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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtgaattctcccttcattattacacaacaaatttaccccctttgacttttgctttatcctcctttattattttttttcagGGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTAGGCATTACAGAAGCCTACTGGGAATACCGACTTAAGCCTTGGGATATGG

Basic information

species Oryza sativa
transcript LOC_Os02g07350.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07350.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G051276_T01 (Zea mays), 3'ss of exon 7
gtaa-agtgaattctcccttcattattacacaacaaatttaccccctttgacttttgctttatcctc----ctttattattttttttcagGGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTAGGCATTACAGAAGCCTACTGGGAATACCGACTTAAGCCTTGGGATATGG
|||| |||        |    ||| ||      || |||| | |  | ||| ||||   | ||||||      |  || |||||||||||||||| ||||| ||||| |||||||||||||||||||||||| |||  || || ||||||||||| ||||||||||||||||||||||| ||||||||||
gtaagagtttgccgaactgcaattgttttt--gcagatttgcaca-tgtgatttttctatcatcctcgaaatatacttcttttttttcagGGAGTGCGAAGGCTAGGGTCTGCTGCTGCTGACATGTCCCACATTGGACTTGGTATTACAGAAGCTTACTGGGAATACCGACTTAAGCCATGGGATATGG
















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|86497781|gb|CI140414.1|CI140414
EST:     CATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGG                         GGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
genomic: CATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGGgtaaagtgaa ... tttttttcagGGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
EST: gi|55409778|gb|CV722154.1|CV722154
EST:     CATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGG                         GGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
genomic: CATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGGgtaaagtgaa ... tttttttcagGGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
EST: gi|29661947|gb|CB658222.1|CB658222
EST:     CATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGG                         GGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
genomic: CATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGGgtaaagtgaa ... tttttttcagGGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
EST: gi|66924326|gb|CX111174.1|CX111174
EST:     CATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGG                         GGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
genomic: CATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGGgtaaagtgaa ... tttttttcagGGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
EST: gi|94362390|gb|CI052303.1|CI052303
EST:     CATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGG                         GGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
genomic: CATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGGgtaaagtgaa ... tttttttcagGGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
EST: gi|88980653|gb|CI022366.1|CI022366
EST:     CATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGG                         GGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
genomic: CATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGGgtaaagtgaa ... tttttttcagGGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
EST: gi|88226163|gb|CI226079.1|CI226079
EST:     GACATTAGCAGG                         GGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
genomic: GACATTAGCAGGgtaaagtgaa ... tttttttcagGGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
EST: gi|88836626|gb|CI010882.1|CI010882
EST:     CATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGG                         GGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
genomic: CATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGGgtaaagtgaa ... tttttttcagGGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
EST: gi|22306217|gb|BQ907439.1|BQ907439
EST:     CATGGGTGACC-ACATAAATTTGTTCAAGGAATACACAGACATTAGCAGG                         GGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA
genomic: CATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGGgtaaagtgaa ... tttttttcagGGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTA

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: 59 (upstream exon), 59 (downstream exon)
Score: 19

GTGGAACAATCACTTCTGGTAACTGGTTTTGGTTATGAACATGATGATGCATGGGTGACCAACATAAATTTGTTCAAGGAATACACAGACATTAGCAGGgtaaagtgaa ... tttttttcagGGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTAGGCATTACAGAAGCCTACTGGGAATACCGACTTAAGCCTTGGGATATGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaaatttaccccctttgacttttgctttatcctcctttattattttttttcagGGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTAGGCATTACAGAAGCCTACTGGGAATACCGACTTAAGCCTTGGGATATGG
              ctttgac  putative branch site (score: 19)
                    cttttgctttatcctc  CT-rich tract
                                     tttattattttttttc  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtgaattctcccttcattattacacaacaaatttaccccctttgacttttgctttatcctcctttattattttttttcagGGAGTACGAAGACTAGGTTCTGCTGCTGCTGACATGTCCCACGTTGCCCTAGGCATTACAGAAGCCTACTGGGAATACCGACTTAAGCCTTGGGATATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC