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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggacttgctcttttctccacatcttctatttcttccctgtataagctcaaatgtttctcccatgaaacaagcctgctgtgaattctttttcctaattgaaacatccgtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGAGCTAACTGCTAATTCTGAATATGCGCGAACGGAGCTACGCCTCTTGGAC

Basic information

species Oryza sativa
transcript LOC_Os07g38360.2
intron # 12
splice site 3'
intron type U2

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|87007445|gb|CI279116.1|CI279116
EST:     CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|87027516|gb|CI272281.1|CI272281
EST:     CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|86488897|gb|CI131530.1|CI131530
EST:     CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|89193003|gb|CI050301.1|CI050301
EST:     CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|86534836|gb|CI175042.1|CI175042
EST:     AAGCCTGCTTCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: AAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|86520168|gb|CI160374.1|CI160374
EST:     CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|86487952|gb|CI130585.1|CI130585
EST:     CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|87018826|gb|CI256711.1|CI256711
EST:     CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|88828716|gb|CI073586.1|CI073586
EST:     CCAATGGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCAAT-GTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|88222664|gb|CI222620.1|CI222620
EST:     CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|29639149|gb|CB644158.1|CB644158
EST:     CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|86500547|gb|CI143180.1|CI143180
EST:     TCAATGTCTGTAAAACCATAAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: TCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|86520400|gb|CI160606.1|CI160606
EST:     CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|86487709|gb|CI130342.1|CI130342
EST:     CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|88849766|gb|CI089872.1|CI089872
EST:     CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACCTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|88903268|gb|CI088806.1|CI088806
EST:     CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|86517221|gb|CI157427.1|CI157427
EST:     CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|87027338|gb|CI270013.1|CI270013
EST:     CAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|88503560|gb|CI431066.1|CI431066
EST:     CCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|88829485|gb|CI074355.1|CI074355
EST:     CAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|87013889|gb|CI271280.1|CI271280
EST:     CCCAATGTCAATGTCTGTAAACCCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|66923414|gb|CX110262.1|CX110262
EST:     TGTAAAACCATCAAGTGATCAGAAGCCTGCTTTTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: TGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|3767888|gb|AU031915.1|AU031915
EST:     AGAAGCNCTGCTGCTG                         GCAAGTNAGATGTCGATGCTCGGANTTCAGGACGCTACTCTGGACTTGCG
genomic: AGAAGC-CTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCG
EST: gi|88547228|gb|CI477509.1|CI477509
EST:     CAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|87028063|gb|CI257223.1|CI257223
EST:     CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|86872933|gb|CI326930.1|CI326930
EST:     AGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: AGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
EST: gi|86498864|gb|CI141497.1|CI141497
EST:     CATCAAGTGATCAGAAGCCTGCTGCTG                         GCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA
genomic: CATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGA

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), 49 (downstream exon)
Score: 11

AGCGGTGTGCCTCACTCTCATATGTCAGCGGCACAATTGACTTTTGGGGCCCCAATGTCAATGTCTGTAAAACCATCAAGTGATCAGAAGCCTGCTGCTGgtaatggact ... gtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGAGCTAACTGCTAATTCTGAATATGCGCGAACGGAGCTACGCCTCTTGGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaaacaagcctgctgtgaattctttttcctaattgaaacatccgtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGAGCTAACTGCTAATTCTGAATATGCGCGAACGGAGCTACGCCTCTTGGAC
                            tcctaat  putative branch site (score: 11)
                                          tccgtctt  putative PPT
                   aattcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatggacttgctcttttctccacatcttctatttcttccctgtataagctcaaatgtttctcccatgaaacaagcctgctgtgaattctttttcctaattgaaacatccgtcttatcagGCAAGTAAGATGTCGATGCTCGGACTTCAGGACGCTACTCTGGACTTGCGAGCTAACTGCTAATTCTGAATATGCGCGAACGGAGCTACGCCTCTTGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT