Sequence
atgc intronic sequence ATGC exonic sequencegtatgattctgctatcgattatttatggataaatctattgctattgctttttaagggtgtccttaattgattgggctaaagtcttgaattgtgtttctccagGTCCTTGGCGGGATGAGAGGAATGATTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGAGGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g33240.3 |
intron # | 4 |
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 4
lower sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 5
gtatgattctgctatcgattatttatggataaatctattgctattgctttttaagggtgtcc-ttaattgattgggctaaagtcttgaattgtgtttctccagGTCCTTGGCGGGATGAGAGGAATGATTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGAGGAG
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gtataata-tactgcttattagttgcctatggat--agttatgttgcttttctagagcatatattaactcatcatgtgaaaatccttaataatgttcctgcagGTCCTTGGTGGAATGAGAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 4
gtatgattctgctatcgattatttatggataaatctattgct--attgctttttaagggtgtccttaattgattgggctaaagtcttgaattgtgtttctccagGTCCTTGGCGGGATGAGAGGAATGATTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGAGGAG
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gtataata-tactgcttatcaattgcctatatatgtatagctttgtcgcttttctaggataatgtt------------------cttgaataatgttcctgcagGTCCTTGGTGGAATGAGAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAG
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G063851_T02 (Zea mays), 3'ss of exon 5
gtatgat---tctgctatcgattatttatggataaatctattgctattgctttttaagggtgtccttaattgattgggctaaagtcttgaattgtgtttctccagGTCCTTGGCGGGATGAGAGGAATGATTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGAGGAG
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gtatgatatattgcttatcaattgtctatggatagttttgttgct------tttatagcatatact-aacttatcctgggaaattcctgaatgatgttcctccagGTCCTTGGTGGAATGAGAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 5
----gtatgattctgctatcgattatttatggataaatctattgctattgctttttaagggtgtccttaattgattgggctaaagtcttgaattgtgtttctccagGTCCTTGGCGGGATGAGAGGAATGATTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGAGGAG
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gtagaaacaatcatgattttcacgtttttggtttgtttatatgattttcaccttccattg-----cataactcatcataatcccctttgaaataa---------agGTTATTGGTGGAATGAGAGGGATGACTGGATTGCTTTGGGAAACCTCATTGCTTGACCCGGAAGAGMapped 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|86904765|gb|CI310558.1|CI310558EST: TTAAATCAGAACATGGGAAGGTCCAGCTTGGAAACATAACTGTTGATATG GTCCTTGGCGGGATGAGAGGAATGATTGGAATGCTTTGGGAAACATCATTG
genomic: TTAAATCAGAACATGGGAAGGTCCAGCTTGGAAACATAACTGTTGATATGgtatgattct ... gtttctccagGTCCTTGGCGGGATGAGAGGAATGATTGGAATGCTTTGGGAAACATCATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttaagggtgtccttaattgattgggctaaagtcttgaattgtgtttctccagGTCCTTGGCGGGATGAGAGGAATGATTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGAGGAG
ggctaaa putative branch site (score: 3)
tgtttctcc putative PPT
ttaattgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgattctgctatcgattatttatggataaatctattgctattgctttttaagggtgtccttaattgattgggctaaagtcttgaattgtgtttctccagGTCCTTGGCGGGATGAGAGGAATGATTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG