Sequence
atgc intronic sequence ATGC exonic sequence...gcattgctgtgaaatgtatgttgttttggcaggcaatgcaccattaataatatgtatatcatgttgttctgatagtgtaacccaatcttaatgcaatcagGAATAGGGTATAATGGATTTCCTAGAGGTTGTTCTGACAATAAGCTACCCTGGGCAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g55974.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g55974.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G03380.1 (Glycine max), 3'ss of exon 3
gcattgctgtgaaatg--tatgttgttttggca-ggcaatgcaccattaataatatgtatatcatgttgttctgatagtgtaacccaatcttaatgcaatcagGAATAGGGTATAATGGATTTCCTAGAGGTTGTTCTGACAATAAGCTACCCTGGGCAAAG
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--------gtaagttcattaggttctcatatcccaattattcactcttttttttttctctctc-tgaaacgcaggtttcttactttgctttttcttctgtcagGAATTGGTTATAATGGATTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCAAAG
upper sequence: LOC_Os01g55974.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G13950.1 (Glycine max), 3'ss of exon 2
gcattgctgtgaaatgtatgttgttttggcaggca-atgcaccattaataatatgtatatcatgttgttctgatagtgtaacccaatcttaatgcaatcagGAATAGGGTATAATGGATTTCCTAGAGGTTGTTCTGACAATAAGCTACCCTGGGCAAAG
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---------------gtaagttcattaaattatcatatccattattcactttatttttct-gtgaaaagcagatttgttactttgctttttcttccgtcagGAATTGGTTATAATGGGTTTCCAAGAGGTTGTTCTGATGACAAGCTACCCTGGGCACAGMapped 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|88395592|gb|CI613114.1|CI613114EST: GTTGGAGCATGCTTGGTTAGACAAGAGGGGATAATCCTAG GAATAGGGTATAATGGATTTCCTAGAGGTTGTT
genomic: GTTGGAGCATGCTTGGTTAGCCAAGAGGGGATAATCCTAGgtaaagttga ... atgcaatcagGAATAGGGTATAATGGATTTCCTAGAGGTTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataatatgtatatcatgttgttctgatagtgtaacccaatcttaatgcaatcagGAATAGGGTATAATGGATTTCCTAGAGGTTGTTCTGACAATAAGCTACCCTGGGCAAAG
tcttaat putative branch site (score: 3)
tatgtatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcattgctgtgaaatgtatgttgttttggcaggcaatgcaccattaataatatgtatatcatgttgttctgatagtgtaacccaatcttaatgcaatcagGAATAGGGTATAATGGATTTCCTAGAGGTTGTTCTGACAATAAGCTACCCTGGGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG