Sequence
atgc intronic sequence ATGC exonic sequencegtacagataaattttcacataagtgctttgcagcagagacaattttgttctgttaaaaactaactttacaaatcaaaaccagATGCGGGCTTTTGCGAAAAGTGGAGAGAACCCTCCTGACGGTTTCATGTGCCCTGGTGGGTGGAAAGTTCTTGTGGACTACTACAATAGTTTGCAAACCG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g02050.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g02050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G158147_T01 (Zea mays), 3'ss of exon 4
----gtacagataaattttcacataagtgctttgcagcagagacaattttgttctgttaaaaactaactttacaaatcaaaaccagATGCGGGCTTTTGCGAAAAGTGGAGAGAACCCTCCTGACGGTTTCATGTGCCCTGGTGGGTGGAAAGTTCTTGTGGACTACTACAATAGTTTGCAAACCG
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gtaggttcgccacaattgtcattcagtt--ttcgtaccagcagtggattactcctgctaaccgttgacctcacatatcaa--ccagATGCGCACTTATGCCAAAACTGGAGAGAATCCTCCAGACGGTTTCATGTGCCCGGGTGGGTGGAAGGTTCTTGTTGACTACTACAACAGCCTGCAAGCTG
upper sequence: LOC_Os04g02050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G06940.1 (Glycine max), 3'ss of exon 4
---------gtacagataaattt-tcacataagtgctttgcagcagagacaattttgttctgttaa-----aaactaactttacaaatcaaaa---ccagATGCGGGCTTTTGCGAAAAGTGGAGAGAACCCTCCTGACGGTTTCATGTGCCCTGGTGGGTGGAAAGTTCTTGTGGACTACTACAATAGTTTGCAAACCG
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acatcacatgtagcaacaagttggtttctgaaatcctttgacaattgggcatctgttctttacaaattttcgtggtttctttaatgatttatatttccagATGCGGGCTTTTGCAAAAAGTGGGGAGAATCCGCCAGAAGGTTTCATGTGCCCAAGTGGGTGGAAGGTTCTTGTCAAATATTATGAAAGTTTGCAGGCAGMapped 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|12404792|gb|AU166393.1|AU166393EST: TCTTTGATCCTTCACGGAGTAAAGATTTTCTGTTCATCTCAGGAACCAAG ATGCGGGCTTTTGCGAAAAGTGGAGAGAACCCTCCTGACGGTTTCATGTGC
genomic: TCTTTGATCCTTCACGGAGTAAAGATTTTCTGTTCATCTCAGGAACCAAGgtacagataa ... tcaaaaccagATGCGGGCTTTTGCGAAAAGTGGAGAGAACCCTCCTGACGGTTTCATGTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcagcagagacaattttgttctgttaaaaactaactttacaaatcaaaaccagATGCGGGCTTTTGCGAAAAGTGGAGAGAACCCTCCTGACGGTTTCATGTGCCCTGGTGGGTGGAAAGTTCTTGTGGACTACTACAATAGTTTGCAAACCG
aactaac putative branch site (score: 1)
ttaaaaactaacttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacagataaattttcacataagtgctttgcagcagagacaattttgttctgttaaaaactaactttacaaatcaaaaccagATGCGGGCTTTTGCGAAAAGTGGAGAGAACCCTCCTGACGGTTTCATGTGCCCTGGTGGGTGGAAAGTTCTTGTGGACTACTACAATAGTTTGCAAACCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA