Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCCTTTCTGTTCTGATTGTACCATTTTGCACTATCTTTGCAATTCTTTGGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTTgtaagactaatttatcttcattcttgtgtggtctttctatattttatatatgaccttgtatggtgtgcttctcactaggaggtgcatttttttttctata...

Basic information

species Oryza sativa
transcript LOC_Os11g24540.2
intron # 8
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 8
lower sequence: GRMZM2G082330_T03 (Zea mays), 5'ss of exon 7
GACCCTTTCTGTTCTGATTGTACCATTTTGCACTATCTTTGCAATTCTTTGGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTTgtaagactaatttatctt-----cattcttgtgtggtctttctatattttatatatgaccttgtatggtgtgcttctcactaggaggtgcatttttttttctata
|| | | ||||||   ||||||||||||||  |  | ||||||||||| |||||||| ||||| |||||||| ||||||||||||||||||||| | || ||||||  |  ||| |||     ||||||| |||  | || || |||| | | | |   ||| |  |||    | |       || ||  ||      |||   |
GATCTTATCTGTTGGAATTGTACCATTTTGTGCGGTGTTTGCAATTCTCTGGGCTGTGTATCGCCATGCTTCATTTGCTTGGATAGGCCAAGACGTTCTGgtaagataatcttaacttacaaccattcttttgttttgttcctctattatgt-tcttttcttttggggt----tgcatgtagagatgtcaatggggaattcccca
















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:     GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTT                         GGAATCTGCCTGATG
genomic: GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTTgtaagactaa ... ttgtcctcagGGAATCTGCCTGATG
EST: gi|2310019|gb|C26174.1|C26174
EST:     GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTT                         GGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCCAAATAT
genomic: GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTTgtaagactaa ... ttgtcctcagGGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTA-CCAAATAT
EST: gi|286796|gb|D15603.1|D15603
EST:     GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTT                         GGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
genomic: GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTTgtaagactaa ... ttgtcctcagGGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
EST: gi|29664759|gb|CB661034.1|CB661034
EST:     GCCAAGACATCCTT                         GGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
genomic: GCCAAGACATCCTTgtaagactaa ... ttgtcctcagGGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
EST: gi|29667214|gb|CB663489.1|CB663489
EST:     GGGCTGTCTATCGGCATGCTTCTTTTGC-TGGATAGGCCAAGACATCCTT                         GGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
genomic: GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTTgtaagactaa ... ttgtcctcagGGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
EST: gi|29641729|gb|CB646736.1|CB646736
EST:     GCTTGGATAGGCCAAGACATCC-T                         GGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
genomic: GCTTGGATAGGCCAAGACATCCTTgtaagactaa ... ttgtcctcagGGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
EST: gi|218478582|gb|FG949084.1|FG949084
EST:     GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTT                         GGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
genomic: GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTTgtaagactaa ... ttgtcctcagGGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
EST: gi|396941284|gb|HO188493.1|HO188493
EST:     GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTT                         GGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
genomic: GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTTgtaagactaa ... ttgtcctcagGGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
EST: gi|27578188|gb|CB000883.1|CB000883
EST:     GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTT                         GGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
genomic: GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTTgtaagactaa ... ttgtcctcagGGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
EST: gi|29677381|gb|CB673656.1|CB673656
EST:     ATAGGCCAAGACATCC-T                         GGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
genomic: ATAGGCCAAGACATCCTTgtaagactaa ... ttgtcctcagGGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
EST: gi|218501626|gb|FG955998.1|FG955998
EST:     GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTT                         GGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
genomic: GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTTgtaagactaa ... ttgtcctcagGGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
EST: gi|58592179|gb|CF990487.1|CF990487
EST:     GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTT                         GGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
genomic: GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTTgtaagactaa ... ttgtcctcagGGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
EST: gi|218504564|gb|FG954781.1|FG954781
EST:     GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTT                         GGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC
genomic: GGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTTgtaagactaa ... ttgtcctcagGGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATC

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), 54 (downstream exon)
Score: 46

GACCCTTTCTGTTCTGATTGTACCATTTTGCACTATCTTTGCAATTCTTTGGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTTgtaagactaa ... ttgtcctcagGGAATCTGCCTGATGATAACTGTGCTTCAAATGGCACGCTTACCAAATATCAGG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCCTTTCTGTTCTGATTGTACCATTTTGCACTATCTTTGCAATTCTTTGGGCTGTCTATCGGCATGCTTCTTTTGCTTGGATAGGCCAAGACATCCTTgtaagactaatttatcttcattcttgtgtggtctttctatattttatatatgaccttgtatggtgtgcttctcactaggaggtgcatttttttttctata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaggtg