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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTCTAAGGCAGCTGAAAAGGCCCGTGCACTTGCGGCTATTTCAGATGAAGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactgcactttctttcagttaattattattttttagcttttgttgaactgagtaactaaatcaaccacaaaattgatgccttattgatatgtcat...

Basic information

species Oryza sativa
transcript LOC_Os04g42010.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g42010.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G096705_T01 (Zea mays), 5'ss of exon 8
GATTCTAAGGCAGCTGAAAAGGCCCGTGCACTTGCGGCTATTTCAGATGAAGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaag--aactgcactttctttcagttaattatta-ttttttagcttttg-ttgaactgagtaactaaatcaaccacaaaattgatgccttattgatatgtcat
||| ||   |||||||| |||||||||||| |||| || ||| |||||||||||||||||| |||||| |||||  | || | ||||||||||||||| |||||   |||| ||  ||||  ||||| |   |   ||| |||| ||    |   |  |  |  || |           | ||||      ||| || | |   
GATCCTGCAGCAGCTGACAAGGCCCGTGCATTTGCAGCCATTGCAGATGAAGGTGGTTTGACTATGAAAGGCCACATAGTCATTTTGGAACCTGTGTCTGgtaaagaaactacagcttctcccagttgacactaggtttcttagtttccaatctgatagcttctctcatctggttttgtagttgaaataaaatt-atttct---
















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|86429750|gb|CI082173.1|CI082173
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|88843313|gb|CI372213.1|CI372213
EST:     TGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTTTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: TGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|33798570|gb|CF325143.1|CF325143
EST:     AGGTGGTTTGA-TATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|86871953|gb|CI332125.1|CI332125
EST:     AGGTGGTTTGATTATGAAGGCCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGCCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|88993134|gb|CI108762.1|CI108762
EST:     ACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: ACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|89197113|gb|CI021953.1|CI021953
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|89193612|gb|CI116245.1|CI116245
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGTCGTTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|86431392|gb|CI085003.1|CI085003
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|86862127|gb|CI330697.1|CI330697
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTT-GAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|86603303|gb|CI112063.1|CI112063
EST:     AGATGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGCCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|88256528|gb|CI358916.1|CI358916
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|86427996|gb|CI073093.1|CI073093
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|88907105|gb|CI089899.1|CI089899
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|86432658|gb|CI086269.1|CI086269
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|86430286|gb|CI082709.1|CI082709
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|88837163|gb|CI078523.1|CI078523
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|86430372|gb|CI082795.1|CI082795
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|88376216|gb|CI533118.1|CI533118
EST:     GGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: GGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|89192806|gb|CI050104.1|CI050104
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|33799670|gb|CF325698.1|CF325698
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|86842260|gb|CI335194.1|CI335194
EST:     TTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: TTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|88218676|gb|CI218525.1|CI218525
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|86425885|gb|CI070982.1|CI070982
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|218478715|gb|FG955118.1|FG955118
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCTG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
EST: gi|88837171|gb|CI078531.1|CI078531
EST:     AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCG                         GTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT
genomic: AGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAAT

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: 75 (upstream exon), 75 (downstream exon)
Score: 9

GATTCTAAGGCAGCTGAAAAGGCCCGTGCACTTGCGGCTATTTCAGATGAAGGTGGTTTGATTATGAAGGGCCATCTTGTTACTTTGGAACCTGTGTCCGgtaagaactg ... tttcattcagGTCAAGCTGAGAAGGATTATTGGAGTGCGATAAAGGGCGGTCAAGGAAAATATAGAGACAATAGAAGTAACAGGGGAAG




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