Sequence
atgc intronic sequence ATGC exonic sequencegtacacatacaatcctattttagtagctgaatcacagattctagattttttgtatgccttctgtttggtgaccatgctcttcatatttccacagCTTGGCATGAGATTCAATGACACAAGAACAAAGTCCTCTATTCTTCATGTTTTCCCATTCAACTCAGAGAAAAAAAGAGGCGGGGTTGCAGTGCATCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g51610.3 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G140328_T02 (Zea mays), 3'ss of exon 19
gtacacatacaatcctattttagtagctgaatcacagattctagattttttgtatgccttctgtttggtgaccatgctcttcatatttccacagCTTGGCATGAGATTCAATGACACAAGAACAAAGTCCTCTATTCTTCATGTTTTCCCATTCAACTCAGAGAAAAAAAGAGGCGGGGTTGCAGTGCATCTG
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gtgca-aaaagatcct-ttatagtagtca---cagagatccttctataggttaatctcttgctattgctaatcatggtcggcacatttttacagCTGGGTATGAAATTCAATGAAACAAGATTGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGTGGGGTTGCAGTGCACCTG
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G391042_T02 (Zea mays), 3'ss of exon 19
gtacacatacaatcctattttagtagctgaatcacagattctagattttttgtatgccttctgtttggtgaccatgctcttcatatttccacagCTTGGCATGAGATTCAATGACACAAGAACAAAGTCCTCTATTCTTCATGTTTTCCCATTCAACTCAGAGAAAAAAAGAGGCGGGGTTGCAGTGCATCTG
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--gtgcaaaaagtccctttgtagtagtttcagcctagatccttccatatgttgatctcttgctatcgctaatcgtggttgtcacatttctacagCTGGGTATGAAATTCAGTGAAACAAGATCGAAGTCATCTATTCTTCATGTATTTCCTTTCAACTCAGAGAAAAAGCGAGGCGGGGTTGCGGTGTACCTG
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 21
gtacacatac-aatcctattttagtagctgaatcacagattctagattttttgtatgccttctgtttggtgaccatgctcttcatat-ttccacagCTTGGCATGAGATTCAATGACACAAGAACAAAGTCCTCTATTCTTCATGTTTTCCCATTCAACTCAGAGAAAAAAAGAGGCGGGGTTGCAGTGCATCTG
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gttcctttgctaacttcctcttattagctacttgataaattttctgtttagagtagaatttttttttttttttaattaacagtaagtgtttcacagATTGGGATGAATTTTGAAGCTGTCAGATCAGGCTCTTCAATTATCCAAGTTTTCCCATTCAACTCAGAGAAAAAACGTGGGGGTGTTGCTATCAAACTG
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 20
gtacacatacaatcctattttagtagctgaatcacagattctagattttttgtatgcct-tctgttt---ggtgaccatgctcttc-atatttcca---cagCTTGGCATGAGATTCAATGACACAAGAACAAAGTCCTCTATTCTTCATGTTTTCCCATTCAACTCAGAGAAAAAAAGAGGCGGGGTTGCAGTGCATCTG
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-------------gttcccctactacctgaa--acatattatctccttttggcatgcatatctatgtcaagttgactttagtcatctatatccttattgcagTTGGGGATGAAGTTTGATGTAATAAGAGAAGAATCCTCAATTCTCCATGTTTTCCCTTTCAACTCAGAGAAAAAGAGAGGTGGTGTTGCAGTACAG---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|29667907|gb|CB664182.1|CB664182EST: AGGTGACTGGATCACCGACCGAAAAGGCTATACTGTCTTGGGGGCTGAAG CTTGGCATGAGATTCAATGACACAAGAACAAAGTCCTCTATTCTTCATGTT
genomic: AGGTGACTGGATCACCGACCGAAAAGGCTATACTGTCTTGGGGGCTGAAGgtacacatac ... atttccacagCTTGGCATGAGATTCAATGACACAAGAACAAAGTCCTCTATTCTTCATGTT
EST:
gi|29685707|gb|CB681982.1|CB681982EST: AGGTGACTGGATCACCGACCGAAAAGGCTATACTGTCTTGGGGGCTGAAG CTTGGCATGAGATTCAATGACACAAGAACAAAGTCCTCTATTCTTCATGTT
genomic: AGGTGACTGGATCACCGACCGAAAAGGCTATACTGTCTTGGGGGCTGAAGgtacacatac ... atttccacagCTTGGCATGAGATTCAATGACACAAGAACAAAGTCCTCTATTCTTCATGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctagattttttgtatgccttctgtttggtgaccatgctcttcatatttccacagCTTGGCATGAGATTCAATGACACAAGAACAAAGTCCTCTATTCTTCATGTTTTCCCATTCAACTCAGAGAAAAAAAGAGGCGGGGTTGCAGTGCATCTG
ctcttcatatttcc CT-rich tract
attttttgtat TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacacatacaatcctattttagtagctgaatcacagattctagattttttgtatgccttctgtttggtgaccatgctcttcatatttccacagCTTGGCATGAGATTCAATGACACAAGAACAAAGTCCTCTATTCTTCATGTTTTCCCATTCAACTCAGAGAAAAAAAGAGGCGGGGTTGCAGTGCATCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG