Sequence
atgc intronic sequence ATGC exonic sequenceGTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAGgtttggattactcgtatatcagagataaaaaaaaatgatgcacacattctagatgatttcttattctgcttagatttaag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g56670.3 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g56670.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G173868_T04 (Zea mays), 5'ss of exon 11
GTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAGgtttggattactcgtatatcagagataaaaaaaaa---tgatgcacacattctagatgatttcttattctgcttagatttaag
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GTACGTGGAGGTTAATATGAACTCTGGTGCTACTGTTTGGCCACTCTTCAATAGTCTGCAGGCATTCTGGCCAGGGCTTCAGgtttgg-ttacacatatttctgataattgatgtggctttgtcgcacatattctagatgattgcttatgctgcttagatttaag
upper sequence: LOC_Os01g56670.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G173868_T02 (Zea mays), 5'ss of exon 11
----------------------------GTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCAC---------TATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTC--AGgtttggattactcgtatatcagagataaaaaaaaatgatgcacacattctagatgatttcttattct--gcttagatttaag
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ATTCTAGATGATTGCTTATGCTGCTTAGATTTAAGGTTTTAGCTGGAGATGTTGATCCTGCTATTCGCACACATGCTGCCTTCTTCAGC-GTCTGGAAAAAgtatggttttacccctgaaggttttaatc-ttgctacatccactgtacaggtaa-tgaaactgttaaactataatagtcaagagtattagcataatctccta
upper sequence: LOC_Os01g56670.3 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv05s0020g04650.t01 (Vitis vinifera), 5'ss of exon 12
GTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAGgtttggattactcgtatatcagagataaaaaaaaatgatgcacacattctagatgatttcttattctgcttagatttaag
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GTATGTGGAGGTAAACATGGATTCTGCTGCTATTGTTTGGCCATTATTTAACAGTTTGCAAGCATTCTGGCCAGGCCTTCAGgtat--tttatctattatttatatattataaattttgcattgtcgattaatcaaaaccgattatcactttggaag-----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|33796226|gb|CF323979.1|CF323979EST: CTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG GTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC
genomic: CTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAGgtttggatta ... tagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC
EST:
gi|58601755|gb|CK012283.1|CK012283EST: CAGTCTCCAGGCATTCTGGCCAGGACTTCAG GTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC
genomic: CAGTCTCCAGGCATTCTGGCCAGGACTTCAGgtttggatta ... tagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC
EST:
gi|88361880|gb|CI682051.1|CI682051EST: CTGTNTGGCCACTATCCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG GTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC
genomic: CTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAGgtttggatta ... tagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC
EST:
gi|88394177|gb|CI684850.1|CI684850EST: CTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAG GTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC
genomic: CTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAGgtttggatta ... tagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTC
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
41 (upstream exon),
50 (downstream exon)
Score:
4GTATGTGGAGGTAAATATGAATTCTGGTGCTACTGTTTGGCCACTATTCAACAGTCTCCAGGCATTCTGGCCAGGACTTCAGgtttggatta ... tagatttaagGTGTTAGCTGGAGATGTTGATCCTGCCATTCGAACTCATGCTGCCTTCTTCAGTGTATGGAAAAAATATGGCTTCACCCCAGAAGGGTTTAATCTTGCTA
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