Sequence
atgc intronic sequence ATGC exonic sequence...tctttgtttacctgttatacttgtaatctcgattttcctattcttatttttgtcagcatttagctattagtgtggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g33240.3 |
intron # | 6 |
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 6
lower sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 7
----------------------------------------------------------------------tctttgtttacctgttatacttgtaatc--tcgattt-tcctattcttattt----ttgtcagcatttagctattagtgt--ggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG
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gtatatgccttcctatattcattcaatttaaatttaaaaatgtgccaaatgtgttctgttaagaatacatttctcgcctatct-ttgtatttccattcctttaatatattttagtttttttcccaattctcatcctatttctataagttttaaggctg-tgttttttttcttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGCTCAACTGTTCCAG
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G063851_T02 (Zea mays), 3'ss of exon 7
----------------------------------------------------------------------tctttgtttacctgttatacttgtaatc--tcgattt-tcctattcttattt----ttgtcagcatttagctattagtgt--ggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG------------------------------------
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gtatatgccttcctatattcattcaatttaaatttaaaaatgtgccaaatgtgttctgttaagaatacatttctcgcctatct-ttgtatttccattcctttaatatattttagtttttttcccaattctcatcctatttctataagttttaaggctg-tgttttttttcttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGCTCAACTGTTCCAGGTATTCTGTGCACACTGCTGTCTGCTTGTGTTATTG
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 7
-tctttgtttacctgttatacttgta-atctcgattttcct--attcttatttttgtcagcatttagctattagtgtggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG
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atctttgtattgccattcctttaatatatctcagttttccccaattctcaccctattt--ctataagttttaagcttg--ctgtttatttttctcttgttttagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGCTCAACTGTCCCAG
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G063909_T04 (Zea mays), 3'ss of exon 6
--tctttgtttacctgttatacttgtaatctcgattttcctattcttatttttgtcagcatttagctattagtgtggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG------------------------------------
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gcttatctttctattgccattcctttaatatttttcagtgttcgccaattcttcccctctttctgtaagt--tttaagcatgtggggtttttcttgttctagGTCCCAACCAAAGATCAAGTTGATGCTCTATCAAAAGAATTGCTTGCGCGCTCAACTGTCCCAGGTATTTTGATCACACCGCTGGCTACTTGTGTTATTG
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 6
--tctttgtttacctgttatacttgtaatctcgattttcctattcttatttttgtcagcatttagctattagtgtggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG
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gcttatctttctattgccattcctttaatatttttcagtgttcgccaattcttcccctctttctgtaagt--tttaagcatgtggggtttttcttgttctagGTCCCAACCAAAGATCAAGTTGATGCTCTATCAAAAGAATTGCTTGCGCGCTCAACTGTCCCAGMapped 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: GTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTCTTTAGACTGGAAAG GTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGT
genomic: GTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTCTTTTGACTGGAAAGgtttggcttt ... tttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGT
EST:
gi|86904765|gb|CI310558.1|CI310558EST: GTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTCTTTTGACTGGAAAG GTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGT
genomic: GTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTCTTTTGACTGGAAAGgtttggcttt ... tttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttgtcagcatttagctattagtgtggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG
gactgat putative branch site (score: 3)
tttgtttc putative PPT
tatttgttt 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
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tctttgtttacctgttatacttgtaatctcgattttcctattcttatttttgtcagcatttagctattagtgtggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG
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