Sequence
atgc intronic sequence ATGC exonic sequencegtacggctcgttccgatctggctcaccatgcagcacaaaccaattgcccttctgctaacatgtaccggttcttgccgccggcgctgcagTTCAATGGCACGGCGACGAAGCCGAGGCTGTCCGTGTTCTGCTCCAACAGGCAGCTCTACGCCATGCTCGTCGACGACCACAACAGGAAGATCCTCTTCT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g07340.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g07340.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G857303_T02 (Zea mays), 3'ss of exon 2
gtacggctcgtt--ccgatctggctcacca--tgcagcacaaa-ccaattgcccttctgctaacatgtaccggttcttg--ccgccggcgct--------gcagTTCAATGGCACGGCGACGAAGCCGAGGCTGTCCGTGTTCTGCTCCAACAGGCAGCTCTACGCCATGCTCGTCGACGACCACAACAGGAAGATCCTCTTCT
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gtacgttccggtgctccacctggttctcaaatttcaggataaggccagctaccaggcagccggtgtaaccaaaccgccgttccgccgactctcgctgtatgcagTTCAACGGCACGGCGACGAAGCCCAGACTCTCGGTGTTCTGCTCCAACCGGCAGCTCTACGCTGTGCTCGCCGACGACCACAACAAGAAGATCCTCTTCT
upper sequence: LOC_Os03g07340.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G479581_T01 (Zea mays), 3'ss of exon 1
-------gtacggctcgtt--ccgatctggctcacca---tgcagcacaaaccaattgc--ccttctgc---taaca-------tgtaccggttcttgccgccggc-gctgcagTTCAATGGCACGGCGACGAAGCCGAGGCTGTCCGTGTTCTGCTCCAACAGGCAGCTCTACGCCATGCTCGTCGACGACCACAACAGGAAGATCCTCTTCT
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gtagtacgaacgttccgatgctccacctgggtcttcgaatttcaggataaaaggcctgcagccggcaggatgtaacgaaaccgccgttccgccgactctcgctggctgctgcagTTCAACGGCACGGCGACGAAGCCCAGGCTCTCGGTGTTCTGCTCCAGCCGGCAGCTCTACGCCGTTCTCGCCGACGACCACAACAAGGAGATCCTCTTCTMapped 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|88397802|gb|CI583120.1|CI583120EST: GCGCGAGGAAGGAGAACCCCAAGGTCAGGAACCGCAGGCTGCAGAAGAAG TTCAATGGCACGGCGACGAAGCCGAGGCTGTCCGTGTTCTGCTCCAACAGG
genomic: GCGCGAGGAAGGAGAACCCCAAGGTCAGGAACCGCAGGCTGCAGAAGAAGgtacggctcg ... ggcgctgcagTTCAATGGCACGGCGACGAAGCCGAGGCTGTCCGTGTTCTGCTCCAACAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaaaccaattgcccttctgctaacatgtaccggttcttgccgccggcgctgcagTTCAATGGCACGGCGACGAAGCCGAGGCTGTCCGTGTTCTGCTCCAACAGGCAGCTCTACGCCATGCTCGTCGACGACCACAACAGGAAGATCCTCTTCT
tgctaac putative branch site (score: 1)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacggctcgttccgatctggctcaccatgcagcacaaaccaattgcccttctgctaacatgtaccggttcttgccgccggcgctgcagTTCAATGGCACGGCGACGAAGCCGAGGCTGTCCGTGTTCTGCTCCAACAGGCAGCTCTACGCCATGCTCGTCGACGACCACAACAGGAAGATCCTCTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA