACGACAAAGGAATGCCAAAATCAAA
ttttaac putative branch site (score: 2)
ctcttattttc CT-rich tract
ttctattttaactctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattaaccaaaaccatttaaaaaatcgttaataaaagccttgtatttctctgccttttgtaattcttatttagctcttctattttaactcttattttcagGTTGAGAGTGAGTTTCAAAAAGCTTACGACAAAGGAATGCCAAAATCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA