Sequence
atgc intronic sequence ATGC exonic sequenceGTATTCCTCAGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTCGAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTTATGAAGGAGAGgtaagcacatagttttagctagttttttaagtttgtgcaaggatagtgttcttgaattacgttttcacactcattcataactgatacggtattcccattgtctgtttctaaaataatataaaactgtgcttcattgccttttag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62040.2 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G032267_T02 (Zea mays), 5'ss of exon 3
GTATTCCTCAGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTCGAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTTATGAAGGAGAGgtaagcacatagttttagctagttttttaagtttgtgcaaggatagtgttct-tgaattacgttttcacactcattcata-actgatacggtattcccattgtctgtttctaaaataatataaaactgtgcttcattgccttttag
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GTACTCCTCAGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTAGAGCTATAGGTTTGCGTATAAAGGAAAACAAAGAGGTTTATGAAGGAGAGgtaagca-at-------gcatggttattaaagcggtaaaacgttaaaacgttatgaaccacctttttaa---catttaaacgttgaaacgaacgttgaaacgtct-tttcag----------------------------------
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G018697_T02 (Zea mays), 5'ss of exon 3
GTATTCCTCAGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTCGAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTTATGAAGGAGAGgtaagcacatagttttagctagtttt----ttaagtttgtgcaaggata-----gtgttcttgaattacgtt--ttcacactcatt--cataactgatacggtat------tcccattgtctgtttctaaaataa-tataaaactgt-gcttcattgccttttag---------------------
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GTACTCCTCGGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTAGAGCTATAGGTTTGCGTATAAAGGAAAACAAAGAGGTTTATGAAGGAGAGgtaagcaatggatatatgcccatgtccaagttaaacgaatactaggctataattgcattagtgatttcctttatttatcaatggttttcattatcgctttgatagctgatgttccacttcgtgcttctataataaatttaccattgttagtctataataaatttaccagtgttgctctgttcctag
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 5'ss of exon 3
GTATTCCTCAGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTCGAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTTATGAAGGAGAGgtaagcacatagttttagctagttttttaagtttgtgcaaggatagtgttcttgaattacgttttcacactcat-tcataactgatacggtattcccattgtctgtttctaaaataatataaaactgtgcttcattgccttttag
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----TCATCAGAGGTAAAGAAAACTGAGATTTTAATGGAAAATTTCCGACGGGCTATTGGTCTACGTATCAAGGAAAATAAGGAAGTGTATGAAGGAGAGGCAAgttatcactgattatgagttttttttgttaatagtttgacttgccagtaatatcatgatctttttgttgtattatcatctttaaatcaagt--agcttctcttttttaggtgacag-------------------------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|33676655|gb|CF304894.1|CF304894EST: GAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTCATGAAGGAGAG GTTACTGAACTT
genomic: GAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTTATGAAGGAGAGgtaagcacat ... tgccttttagGTTACTGAACTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTATTCCTCAGAGGTCAAGAAAACTGAGGTGCTGATGGAAAATTTCCGTCGAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTTATGAAGGAGAGgtaagcacatagttttagctagttttttaagtttgtgcaaggatagtgttcttgaattacgttttcacactcattcataactgatacggtattcccattgtctgtttctaaaataatataaaactgtgcttcattgccttttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA