Sequence
atgc intronic sequence ATGC exonic sequenceCCTCAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGGTAACGCGCCACGCCGCGGACCCAAATCTTTGCTGCTGCTGCCGCGTgtatgatccactctcctcgcctgttcggcagctattctgctttacttttctttcttgtttgcttcggatttactagtagcatatgcgcgccgaggtgttt...
Basic information
species | Oryza sativa |
transcript | LOC_Os11g28340.2 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g28340.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G031802_T02 (Zea mays), 5'ss of exon 1
-----------------------------------------------CCTCAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGGTAACGCGCCACGCCGCGGACCCAAATCTTTGCTGCTGCTGCCGCGTgtatgatcc-actctcctcgcctgttcg-gcagctattctgctttacttttctttcttgtttgcttcggatttactagtagcatatgcgcgccgaggtgttt
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GGATCGGAGATGAACGTGTTCCGGCTGGCGGGGGACATGACCCACCTCCTCAGCGTGGTAGTGCTGCTCCTCAAGATCCATACCATCAAGTCCTGCGCAGgta-cgcccttctcttc----ccctctccgccccactgggatcagggctaggattctaggaaccgaaactaattgcgctgccatttctccgtattttaacgactg--------------------------------------------
upper sequence: LOC_Os11g28340.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ33020 (Selaginella moellendorffii), 5'ss of exon 1
CCTCAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGGTAACGCGCCACGCCGCGGACCCAAATCTTTGCTGCTGCTGCCGCGTgtatgatccactctcctcgcctgttcggcagctattctgctttacttttctttcttgtttgcttcggatttactagtagcatatgcgcgccgaggtgttt
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-------------------GCAGCAGCGATGAATATCTTCCGGCTCTGCGGCGACATGACCCATCTCCTCAGCGTCGTGGTGCTGCTGCTCAAGATCCAC--ACCATCAAGTCTTG-CGCCGgtaagggaagagagaaaattt--tcttcgattcttttgatttcgtgctgcttagaaatctttgcgcag----------
upper sequence: LOC_Os11g28340.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ30337 (Selaginella moellendorffii), 5'ss of exon 1
CCTCAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGGTAACGCGCCACGCCGCGGACCCAAATCTTTGCTGCTGCTGCCGCGTgtatgatccactctcctcgcctgttcggcagctattctgctttacttttctttcttgtttgcttcggatttactagtagcatatgcgcgccgaggtgttt
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-------------------GCAGCAGCGATGAATATCTTCCGGCTCTGCGGCGACATGACCCATCTCCTCAGCGTCGTGGTGCTGCTGCTCAAGATCCAC--ACCATCAAGTCTTG-CGCCGgtaagggaagagagaaaattt--tcctcgattcttttgatttcgtgctgcttagaaatctttgcgcag----------Mapped 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|88730213|gb|CI753828.1|CI753828EST: CAGGTAACGCGCCACGCCGCGGACCCAAATCTTTGCTGCTGCTGCCGCGT GCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
genomic: CAGGTAACGCGCCACGCCGCGGACCCAAATCTTTGCTGCTGCTGCCGCGTgtatgatcca ... ctttttgcagGCATATCTCTAAAGACCCAGGAGCTATATGCACTTGTGTTTGCTGCTCGTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CCTCAGCGTGGTGGTGCTCCTCCTGAAGATCCACACCATCAAGTCCTGCGCAGGTAACGCGCCACGCCGCGGACCCAAATCTTTGCTGCTGCTGCCGCGTgtatgatccactctcctcgcctgttcggcagctattctgctttacttttctttcttgtttgcttcggatttactagtagcatatgcgcgccgaggtgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cggcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcgccg