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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACCATAGTTCAGGGCCTGAGGAACACAGACGATTCTATCTCTACAATGATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagccctacagcagctaccctgttcttgtttctttctacatcagtaggcttaagtaattctgaccaatagcattgctagcatgtaggtttcagta...

Basic information

species Oryza sativa
transcript LOC_Os09g33520.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g33520.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G822842_T01 (Zea mays), 5'ss of exon 3
---CAACCATAGTTCAGGGCCTGAGGAACACAGACGATTCTATCTCTACAATGATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagc----------cctacagcagctaccctgttcttgttt--ctttctacatcagtaggcttaagtaattctgaccaatagcattgctagcatgtaggtttcagta
   ||  |  |||    || |||||||| | ||| |||| ||||| ||||||||| ||||||||||||||||||| || ||||||||  | || ||||||||||||||  ||             ||    |   | |   | | ||||  || ||| ||| |  |    ||  | ||| |  |  ||   |  |  || || |           
ACACAGTCGCAGT---AGGACTGAGGAAGAGAGAAGATTTTATCTTTACAATGATATTAGAGTTGTCTTTCCTCAGAGGCACTCAGACTCTGACGAAGGCGAGgtatgtggcaactatttatttcacccttgtagcacaactttagtttaactctctccattacaaattatagttcattttagctcatcttaa-gtcagaattt-----------
















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|88276813|gb|CI395976.1|CI395976
EST:     TGTTAGAGTT-TCTTTCCTCAAAGACACTCAGATGCAGATGAAGGGCGAG                         CTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAG
genomic: TGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGG-CGAGgtatgcagcc ... ttccctgcagCTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAG
EST: gi|88446797|gb|CI526630.1|CI526630
EST:     ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAG                         CTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagcc ... ttccctgcagCTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|88251177|gb|CI349407.1|CI349407
EST:     ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAG                         CTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagcc ... ttccctgcagCTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|88253435|gb|CI352061.1|CI352061
EST:     ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAG                         CTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagcc ... ttccctgcagCTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|88276039|gb|CI396643.1|CI396643
EST:     ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAG                         CTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagcc ... ttccctgcagCTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|4879921|gb|AU064220.1|AU064220
EST:     ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAG                         CTGCGGGTCGAGCACGACTTNCCTGCTGATCCCAAGTACTTNGACATAAGC
genomic: ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagcc ... ttccctgcagCTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|88991537|gb|CI019715.1|CI019715
EST:     ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAG                         CTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagcc ... ttccctgcagCTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|88462813|gb|CI519725.1|CI519725
EST:     ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAG                         CTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagcc ... ttccctgcagCTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|88261204|gb|CI364780.1|CI364780
EST:     ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAG                         CTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagcc ... ttccctgcagCTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|88515446|gb|CI443100.1|CI443100
EST:     ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAG                         CTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagcc ... ttccctgcagCTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|86851930|gb|CI316499.1|CI316499
EST:     ATGTTAGAGTTTTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAG                         CTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagcc ... ttccctgcagCTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|88260809|gb|CI361397.1|CI361397
EST:     ATGTTAGAGTTTTCTTTCCTCAAAGACACTCAGATGCGGATGAAGGCGAG                         CTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagcc ... ttccctgcagCTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
EST: gi|88260407|gb|CI362700.1|CI362700
EST:     ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAG                         CTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC
genomic: ATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagcc ... ttccctgcagCTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGC

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: 71 (upstream exon), 75 (downstream exon)
Score: 11

CAACCATAGTTCAGGGCCTGAGGAACACAGACGATTCTATCTCTACAATGATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagcc ... ttccctgcagCTGCGGGTCGAGCACGACTTCCCTGCTGATCCCAAGTACTTCGACATAAGCAACTGATATTTACTCGCGCACTTCACATGAAATCTGTATATATCATACC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACCATAGTTCAGGGCCTGAGGAACACAGACGATTCTATCTCTACAATGATGTTAGAGTTGTCTTTCCTCAAAGACACTCAGATGCAGATGAAGGCGAGgtatgcagccctacagcagctaccctgttcttgtttctttctacatcagtaggcttaagtaattctgaccaatagcattgctagcatgtaggtttcagta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG