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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATTTTGAGCCAGCCAATGTGCTCCTTGGTAATGGATTCTCAGTACGTGTCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatctagtgttgtacaccaaccttgtggttgtgatacttcggcttttccgtcgcaagcagttctgatacatttcctaaaattcctgaagtccaatt...

Basic information

species Oryza sativa
transcript LOC_Os02g07960.3
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07960.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G335638_T01 (Zea mays), 5'ss of exon 14
GAATTTTGAGCCAGCCAATGTGCTCCTTGGTAATGGATTCTCAGTACGTGTCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatctagtgttgtacaccaaccttgtggttgt-gatacttcggcttttccgtcgcaagcagttctgatacatttcctaaaattcctgaagtccaatt-----
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GAATTTTGAACCAGCCAACGTGCTCCTCGACAATAGATGCTCAGTGCGTGTTGCTGAATGTGGGCTGGCACAATTGATGGCGTCTGGTTCTGTTACACAGgtaacctcttcgatt------cagctttgccgttatcaataatacaaaattgtggctgaaagaactgaactcatagcgcatacacttcatggtgcacggatcacgg
















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|58669825|gb|CK058511.1|CK058511
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29621906|gb|CB626917.1|CB626917
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29656568|gb|CB652843.1|CB652843
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|58611356|gb|CK039068.1|CK039068
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29626065|gb|CB631076.1|CB631076
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29626028|gb|CB631039.1|CB631039
EST:     GCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TCGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: GCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29640907|gb|CB645914.1|CB645914
EST:     CAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: CAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|66927345|gb|CX114193.1|CX114193
EST:     GGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: GGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29674397|gb|CB670672.1|CB670672
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29671438|gb|CB667713.1|CB667713
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29638004|gb|CB643013.1|CB643013
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT

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: 72 (upstream exon), 62 (downstream exon)
Score: 26

GAATTTTGAGCCAGCCAATGTGCTCCTTGGTAATGGATTCTCAGTACGTGTCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCATGAAGCTGGGACTTTTACCTACCGAAGTGATGTTTACAGTTTTGGCGTGG




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