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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGATAATGGCTATAGGAACCATAGTTTGTGCTTCACTCTGGACTGAATTTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgacttttgtgctttacctttctatccaaattatgtcattttaattttatattttcacacacatatggtagcacattcatacccattttctcttgg...

Basic information

species Oryza sativa
transcript LOC_Os11g24540.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g24540.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G082330_T03 (Zea mays), 5'ss of exon 5
GTGGATAATGGCTATAGGAACCATAGTTTGTGCTTCACTCTGGACTGAATTTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgacttttgtgctttacctttctatccaaatt--atgtcattttaattttatattttcacacacatatggtagcacattcatacccattttctcttgg---------
 |||||||||||| |||| |||||||| ||||||||||||||||||||||||||| |||| || || ||||||||||||||||||||| ||||  | ||||||| ||  |||||||         ||| ||||| |  ||| ||||| |  ||| |||||  |   |   |    |   ||||||| ||||||   ||   |         
ATGGATAATGGCTGTAGGCACCATAGTCTGTGCTTCACTCTGGACTGAATTTGTTACATGTGAACAGGTTGATGAGCGTTATAATCAGCTGACCAGAAAGgtttgga--tttgtgc---------ctacccaaagtgaatggcatttcatgtttgtatttatatgtatgcactccaatgcattcattcccattgcttcagcgcattggaca
















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|29667215|gb|CB663490.1|CB663490
EST:     TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAG                         GATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
genomic: TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgactt ... tgctaaacagGATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
EST: gi|218487041|gb|FG950201.1|FG950201
EST:     TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAG                         GATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
genomic: TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgactt ... tgctaaacagGATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
EST: gi|88688575|gb|CI732151.1|CI732151
EST:     TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAG                         GATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
genomic: TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgactt ... tgctaaacagGATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
EST: gi|300215497|gb|HO088123.1|HO088123
EST:     TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAG                         GATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
genomic: TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgactt ... tgctaaacagGATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
EST: gi|88688415|gb|CI731991.1|CI731991
EST:     TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAG                         GATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
genomic: TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgactt ... tgctaaacagGATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
EST: gi|88691769|gb|CI733346.1|CI733346
EST:     TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAG                         GATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
genomic: TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgactt ... tgctaaacagGATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
EST: gi|88691004|gb|CI735083.1|CI735083
EST:     TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAG                         GATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
genomic: TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgactt ... tgctaaacagGATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
EST: gi|218478582|gb|FG949084.1|FG949084
EST:     ATCAGTTGACACGGAAG                         GATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
genomic: ATCAGTTGACACGGAAGgttttgactt ... tgctaaacagGATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
EST: gi|88690551|gb|CI734630.1|CI734630
EST:     TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAG                         GATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
genomic: TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgactt ... tgctaaacagGATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
EST: gi|396941284|gb|HO188493.1|HO188493
EST:     TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAG                         GATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
genomic: TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgactt ... tgctaaacagGATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
EST: gi|88688359|gb|CI731935.1|CI731935
EST:     TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAG                         GATGGGCCTAATTCTGGAACAAACCAACAGAGAAGATAAAGAAATCTTCGA
genomic: TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgactt ... tgctaaacagGATGGGCCTAATTCTGGAAC-AACCAACAGAGAAGATAAAGAAATCTTCGA
EST: gi|88691243|gb|CI733827.1|CI733827
EST:     TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAG                         GATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
genomic: TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgactt ... tgctaaacagGATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
EST: gi|58592179|gb|CF990487.1|CF990487
EST:     TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAG                         GATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
genomic: TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgactt ... tgctaaacagGATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
EST: gi|29664758|gb|CB661033.1|CB661033
EST:     TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAG                         GATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG
genomic: TTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgactt ... tgctaaacagGATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAG

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: 75 (upstream exon), 68 (downstream exon)
Score: 64

GTGGATAATGGCTATAGGAACCATAGTTTGTGCTTCACTCTGGACTGAATTTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgactt ... tgctaaacagGATGGGCCTAATTCTGGAACAACCAACAGAGAAGATAAAGAAATCTTCGAGATCAGTGCCAAGGGGGCTATTGTTTTTATTTTAGTAGCTTCAGTTTTCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGATAATGGCTATAGGAACCATAGTTTGTGCTTCACTCTGGACTGAATTTGTTGCATGCGAGCAAGTTGATGAGCGTTATAATCAGTTGACACGGAAGgttttgacttttgtgctttacctttctatccaaattatgtcattttaattttatattttcacacacatatggtagcacattcatacccattttctcttgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG