Sequence
atgc intronic sequence ATGC exonic sequenceTTCTTATTATGACATAAGAGCAGCCCAAAATGCAATGAGAGCGCTGCATAGCAAGCCTCTGGGGCTGATGAAACTTGATGTGCAATTTTCTTTTCCTAAGgtatgcataataatatcagtagttttgaattaggcatgctacctaatctatatatcttccttatcatgccatttgttacttgggcaatgttgttctgttt...
Basic information
species | Oryza sativa |
transcript | LOC_Os05g01240.2 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g01240.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G156956_T01 (Zea mays), 5'ss of exon 5
TTCTTATTATGACATAAGAGCAGCCCAAAATGCAATGAGAGCGCTGCATAGCAAGCCTCTGGGGCTGATGAAACTTGATGTGCAATTTTCTTTTCCTAAGgtatgcataataatatcagtagttttgaattaggcatgctacctaatctata---tatcttccttatcatgccatttgttacttgggcaatgttgttctgttt
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GTCTTACTATGACATTAGAGCTGCACAGGACGCAGTGAGAGCAGTCCATAACAAACCTCTGGGGCTGATGAAACTTGATGTTCAATTTTCCCTTCCTAAGgtagacacactag---cacttttcttgcagtggaaatgtttagtaacctgtcccctgtttaatctgttaaattaatttgtcattatacaactggtttatgcct
upper sequence: LOC_Os05g01240.3 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 5'ss of exon 6
TTCTTATTATGACATAAGAGCAGCCCAAAATGCAATGAGAGCGCTGCATAGCAAGCCTCTGGGGCTGATGAAACTTGATGTGCAATTTTCTTTTCCTAAGgtatgcataataatatcagtag-ttttgaattaggcatgctacc------taatctatatatcttccttatcatgccatttgttacttgggcaatgtt----gttctgttt-----------------------------------------------------------------------------------
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TTCTTATTATGATATAAGGGCAGCCAGAAATGCAATGAGAGCCCTTCAGAATAAGCCACTGAGACGGAGGAAACTTGATATTCATTATTCAATTCCAAAGgtatgttgagcatgttcaaaaaatcttgctgcacacatgatattgttttacagttatcatattcagtgttttgtgttagcattatcattgacaatgctttggatgctatttgggtttgtgtttattgaaatggttctgcatgtcaaggtgatgctttgttgtttgatgttctttttaactcggtgttatgttag
upper sequence: LOC_Os05g01240.3 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv01s0150g00090.t01 (Vitis vinifera), 5'ss of exon 7
TTCTTATTATGACATAAGAGCAGCCCAAAATGCAATGAGAGCGCTGCATAGCAAGCCTCTGGGGCTGATGAAACTTGATGTGCAATTTTCTTTTCCTAAGgtatgcataataatatcagtagttttgaattaggcatgctacctaatctatatatcttccttatcatgccatttgttacttgggcaatgttgttctgttt------
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CTCATATTATGATATAAGAGCAGCCCGAAATGCAATGAGAGCACTCCAGAACAAACCATTGAGGCGTAGGAAGCTTGACATTCATTATTCTATTCCAAAGgtgtg-atactt-tattttca-tcctatgtagagcatgtggc---atttcttgctttgattaagtaatcctcatgttagctttgtagttatcacttgttaggataaMapped 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|58606065|gb|CK034098.1|CK034098EST: GCAAGCCTCTGGGGCTGATGAAACTTGATGTGCAATTTTCTTTTCCTAAG GAAAATGTTCCAGGCAAGGATATTGATAAGGGAATGTTGGTGGTATCTAAC
genomic: GCAAGCCTCTGGGGCTGATGAAACTTGATGTGCAATTTTCTTTTCCTAAGgtatgcataa ... actttgctagGAAAATGTTCCAGGCAAGGATATTGATAAGGGAATGTTGGTGGTATCTAAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTCTTATTATGACATAAGAGCAGCCCAAAATGCAATGAGAGCGCTGCATAGCAAGCCTCTGGGGCTGATGAAACTTGATGTGCAATTTTCTTTTCCTAAGgtatgcataataatatcagtagttttgaattaggcatgctacctaatctatatatcttccttatcatgccatttgttacttgggcaatgttgttctgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT