Sequence
atgc intronic sequence ATGC exonic sequenceATGGCACATTATCAAGGATGTGCCTAATCCACAATTTCGCCACATAATACTGGAGAACAACGAAAACAAACCTGTGACAAACAGCAGGGATACACAAGAGgtatttattcaattacctagagattttttatttttttatactcatgatctcaagccatctgcttgtacgtagtattcataaatttcccatcctgtcttcc...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g48790.3 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g48790.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G169116_T01 (Zea mays), 5'ss of exon 8
ATGGCACATTATCAAGGATGTGCCTAATCCACAATTTCGCCACATAATACTGGAGAACAACGAAAACAAACCTGTGACAAACAGCAGGGATACACAAGAGgtatttattcaattacctag--agattttttat--ttttttatact-catgatctcaagccatctgcttgtacgtagtattcata--aatttcccatcctgtcttcc
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ATGGCACATTATTAAGGATGTTCCCAATCCACAATTTCGCCATATAATTTTGGAGAATAATGAGAATAAACCTGTGACAAACAGCAGGGACACGCAAGAGgtattccttccaatacctagcaagagtgtctgtggtattttttacagcaagaggttgagctttctaagttaattctcatttcatggcaatatgtgaggaa-------
upper sequence: LOC_Os01g48790.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G127780_T02 (Zea mays), 5'ss of exon 7
ATGGCACATTATCAAGGATGTGCCTAATCCACAATTTCGCCACATAATACTGGAGAACAACGAAAACAAACCTGTGACAAACAGCAGGGATACACAAGAGgtatttattcaattacctag--agattttttatttttttatact-catgatctcaagccatctgcttgtacgtagtattcataa-atttcccatcctgtcttcc
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ATGGCACATTATCAAGGATGTTCCCAATCCACAATTTCGCCATATAATTTTGGAGAATAATGAGAATAAACCTGTGACAAACAGCAGGGACACACAAGAGgtattccttccaatacctagcaagagttcttggtattttttatgacaagtggttgagctttctaagttaattctcatttcatggcaatatatgtcaggaa----
upper sequence: LOC_Os01g48790.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA15G41960.1 (Glycine max), 5'ss of exon 7
ATGGCACATTATCAAGGATGTGCCTAATCCACAATTTCGCCACATAATACTGGAGAACAACGAAAACAAACCTGTGACAAACAGCAGGGATACACAAGAGgtatttatt--caattacctagagattttttatttttttatactcatgatctcaagccatctgcttgtacgtagtattcataaatttcccatcctgtcttcc--
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ATGGCACATTATAAAGGATGTTCCAAATCCTCAACTACGGCATATAATACTCGAGAATAATGATCACAAGCCTGTTACAAGCAGTAGAGACACACAAGAGgtttgcattttctagtaaaaacagaaatctactgagaaagtcttagttgtttctt-ctgtatgctt-tac-taatgtctatgtcttctatgtttcttttttcag
upper sequence: LOC_Os01g48790.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA08G17240.2 (Glycine max), 5'ss of exon 7
ATGGCACATTATCAAGGATGTGCCTAATCCACAATTTCGCCACATAATACTGGAGAACAACGAAAACAAACCTGTGACAAACAGCAGGGATACACAAGAGgtatttattcaattacctagagattttttatttttttatactcatgatctcaagccatctgcttgtacgtagtat--tcataaatttcccatcctgtcttcc
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ATGGCACATTATAAAGGATGTTCCAAATCCTCAACTACGCCACATAATACTCGAGAATAATGATCACAAGCCTGTCACAAATAGTAGAGACACACAAGAGgtatgcatccatagtaaaagcaacaatctactgacgaagtcttggttgtttcttctgtatgcttactcatcatgtctttgttgattccactttcag------
upper sequence: LOC_Os01g48790.3 (Oryza sativa), 5'ss of exon 4
lower sequence: AT1G79270.1 (Arabidopsis thaliana), 5'ss of exon 7
ATGGCACATTATCAAGGATGTGCCTAATCCACAATTTCGCCACATAATACTGGAGAACAACGAAAACAAACCTGTGACAAACAGCAGGGATACACAAGAGgtatttattcaattacctagagattttttatttttttatactcatgatctcaagccatctgcttgtacgtagtattcataaatttcccatcctgtcttcc
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GTGGCACATCATCAAAGATGTTCCAAATCCGCAACTACGACATATCATACTAGAGAACAATGAGAACAAGCCTGTAACCAATAGCAGAGACACACAAGAGgtaaca--ttagttccttaataggcttaaggaagtgaat---cattatcaagagctaatctcatct-catactgtttaaacattgtccttcatatatag-
upper sequence: LOC_Os01g48790.3 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv19s0085g01100.t01 (Vitis vinifera), 5'ss of exon 7
ATGGCACATTATCAAGGATGTGCCTAATCCACAATTTCGCCACATAATACTGGAGAACAACGAAAACAAACCTGTGACAAACAGCAGGGATACACAAGAGgtatttattcaattacctagagattttttatttttttatactcatgatctcaagccatctgcttgtacgtagtattcataaatttcccatc-ctgtcttcc--------
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GTGGCACATCATAAAAGATGTTCCAAACCCACAGTTGCGGCATATAATACTTGAGAACAACGACAACAAGCCTGTGACCAATAGCAGAGACACACAGGAGgtgcgca--caacaaactg----ttctctatctcatagaatttgttttctt----caatttcttgtgcttccttccaactaatcttgttttgttgtcatcctttttcagMapped 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|29640181|gb|CB645190.1|CB645190EST: TGGAGAACAACGAAAACAAACCTGTGACAAACAGCAGGGATACACAAGAG GTCAAGTTTCCACAAGGTTCAGAGATGCTGAACA
genomic: TGGAGAACAACGAAAACAAACCTGTGACAAACAGCAGGGATACACAAGAGgtatttattc ... ggcaattcagGTCAAGTTTCCACAAGGTTCAGAGATGCTGAACA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATGGCACATTATCAAGGATGTGCCTAATCCACAATTTCGCCACATAATACTGGAGAACAACGAAAACAAACCTGTGACAAACAGCAGGGATACACAAGAGgtatttattcaattacctagagattttttatttttttatactcatgatctcaagccatctgcttgtacgtagtattcataaatttcccatcctgtcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA