Sequence
atgc intronic sequence ATGC exonic sequenceGCATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAGgtgagatacatgactacctgttctgatcttaagactaaataaaattttctgtttttagttgtagtaggtgatggacctcttttaatttgtaatgtagggttgcttataatgatcgaatgttcatatgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g27350.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G064212_T02 (Zea mays), 5'ss of exon 4
GCATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAGgtgagatacatgactacctgttc--tgatcttaagactaaataaa-attttctgtttttagttgtagtaggtgatggacctcttttaatttgtaatgtagggttgcttataatgatcgaatgttcatatgcag
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GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagagat-atggcttgaccaccaatgcaaagaaaaaatgaggaatttctgct--cagttatagtaggtgatggagctcttt-aattcttaatgtagggttgcttataattaccaaatgttcatatgcag
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G064212_T02 (Zea mays), 5'ss of exon 4
GCATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAGgtgagatacatgactacctgttc--tgatcttaagactaaataaa-attttctgtttttagttgtagtaggtgatggacctcttttaatttgtaatgtagggttgcttataatgatcgaatgttcatatgcag
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GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagagat-atggcttgaccaccaatgcaaagaaaaaatgaggaatttctgct--cagttatagtaggtgatggagctcttt-aattcttaatgtagggttgcttataattaccaaatgttcatatgcag
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G458441_T01 (Zea mays), 5'ss of exon 4
GCATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAGgtgagata--catgact--acc--tgttctgatctt---------------aagactaaataaaattttctgtttttagtt--gtagtaggtgatggacctcttttaatttgtaatgtagggttgcttataatgatcgaatgttcatatgcag
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GCGCTGATTTTTCACCACCTTGGAAGATCTTGTAGAAAGCCCCCAGAGAAGgtgagagagatatggcttgaccattgctctggtccttattagaggttcaccaatgcaaagaaaaaatgaggaatttctgctcagttataggtgatggagctcttt-aattcttaatgtagggttgcttataattaccaaatgttcatatgcag
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G458441_T01 (Zea mays), 5'ss of exon 4
GCATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAGgtgagata--catgact--acc--tgttctgatctt---------------aagactaaataaaattttctgtttttagtt--gtagtaggtgatggacctcttttaatttgtaatgtagggttgcttataatgatcgaatgttcatatgcag
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GCGCTGATTTTTCACCACCTTGGAAGATCTTGTAGAAAGCCCCCAGAGAAGgtgagagagatatggcttgaccattgctctggtccttattagaggttcaccaatgcaaagaaaaaatgaggaatttctgctcagttataggtgatggagctcttt-aattcttaatgtagggttgcttataattaccaaatgttcatatgcag
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G410085_T01 (Zea mays), 5'ss of exon 3
GCATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAGgtgagatacatgactacctgttctgatcttaagactaaataaaattttctgtttttagttgtagtaggtgatggacctcttttaatttgtaatgtagggttgcttataatgatcgaatgttcatatgcag
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GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagagat-atggcttgaccattgctctggtccttattagaggttc-accaatgcaaagaaaaaatgaggaatgtctgctcagttatag-gtaatggagc---------------------------
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G442425_T01 (Zea mays), 5'ss of exon 3
GCATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAGgtgagata--catgact--acc--tgttctgatctt---------------aagactaaataaaattttctgtttttagtt--gtagtaggtgatggacctcttttaatttgtaatgtagggttgcttataatgatcgaatgttcatatgcag
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GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagagatatggcttgaccattgctctggtccttattagaggttcaccaatgcaaagaaaaaatgaggaatttctgctcagttataggtgatggagctcttt-aattcttaatgtagggttgcttataattaccaaatgttcatatgcag
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G442425_T01 (Zea mays), 5'ss of exon 3
GCATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAGgtgagata--catgact--acc--tgttctgatctt---------------aagactaaataaaattttctgtttttagtt--gtagtaggtgatggacctcttttaatttgtaatgtagggttgcttataatgatcgaatgttcatatgcag
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GCGCTGATTTTTCACCACCTTGGAAGATCTTGGAGAAAGCCCCCAGAGAAGgtgagagagatatggcttgaccattgctctggtccttattagaggttcaccaatgcaaagaaaaaatgaggaatttctgctcagttataggtgatggagctcttt-aattcttaatgtagggttgcttataattaccaaatgttcatatgcag
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G173682_T01 (Zea mays), 5'ss of exon 3
GCATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAGgtgagatacatg---actacctgttctgatct----------------taagact-----aaataaaattt-----tctgtttttagttgtagtaggtgatggacctcttttaatttgtaatgtagggttgcttataatgatcgaatgttcatatgcag
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GCACTGATTTTTCACCATCTTGGAAGATCTTGGAGAAAGCCATCAGAGAAGgtgagagatatatgaattggctattctggtctgtaccagaggttcacctgtgacctgtgcaaagaaaaatgaggaacatcggctcagttatagtagatgatggagttcttttaattcttaatgtagggttgcttataatgaccaaatgttcatatgcag
upper sequence: LOC_Os03g27350.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G173682_T01 (Zea mays), 5'ss of exon 3
GCATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAGgtgagatacatg---actacctgttctgatct----------------taagact-----aaataaaattt-----tctgtttttagttgtagtaggtgatggacctcttttaatttgtaatgtagggttgcttataatgatcgaatgttcatatgcag
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GCACTGATTTTTCACCATCTTGGAAGATCTTGGAGAAAGCCATCAGAGAAGgtgagagatatatgaattggctattctggtctgtaccagaggttcacctgtgacctgtgcaaagaaaaatgaggaacatcggctcagttatagtagatgatggagttcttttaattcttaatgtagggttgcttataatgaccaaatgttcatatgcagMapped 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|58653596|gb|CK042276.1|CK042276EST: CATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAG CCGTATAGCCCTGAATATATAGGGATCTTACACATGTTTGGTGATTCTGAA
genomic: CATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAGgtgagataca ... tcatatgcagCCGTATAGCCCTGAATATATAGGGATCTTACACATGTTTGGTGATTCTGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCATTGATTTTCCACCATCTTGGAAGGTCTTGGAGAAAGCCCTCACAGAAGgtgagatacatgactacctgttctgatcttaagactaaataaaattttctgtttttagttgtagtaggtgatggacctcttttaatttgtaatgtagggttgcttataatgatcgaatgttcatatgcag
- - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - GGAGAA