Sequence
atgc intronic sequence ATGC exonic sequence...gttcaaagtatattaaatcagcaccttatgttcatatattgtgcatataaaatgtgcattgtgttcttctcctgatttatttgctttgctttgctttcagCCCTGTCCCATCTGCTTCGAAAAGATTACAAGAGATATGTTAAATCATATCACCATGCAACATGGTTACTTGTTCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g48190.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g48190.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G069018_T01 (Zea mays), 3'ss of exon 2
----gttcaaagtatattaaatcagcaccttatgttcatatattgtgcatataaaatgtgcattgtgttcttctcctgatttatttgctttgctttgctttcagCCCTGTCCCATCTGCTTCGAAAAGATTACAAGAGATATGTTAAATCATATCACCATGCAACATGGTTACTTGTTCAAG
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cctcatactggttttgtttacgctgtactgtaaagactgctagcagatgtagacactagacat-gtagtgttctc---attttcatttttttctctcatttcagCCCTGCCCCATTTGCTCCCAAAGGATTACAAGGGATATGCTTAACCATATCACCATGCAACATGGTTACTTGTTCAAG
upper sequence: LOC_Os01g48190.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G014066_T01 (Zea mays), 3'ss of exon 2
-gttcaaagtatattaaatcagcaccttatgttcatatattgtgcatataaaatgtgcattgtgttcttctcctgattt--atttgctttgctttgctttcagCCCTGTCCCATCTGCTTCGAAAAGATTACAAGAGATATGTTAAATCATATCACCATGCAACATGGTTACTTGTTCAAG
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cattcaaaatgcgcacctcatactacttttgtt--tatgctacac-tgtagactgctagcagaggtagtgttctcatttccatttttctctctctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATGACCATGCAGCATGGTTACCTGTTCAAGMapped 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|33381970|gb|CF197313.1|CF197313EST: CCCTCTGCGCCCACCTCGAGGAGGACCACCCCTACGAGCCCCACACCGCG CCCTGTCCCATCTGCTTCGAAAAGATTACAAGAGATATGTTAAATCATATC
genomic: CCCTCTGCGCCCACCTCGAGGAGGACCACCCCTACGAGCCCCACACCTCGgtgagctcct ... ttgctttcagCCCTGTCCCATCTGCTTCGAAAAGATTACAAGAGATATGTTAAATCATATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataaaatgtgcattgtgttcttctcctgatttatttgctttgctttgctttcagCCCTGTCCCATCTGCTTCGAAAAGATTACAAGAGATATGTTAAATCATATCACCATGCAACATGGTTACTTGTTCAAG
tcctgat putative branch site (score: 3)
ctttgctttgctttc putative PPT
tgatttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcaaagtatattaaatcagcaccttatgttcatatattgtgcatataaaatgtgcattgtgttcttctcctgatttatttgctttgctttgctttcagCCCTGTCCCATCTGCTTCGAAAAGATTACAAGAGATATGTTAAATCATATCACCATGCAACATGGTTACTTGTTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA