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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattctaagcactcagctaagaatatctgcaaacttgttctagtttccgtggctataatgtgtgaatgattttgttccccttggacacagCCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCAGAGGTGTCGTCTACAGGGGAGTCAATTTGCTCGCTACGGTTCGCAGCAC

Basic information

species Oryza sativa
transcript LOC_Os07g01490.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g01490.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G436981_T02 (Zea mays), 3'ss of exon 15
gtaaattctaagcactcagctaagaatatctgcaaacttgttctagtttccgtggctataatgtgtgaatgattttgttccccttggacacagCCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCAGAGGTGTCGTCTACAGGGGAGTCAATTTGCTCGCTACGGTTCGCAGCAC
|||   |     |||      |    | || || ||   |||  |  ||   |||    ||    | | ||||  | ||  |     |||||||| || || ||||| |||||||||||||| |||||||||||||||||||| || | ||| || |||||||||||  |||||||  | ||||| || ||| 
gtattgttccgacac------attggtttcggctaaaa-gtttaatcttaaatggtatcaagtactaactgatgcttttggc----aacacagCCGTGTCTCGGAGGGGACTCGAAGACACTGATGTTTGTGAATCTGTCTCCTGAAGCGTCCTCGACAGGGGAGTCTCTTTGCTCATTGCGGTTTGCTGCAA
















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|88286255|gb|CI522555.1|CI522555
EST:     TACTTGCTACAN                         CCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCA
genomic: TACTTGCTACAGgtaaattcta ... ttggacacagCCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCA
EST: gi|86482699|gb|CI125332.1|CI125332
EST:     AAGAGGAGCACGTTCCGTTCAGGAACTCAAAATTAACGTACTTGCTACAG                         CCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCA
genomic: AAGAGGAGCACGTTCCGTTCAGGAACTCAAAATTAACGTACTTGCTACAGgtaaattcta ... ttggacacagCCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCA
EST: gi|58686047|gb|CK074734.1|CK074734
EST:     AAGAGGAGCACGTTCCGTTCAGGAACTCAAAATTAACGTACTTGCTACAG                         CCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCA
genomic: AAGAGGAGCACGTTCCGTTCAGGAACTCAAAATTAACGTACTTGCTACAGgtaaattcta ... ttggacacagCCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCA
EST: gi|88989368|gb|CI043867.1|CI043867
EST:     AAGAGGAGCACGTTCCGTTCAGGAACTCAAAATTAACGTACTTGCTACAG                         CCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCA
genomic: AAGAGGAGCACGTTCCGTTCAGGAACTCAAAATTAACGTACTTGCTACAGgtaaattcta ... ttggacacagCCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCA
EST: gi|58681647|gb|CK070334.1|CK070334
EST:     AAGAGGAGCACGTTCCGTTCAGGAACTCAAAATTAACGTACTTGCTACAG                         CCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCA
genomic: AAGAGGAGCACGTTCCGTTCAGGAACTCAAAATTAACGTACTTGCTACAGgtaaattcta ... ttggacacagCCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCA
EST: gi|88273313|gb|CI388769.1|CI388769
EST:     AAGAGGAGCACGTTCCGTTCAGGAACTCAAAATTAACGTACTTGCTACAG                         CCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCA
genomic: AAGAGGAGCACGTTCCGTTCAGGAACTCAAAATTAACGTACTTGCTACAGgtaaattcta ... ttggacacagCCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCA
EST: gi|58684836|gb|CK073523.1|CK073523
EST:     TACTTGCTACAG                         CCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCA
genomic: TACTTGCTACAGgtaaattcta ... ttggacacagCCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCA

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: 42 (upstream exon), 64 (downstream exon)
Score: 10

TAATAAGAGCCTCTCATGCTTGAGCGATGTAATCTTCTCCATTGCAAAGAAAGAGGAGCACGTTCCGTTCAGGAACTCAAAATTAACGTACTTGCTACAGgtaaattcta ... ttggacacagCCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCAGAGGTGTCGTCTACAGGGGAGTCAATTTGCTCGCTACGGTTCGCAGCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttctagtttccgtggctataatgtgtgaatgattttgttccccttggacacagCCATGCCTTGGAGGAGACTCGAAGACACTTATGTTTGTGAATCTGTCTCCAGAGGTGTCGTCTACAGGGGAGTCAATTTGCTCGCTACGGTTCGCAGCAC
                                  ttttgttcccctt  CT-rich tract
                             aatgatttt  TA-rich tract