Sequence
atgc intronic sequence ATGC exonic sequenceCTTTGATTGAGTCTGACGCAGAAGGCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCGgtaatctggataagcaatcagtgaatgtataccttggcattttctgatccacattatatccaactaacttctctaccttttag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g39380.3 |
intron # | 17 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g39380.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G074572_T01 (Zea mays), 5'ss of exon 16
CTTTGATTGAGTCTGACGCAGAAGGCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCGgtaatctggataa---------gcaatcagtgaatgtataccttggcattttctgatccacattatatccaactaacttctctaccttttag
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CTTTGATTGAGTCTGACGCAGAAGGCATCGGGGGAAGTGGCTTTGTTGAATGCATCAGAGAGCATATTCATTCGgtaatctggatcttaggatcttgcaattgataaatctttactcgggcactttctaatgcactttatatcttgctgtactatct---ttgtag
upper sequence: LOC_Os01g39380.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GLYMA08G04510.1 (Glycine max), 5'ss of exon 16
CTTTGATTGAGTCTGACGCAGAAGGCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCGgt----aatctggataagc---aatcagtgaatgtatacct-------tggcattttctgatccacattatatccaactaacttctctaccttttag---------
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CTTTGATTGAATCTGATGCAGAGGGGATTGGCGGTAGTGGATTTGTTGAATGTATAAGAGAGCATATACATTCGgtttgtagctctatttagctccaactgataattatttatttctttatttataatttcttgttctggaatctggtacaatgaatcttatgctagattgttttaccag
upper sequence: LOC_Os01g39380.2 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv17s0000g03950.t01 (Vitis vinifera), 5'ss of exon 16
CTTTGATTGAGTCTGACGCAGAAGGCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCGgtaatctggataagcaatcagtgaatgtataccttggcattttctgatccacattatatccaactaacttctctaccttt-tag----
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CTTTGATTGAGTCTGATGCGGAAGGAATTGGCGGTAGTGGATTTGTTGAGTGTATAAGGGAGCACATACATTCAgtaag-tagctctacaaagggtatat---tgcttaaatattttttcacaggaatga--gctaactttttactggatttctgttgtcag
upper sequence: LOC_Os01g39380.2 (Oryza sativa), 5'ss of exon 16
lower sequence: EFJ15218 (Selaginella moellendorffii), 5'ss of exon 16
CTTTGATTGAGTCTGACGCAGAAGGCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCGgtaatctggataagcaatcagtgaatgtataccttggcattttctgatccacattatatccaactaacttctctaccttttag
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CTTTGATTGAGTCCGATGCGGAAGGTATTGGTGGAAGTGGATTTGTTGAGTGTGTCAGGGAGCATATTCACTCGgtaagctaaat--gtttttggtacacgc-tgttctaaagctcgaacctttgcag-----------------------------
upper sequence: LOC_Os01g39380.2 (Oryza sativa), 5'ss of exon 16
lower sequence: EFJ09845 (Selaginella moellendorffii), 5'ss of exon 16
CTTTGATTGAGTCTGACGCAGAAGGCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCGgtaatctggataagcaatcagtgaatgtataccttggcattttctgatccacattatatccaactaacttctctaccttttag
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CTTTGATTGAGTCCGATGCGGAAGGTATTGGTGGAAGTGGATTTGTTGAGTGTGTCAGGGAGCATATTCACTCGgtaagctaaatggtt--ttggtacacgc-tgttctaaagctcgaacctttgcag-----------------------------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|163926735|gb|EG713751.1|EG713751EST: GCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCG GGTTGGCAATGCCGATTAACTGATGAACAGTTTATTGCTGTAAAAGAACTG
genomic: GCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCGgtaatctgga ... taccttttagGGTTGGCAATGCCGATTAACTGATGAACAGTTTATTGCTGTAAAAGAACTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTTTGATTGAGTCTGACGCAGAAGGCATTGGGGGTAGTGGCTTTGTTGAGTGCATCAGAGAGCATATTCATTCGgtaatctggataagcaatcagtgaatgtataccttggcattttctgatccacattatatccaactaacttctctaccttttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA