Sequence
atgc intronic sequence ATGC exonic sequenceCTTGTGAAACTCATTGGTTACTATAGTAACCGTGAGTCATCACAGAACCTACTGTGCTATGAGCTTGTTCCTAATGGAAGCCTAGAGGCTTGGCTTCATGgtatggccaattgagtcaactatttctccttctgaaattgctgcataagttccactcagttgcagttgaatgtggtccttcattgtttaattaattagtggtgatcatgtaatcatgatacaccttgactcttgagtctctgactacttacatttttttcaggtacattgggagctag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g14932.3 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g14932.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G180065_T03 (Zea mays), 5'ss of exon 5
CTTGTGAAACTCATTGGTTACTATAGTAACCGTGAGTCATCACAGAACCTACTGTGCTATGAGCTTGTTCCTAATGGAAGCCTAGAGGCTTGGCTTCATGgtatggccaattgagtcaactatttctccttctgaaattgctg--cataagttccactc-agttgcagttgaatgtggtccttcattgtttaattaattagtggtgatcatgtaatcatgatacaccttgactcttgagtctctgactacttacatttttttcaggtacattgggagctag
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CTTGTGAAACTGATTGGTTATTACAGCAGCCGTGAATCATCACAGAACCTTCTTTGTTATGAGCTTGTTCCCAATGGAAGCCTAGAGGCTTGGCTTCATGgtacgatctattgcatc------ttctcttaccaaatcctctgtgcataggccccattttatttgcacctgaacctactatttca--gtttgtttg---------gaccatgtaact----------------------------------------------------------------
upper sequence: LOC_Os01g14932.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA02G01480.1 (Glycine max), 5'ss of exon 4
CTTGTGAAACTCATTGGTTACTATAGTAACCGTGAGTCATCACAGAACCTACTGTGCTATGAGCTTGTTCCTAATGGAAGCCTAGAGGCTTGGCTTCATGgtatggccaattgagtcaactatttctccttctgaaattgctgcataagttccactcagttgcagttgaatgtggtccttcattgtttaattaattagtggtgatcatgtaatcatgatacaccttgactcttgagtctctgactacttacatttttttcaggtacattgggagctag
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CTTGTAAAACTAGTGGGATACTATAGCAACCGTGACTCATCACAAAATCTACTTTGCTACGAGCTTGTCCCAAATGGAAGCTTGGAGGCCTGGCTTCATGgta------at-------ataatttctc------aaatcatggcatcagctctgtaatcttgaaatgacatgttttgcttctt--ccaaatttac-aataacgtttaagaaagtat--tttactgtgcttaattaaaattgg----ccttgatttgtcctag----------------
upper sequence: LOC_Os01g14932.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA19G40500.1 (Glycine max), 5'ss of exon 5
CTTGTGAAACTCATTGGTTACTATAGTAACCGTGAGTCATCACAGAACCTACTGTGCTATGAGCTTGTTCCTAATGGAAGCCTAGAGGCTTGGCTTCATGgtatggccaattgagtcaactatttctccttctgaaattgctgcataagttccactcagttgca-gttgaatgtggtccttcattgtttaattaattagtggtgatcatgtaatcatgatacaccttgactcttgagtctctgactacttacatttttttcaggtacattgggagctag
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CTTGTAAAACTAGTGGGATACTTCATTAATCGTGACTCATCACAAAATTTACTTTGCTATGAGCTTGTCCCTAATGGAAGTTTGGAGGCTTGGCTTCATGgtaatgg-aattttccgaatcatggtttcagct----ttttagcattgaat-------gttacatgttttttttgttctattattgacttattg-ttcttagt-atagttttctcaaaacgtgttttatgccctaaattgaaatcggccttgatttggcccggcag-------------
upper sequence: LOC_Os01g14932.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA10G01520.1 (Glycine max), 5'ss of exon 4
CTTGTGAAACTCATTGGTTACTATAGTAACCGTGAGTCATCACAGAACCTACTGTGCTATGAGCTTGTTCCTAATGGAAGCCTAGAGGCTTGGCTTCATGgtatggccaattgagtcaactatttctccttctgaaattgctgcataagttccactcagttgcagttgaatgtggtccttcattgtttaattaattagtggtgatcatgtaatcatgatacaccttgactcttgagtctctgactacttacatttttttcaggtacattgggagctag
