Sequence
atgc intronic sequence ATGC exonic sequencegtaagcacatagttttagctagttttttaagtttgtgcaaggatagtgttcttgaattacgttttcacactcattcataactgatacggtattcccattgtctgtttctaaaataatataaaactgtgcttcattgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGAAAAAGCATTAGCCATGTAATCATAGGTCTGAAGACTGTAAAAGGGACTA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62040.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G018697_T02 (Zea mays), 3'ss of exon 3
----------------------------------gtaagcacatagttttagctagttttttaagtttgtgcaaggat-agtgttcttgaattacgttttcaca--------ctcattcataactgatacggta---ttcccattgtctgtttctaaaataatataaaactgtgcttcattgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGAAAAAGCATTAGCCATGTAATCATAGGTCTGAAGACTGTAAAAGGGACTA
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gtaagcaatggatatatgcccatgtccaagttaaacgaatactaggctataattgcattagtgatttcctttatttatcaatggttttcattatcgctttgatagctgatgttccacttcgtgcttctataataaatttaccattgttag--tctataataa-atttaccagtgttgctctgt-tcctagGTTACTGAACTTTCCCCAGAAGAGGCTGAGAGTACAACTGGTGGATATGCAAAAAGCATTAGCCATGTAATCATCAGCTTAAAGACTGTTAAAGGGACTA
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G032267_T02 (Zea mays), 3'ss of exon 3
gtaagcacatagttttagctagttttttaagtttgtgcaaggatagtgttcttgaattacgttttcacactcattcataactgatacggta-----ttcccattgtctgtttctaaaataatataaaactgtgcttcattgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGAAAAAGCATTAGCCATGTAATCATAGGTCTGAAGACTGTAAAAGGGACTA
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--------------------------------------------agtggtttt--atttatttatca-actgtttcattatcgctttggtagctaatgttcacttcttgcttctataatag-atataccaatgttgctctgt-tcctagGTTATTGAACTTTCCCCAGAAGAGGCTGAGAGCACAACTGGTGGATATGCGAAAAGCATTAGCCACGTAATCATTGGCTTAAAGACTGTCAAAGGGACTA
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 3
gtaagcacatagttttagctagttttttaagtttgtgcaaggatagtgttcttgaattacgttttcacactcattcataactgatacggtattcccattgtc-tgtttctaaaataatataaaactgtgcttcattgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGAAAAAGCATTAGCCATGTAATCATAGGTCTGAAGACTGTAAAAGGGACTA-------
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-------------------------------gttat-cactgattatgagttt--tttttgttaatagtttgacttgccagtaatatcatgatctttttgttgtattatcatctttaaatcaagtagcttctc----ttttttaggtgacagAACTCTCCCCAGAAGAAACTGAGAGCACAACAGGTGGTTATGGAAAAAGCATTAGCCATGTGATTATTGGATTAAAAACTGTGAAGGGAACCAAGCAGCTMapped 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
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattcccattgtctgtttctaaaataatataaaactgtgcttcattgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGAAAAAGCATTAGCCATGTAATCATAGGTCTGAAGACTGTAAAAGGGACTA
ttctaaa putative branch site (score: 2)
cttcattgcctttt putative PPT
attgtctgtttctaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcacatagttttagctagttttttaagtttgtgcaaggatagtgttcttgaattacgttttcacactcattcataactgatacggtattcccattgtctgtttctaaaataatataaaactgtgcttcattgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGAAAAAGCATTAGCCATGTAATCATAGGTCTGAAGACTGTAAAAGGGACTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA