Sequence
atgc intronic sequence ATGC exonic sequenceCAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGTGTTACTCAAATAAAAGCATACTTTGGTTTGTCTGGAGGgtgggatagctttatcatctaattttgattgattatatgtctgtatggttatcatcattattaaagaattgcttctcctgagtcttgattagttttctat...
Basic information
species | Oryza sativa |
transcript | LOC_Os05g50170.1 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G325504_T01 (Zea mays), 5'ss of exon 3
CAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGTGTTACTCAAATAAAAGCATACTTTGGTTTGTCTGGAGGgtgggatagctttatcatctaattttgattgat-tatatgtctgtatggttatcatcat-tattaaagaattgctt-ctcctgagtcttgattagttttctat
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TGGCCTGCACTCTCTTAGAGCAAGCAATTAAGGAATCTAAGGGAGAGAATACCTATTGGAATGTGGCTCAAATAAAAGCATATTTTGGTTTATCTGGAGGgtgagaacttgaaagcctcgacatctgtttaatgtctgtaaatttacatttttaatcatatatcatattattaatcatttctcaatagtg-ccagcacata--
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G406177_T01 (Zea mays), 5'ss of exon 6
CAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGTGTTACTCAAATAAAAGCATACTTTGGTTTGTCTGGAGGgtgggat------agctttatcatctaattttgattgattatatgtctgtatggtta-tcat-cattat-taaagaattgcttctcctgagtcttgattagttttctat
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CGGCCTGCGCTCTCTTAGAGCAAGCAATTAAGGAATCTAAGGGAGAGAATACCTATTGGAATGTGGCTCAAATAAAAGCATATTTTGGTTTATCTGGAGGgtgagaacttgaaagcctcggcatctgtttt--aatgtctgtaaatttacatttttaatcatatatcatattattaatcatttctcaatagtgccagcacat-------
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM5G854930_T01 (Zea mays), 5'ss of exon 7
CAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGTGTTACTCAAATAAAAGCATACTTTGGTTTGTCTGGAGGgtgggat------agctttatcatctaattttgattgattatatgtctgtatggttatcatcattattaaagaattgcttctcctgagtcttgattagttttctat
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CGGCCTGCGCTCTCTTAGAGCAAGCAATTAAGGAATCTAAGGGAGAGAATACCTATTGGAATGTGGCTCAAATAAAAGCATATTTTGGTCTATCTGGAGGgtgagaacttgaaagcctcggtatatgtttt--aatgtctgtaaatttacatttttaagagattcatttattaatcatttctcaatagtgccagtacataag----
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM5G854930_T01 (Zea mays), 5'ss of exon 9
--------------------------------------CAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGTGTTACTCAAATAAAAGCATACTTTGGTTTGTCTGGAGGgtgggatagctttatcatctaattttgattgattatatgtctgtatggttatcatcattattaaagaattgcttctcctgagtcttgattagttttctat
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AATCTACTTGATGGGTCAATCAGCAGGAGCACATATCGCGGCCTGCGCTCTCTTAGAGCAAGCAATTAAGGAATCTAAGGGAGAGAATACCTATTGGAATgtggctcaaataaaagcatattttggtctatctggagggtgaga--acttgaaagcctcggtata--tgttttaatgtctgtaaatttacatttttaatcatat----------------------------------
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G437845_T01 (Zea mays), 5'ss of exon 7
CAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGTGTTACTCAAATAAAAGCATACTTTGGTTTGTCTGGAGGgtgggat------agctttatcatctaattttgattgattatatgtctgtatggtta-tcat-cattat-taaagaattgcttctcctgagtcttgattagttttctat
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TGGCCTGCGCTCTCTTAGAGCAAGCAATTAAGGAATCTAAGGGAGAGAATACCTATTGGAATGTGGCTCAAATAAAAGCATATTTTGGTTTATCTGGAGGgtgagaacttgaaagcctcgacatctgtttt--aatgtctgtaaatttacatttttaatcatatatcatattattaatcatttctcaatagtgccagcacat-------
upper sequence: LOC_Os05g50170.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT3G02410.2 (Arabidopsis thaliana), 5'ss of exon 7
CAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGTGTTACTCAAATAAAAGCATACTTTGGTTTGTCTGGAGGgtgggata----gctttatcatctaattttgattgat-tatatgtctgtatggttatcatc--attattaaagaattgcttctcctgagt---cttgattagttttctat
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CTTCTTGTGCTCTCTTTGAACAAGCTATTAAAGAATCAAGAGGGGAGAGCATCTCATGGAGTGTATCTCAGATTAAAGCTTACTTTGGTTTATCTGGAGGgtaatttactaaacttggtgacactatgaagcttaaaacgtttttcaaagggtttcttatccagtaattcagaatctactcaccatttgtaaacttgaacag--------Mapped 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|66926863|gb|CX113711.1|CX113711EST: ATTTCATGGAGTGTTACTCAAATAAAAGCATACTTTGGTTTGTCTGGAGG ATACAACATTGAAAATTTGGTTGATCATTTCCATGAACGTGGTCTTTACCG
genomic: ATTTCATGGAGTGTTACTCAAATAAAAGCATACTTTGGTTTGTCTGGAGGgtgggatagc ... ctgtttgcagATACAACATTGAAAATTTGGTTGATCATTTCCATGAACGTGGTCTTTACCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAGCATGCGCTCTTTTGGAACAAGCGGCTAAAGAATCTAGGGGAGAGCAGATTTCATGGAGTGTTACTCAAATAAAAGCATACTTTGGTTTGTCTGGAGGgtgggatagctttatcatctaattttgattgattatatgtctgtatggttatcatcattattaaagaattgcttctcctgagtcttgattagttttctat
- - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctcc