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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCATTCCTGTTTTTCGGGAGCAAGCTGAGCAACTATTGAACTCTTCCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgcttctcctgttatgtaattaatactgtagcaagtactagtatagctgcgatacttaacagagatgcatttcttag

Basic information

species Oryza sativa
transcript LOC_Os09g34910.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g34910.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G164956_T01 (Zea mays), 5'ss of exon 11
TGTCATTCCTGTTTTTCGGGAGCAAGCTGAGCAACTATTGAACTCTTCCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgctt-ctcctgttatgtaattaatactgtagcaagtactag-tat----agctgcgatacttaacagagatgcatttcttag
||| |||||||| ||  || ||||||| |||||  |  | | |||||||    ||||||| | |||  | || |||||||| ||||| |||||||||||||||||||| ||| |  ||  |    |    | |     |  |||| |||    |||| || ||  ||||||| ||   |  |||||
TGTTATTCCTGTCTTCAGGCAGCAAGCAGAGCAGTTGCTAAGCTCTTCCACTCTGTCTGCGGCTGACTTGCTTGCCAAAGCTCTTGCAAAGGCAGTTgtaagttgctttctcgttctacatttccaggtttctgctctgctctagatattggcagctccg-taactaacagaaatatgtaccttag

upper sequence: LOC_Os09g34910.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G149520_T01 (Zea mays), 5'ss of exon 7
TGTCATTCCTGTTTTTCGGGAGCAAGCTGAGCAACTATTGAACTCTTCCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgcttctcctgttatgtaattaatactgtagcaa-gtactag-tatagct-gcgatacttaacagagatgcatttcttag
||| |||||| | ||  || ||||||| |||||  |  | | ||||||| |  ||||||||| |||  | || |||||||||||||| ||||||||||||||||||||   |  | |  |  |  |   | | ||   |  |||| ||| |   |    |  ||||||| ||   | ||||||
TGTTATTCCTATCTTCAGGCAGCAAGCAGAGCAGTTGCTAAGCTCTTCCAGTCTGTCTGCAGCTGACTTGCTTGCCAAAGCACTTGCAAAGGCAGTTgtaagttgctttcacgttcagcttttccaggtttttgctctgctctagatattgtcagttggaactaacagaaatatgtgtcttag
















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|29679594|gb|CB675869.1|CB675869
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|218480006|gb|FG954443.1|FG954443
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|29622801|gb|CB627812.1|CB627812
EST:     TAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: TAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|29637933|gb|CB642942.1|CB642942
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|29672112|gb|CB668387.1|CB668387
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|218486017|gb|FG967018.1|FG967018
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|218497196|gb|FG952158.1|FG952158
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTAT
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTAT
EST: gi|218489960|gb|FG943973.1|FG943973
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAA
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAA
EST: gi|29628389|gb|CB633400.1|CB633400
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|87023726|gb|CI286477.1|CI286477
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|87008347|gb|CI301105.1|CI301105
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|218502440|gb|FG963347.1|FG963347
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|87035352|gb|CI189974.1|CI189974
EST:     TAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: TAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|29636722|gb|CB641731.1|CB641731
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|29687238|gb|CB683513.1|CB683513
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|29662539|gb|CB658814.1|CB658814
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|218487667|gb|FG948994.1|FG948994
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|218495874|gb|FG947056.1|FG947056
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|29662538|gb|CB658813.1|CB658813
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGTGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
EST: gi|29672113|gb|CB668388.1|CB668388
EST:     CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTT                         GGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC
genomic: CCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCAC

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), 74 (downstream exon)
Score: 102

TGTCATTCCTGTTTTTCGGGAGCAAGCTGAGCAACTATTGAACTCTTCCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgct ... catttcttagGGCTACACGGACATAAAGAAGAGATCCTTGCTGTCTTCTATGGACAACCACACTACATTACTTCTTCAAACTGGTCGATCGGTGTATGCAGCAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCATTCCTGTTTTTCGGGAGCAAGCTGAGCAACTATTGAACTCTTCCGGGATGTCTGCAGTTGATCTACTAGCCAAAGCACTTGCGAAGGCAGTTgtaagttgcttctcctgttatgtaattaatactgtagcaagtactagtatagctgcgatacttaacagagatgcatttcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG