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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTAATGTGTCAGAACAAGATGCCATTGACCCAGTTTTAATCAATCTTTTAGTAAGGCTACGCAATCTCCAGgtaatcatttatgacaagcatactgacatgctcgcatgcattactgtttaatggcattatgcagaacgatttgcattactttaccatgcttattatggaa...

Basic information

species Oryza sativa
transcript LOC_Os03g05330.1
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05330.1 (Oryza sativa), 5'ss of exon 24
lower sequence: GRMZM2G086093_T01 (Zea mays), 5'ss of exon 13
GTTCTTAATGTGTCAGAACAAGATGCCATTGACCCAGTTTTAATCAATCTTTTAGTAAGGCTACGCAATCTCCAGgtaatcatttatgacaagcatactgacat----gctcgcatgcattactgtttaatggcat-tatgcagaacgatttgcattactttaccatgcttattatggaa
|| |||||| ||||||||||||||||  |||  ||| | ||||| ||||| ||||||||||| || ||||| |||||||| ||     |||||| |  ||   |    | ||  ||||  |  ||    |    ||  |||    || || |   |    | | |  || ||  |     
GTCCTTAATTTGTCAGAACAAGATGCTGTTGGTCCAATCTTAATAAATCTCTTAGTAAGGCTGCGAAATCTTCAGgtaattatccggaacaagctttttggttttgctgttctaatgccatgatgcaggacaatatgcatgttagactatgtaattaggctgatccagcctacca-----
















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|58677430|gb|CK066117.1|CK066117
EST:     CCATTGACCCAGTTTTAATCAATCTTTTAGTAAGGCTACGCAATCTCCAG                         GTTTCGATGAATACGAAAATGAGGTCCAATGCGTTTGCAGCTTATGGTGCT
genomic: CCATTGACCCAGTTTTAATCAATCTTTTAGTAAGGCTACGCAATCTCCAGgtaatcattt ... tttgcttcagGTTTCGATGAATACGAAAATGAGGTCCAATGCGTTTGCAGTTTATGGTGCT
EST: gi|218481123|gb|FG968746.1|FG968746
EST:     CCATTGACCCAGTTTTAATCAATCTTTTAGTAAGGCTACGCAATCTCCAG                         GTTTCGATGAATACGAAAATGAGGTCCAATGCGTTTGCAGCTTATGGTGCT
genomic: CCATTGACCCAGTTTTAATCAATCTTTTAGTAAGGCTACGCAATCTCCAGgtaatcattt ... tttgcttcagGTTTCGATGAATACGAAAATGAGGTCCAATGCGTTTGCAGTTTATGGTGCT
EST: gi|42591926|gb|CK738412.1|CK738412
EST:     CCATTGACCCAGTTTTAATCAATCTTTTAGTAAGGCTACGCAATCTCCAG                         GTTTCGATGAATACGAAAATGAGGTCCAATGCGTTTGCAGCTTATGGTGCT
genomic: CCATTGACCCAGTTTTAATCAATCTTTTAGTAAGGCTACGCAATCTCCAGgtaatcattt ... tttgcttcagGTTTCGATGAATACGAAAATGAGGTCCAATGCGTTTGCAGTTTATGGTGCT
EST: gi|58659604|gb|CK048284.1|CK048284
EST:     ATCAATCTTTTAGTAAGGCTACGCAATCTCCAG                         GTTTCGATGAATACGAAAATGAGGTCCAATGCGTTTGCAGCTTATGGTGCT
genomic: ATCAATCTTTTAGTAAGGCTACGCAATCTCCAGgtaatcattt ... tttgcttcagGTTTCGATGAATACGAAAATGAGGTCCAATGCGTTTGCAGTTTATGGTGCT
EST: gi|33681327|gb|CF309566.1|CF309566
EST:     AATCAATCTTTTAGTAAGGCTACGCAATCTCCAG                         GTTTCGATGAATACGAAAATGAGGTCCAATGCGTTTGCAGTTTATGGTGCT
genomic: AATCAATCTTTTAGTAAGGCTACGCAATCTCCAGgtaatcattt ... tttgcttcagGTTTCGATGAATACGAAAATGAGGTCCAATGCGTTTGCAGTTTATGGTGCT

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: 60 (upstream exon), 71 (downstream exon)
Score: 5

GTTCTTAATGTGTCAGAACAAGATGCCATTGACCCAGTTTTAATCAATCTTTTAGTAAGGCTACGCAATCTCCAGgtaatcattt ... tttgcttcagGTTTCGATGAATACGAAAATGAGGTCCAATGCGTTTGCAGTTTATGGTGCTTTAAGTGCCTATGGTGTAGGTTCACAGCAGTTTCTTGAGCAG




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