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CTTGTAAAACTAGTGGGATACTATAGCAATCGCGACTCATCACAAAATCTACTTTGCTATGAGCTTGTCGCAAATGGAAGCTTGGAGGCCTGGCTTCATGgta------at-------ataatttctc------aaatgatggcaccagctctgtaatcttgaaattacatgtttttcttcttccaagtttacaataatgttggttcagaaactatttta-----ttatgcttaa--ttgaaattggccttggtttttcctag---------------
upper sequence: LOC_Os01g14932.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA03G37910.1 (Glycine max), 5'ss of exon 6
CTTGTGAAACTCATTGGTTACTATAGTAACCGTGAGTCATCACAGAACCTACTGTGCTATGAGCTTGTTCCTAATGGAAGCCTAGAGGCTTGGCTTCATGgtatggccaattgagtcaactatttctccttctgaaattgctgcataagttccactcagttgcagttgaatgtggtccttcattgtttaattaattagtggtgatcatgtaatcatgatacaccttgactcttgagtctctgactacttacatttttttcaggtacattgggagctag
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CTTGTAAAACTAGTGGGATACTTTAGTAATCGTGACTCATCACAAAATGTACTTTGCTATGAGCTTGTCCCTAATGGAAGTTTGGAGGCTTGGCTTCATGgtaatgt-aatttttcgaatcatgggttcagcttttagcattgtatggtacatgctttctt-----------tgttctattattgacttattg--tacttagtatagttttctcaatgtgtgttttatgccttaaactgaaatcggccttgattttgcccggcag-------------
upper sequence: LOC_Os01g14932.3 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G02010.1 (Arabidopsis thaliana), 5'ss of exon 5
CTTGTGAAACTCATTGGTTACTATAGTAACCGTGAGTCATCACAGAACCTACTGTGCTATGAGCTTGTTCCTAATGGAAGCCTAGAGGCTTGGCTTCATGgtatggccaattgagtcaactatttctccttctgaaattgctgcataagttccactcagttgcagttgaatgtggtccttcattgtttaattaattagtggtgatcatgtaatcatgatacaccttgactcttgagtctctgactacttacatttttttcaggtacattgggagctag
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CTTGTGAAACTTGTGGGTTACTATAGTAGTCGAGATTCTTCTCAGCACCTACTTTGTTATGAGCTTGTTCCAAATGGCAGCCTCGAGGCTTGGCTCCATGgtaatatc-----------tcctctttgcttccc---ttgctgcctatttttagatctgacattgtcaaaagtagttattgtacactgagttcatctacaagagtggtttatttaagtcat-tgtttatgcttcag------------------------------------------
upper sequence: LOC_Os01g14932.3 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv07s0005g01590.t01 (Vitis vinifera), 5'ss of exon 4
CTTGTGAAACTCATTGGTTACTATAGTAACCGTGAGTCATCACAGAACCTACTGTGCTATGAGCTTGTTCCTAATGGAAGCCTAGAGGCTTGGCTTCATGgtatggccaattgagtcaactatttctccttctgaaattgctgcataagttccactcagttgcagttgaatgtggtccttcattgtttaattaattagtggtgatcatgtaatcatgatacaccttgactcttgagtctctgactactta-catttttttcaggtacattgggagctag
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CTTGTGAAACTTGTGGGTTACTATAGCAATCGTGACTCTTCACAAAATCTCCTTTGTTATGAGCTTGTCCCAAATGGAAGCTTAGAGGCCTGGCTCCATGgta-gtttgctttcttgaaccacagatt-taatgaaat--cctcatatatttatctctctttccattgtcccta-ttatggattgtgtatct---tggaaaaaaatataaaactctg-tacttttgg------gagattttcaatacatagtattgacaatggtcctgttctgctccagMapped 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|58681155|gb|CK069842.1|CK069842EST: GCTTG-TCCTAATGGAAGCCTAGAGGCTTGGCTTCATG CCGCCCC-TGGACTGGGACACTAGAATGAGGATAGCACTAGATGCTGCCA-
genomic: GCTTGTTCCTAATGGAAGCCTAGAGGCTTGGCTTCATGgtatggccaa ... tgggagctagCCGCCCCTTGGACTGGGACACTAGAATGAGGATAGCACTAGATGCTGCCAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTTGTGAAACTCATTGGTTACTATAGTAACCGTGAGTCATCACAGAACCTACTGTGCTATGAGCTTGTTCCTAATGGAAGCCTAGAGGCTTGGCTTCATGgtatggccaattgagtcaactatttctccttctgaaattgctgcataagttccactcagttgcagttgaatgtggtccttcattgtttaattaattagtggtgatcatgtaatcatgatacaccttgactcttgagtctctgactacttacatttttttcaggtacattgggagctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG