Sequence
atgc intronic sequence ATGC exonic sequenceTCCAACAACGACATCCCGGCTCCCAACAACACCCTCCCCACCATCATCACCAAGTTCAAGCTCCAGGGCCTCGACATCGTCGACCTCGTCGCCCTCCTCGgtatttatattatgtcgcatatgatttataatctatcctttatatatattgttacgacttaacctatttgtcagtgactgttgttatatagcgctagtga...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g36240.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g36240.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G023840_T01 (Zea mays), 5'ss of exon 3
TCCAACAACGACATCCCGGCTCCCAACAACACCCTCCCCACCATCATCACCAAGTTCAAGCTCCAGGGCCTCGACATCGTCGACCTCGTCGCCCTCCTCGgtatttatat-tatgtcgc-----atatgatttataatctatcctttatat-atattgttacgacttaacctatttgtcagtgactgttgttatatagcgctagtga
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TCCAACAACGACATCCCTGCTCCCAACAACACTCTCCCCACCATCATCACAAAGTTCAAGCTCCAGGGCCTCGACATCGTCGACCTCGTCGCACTCCTCGgtacgtacgtatacctagctactagtatcctgcacgat-tatcttctacatgatgcagctggggctttacagaagcatc---tagcgtcttcatgtcacgatcc---
upper sequence: LOC_Os01g36240.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G66390.1 (Arabidopsis thaliana), 5'ss of exon 3
TCCAACAACGACATCCCGGCTCCCAACAACACCCTCCCCACCATCATCACCAAGTTCAAGCTCCAGGGCCTCGACATCGTCGACCTCGTCGCCCTCCTCGgtatttatattatgtcgcatatgatttataatctatcctttatatatattgttacgacttaacctatttgtcagtgactgttgttatatagcgctagtga
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TCCAACAACGACATTCCTGCTCCAAACAACACTTTCCAAACCATCCTCACTAAGTTCAAGCGTCAAGGCCTTGATCTCGTCGATCTTGTCTCCCTCTCAGgtatacatatc-tatc-catctttattacacgaaacattttcaataacttattacacttt----taagaagcggatacatatgatttatag---------
upper sequence: LOC_Os01g36240.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv04s0023g02570.t01 (Vitis vinifera), 5'ss of exon 3
TCCAACAACGACATCCCGGCTCCCAACAACACCCTCCCCACCATCATCACCAAGTTCAAGCTCCAGGGCCTCGACATCGTCGACCTCGTCGCCCTCCTCGgta---tttatattatgtcgcatatgatttataatctatcctttatatatattgttacgacttaacctatttgtcagtgactgttgttatatagcgctagtga
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TCCAACAACAACATTCCTGCTCCAAACAACACCTTCCAGACCATTCTCACCAAGTTCAAGCTACACGGGCTTAACATCGTGGATCTTGTTGCTCTATCTGgtaaaattgatgaaagtttttaactacttttttacaggaactccctgatgattgtaagaagcagatatggttaatttttcttctgataattgagtgcag----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|6449619|gb|AU081561.1|AU081561EST: CAAGTTCAAGCTCCAGGGCCTCGACATCGTCGACCTCGTCGCCCTCCTCG GTAGCCACACCATCGGCGACTCCCGGTGCACGAGCTTCCGGCAGCGGCTGT
genomic: CAAGTTCAAGCTCCAGGGCCTCGACATCGTCGACCTCGTCGCCCTCCTCGgtatttatat ... tgactgacagGTAGCCACACCATCGGCGACTCCCGGTGCACGAGCTTCCGGCAGCGGCTGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCCAACAACGACATCCCGGCTCCCAACAACACCCTCCCCACCATCATCACCAAGTTCAAGCTCCAGGGCCTCGACATCGTCGACCTCGTCGCCCTCCTCGgtatttatattatgtcgcatatgatttataatctatcctttatatatattgttacgacttaacctatttgtcagtgactgttgttatatagcgctagtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC