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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgattttgccatatacattatttacttccttgtgatccattagttccactaaggcttcacgtatagaacaatatagttgtgcgctggttgtctat...

Basic information

species Zea mays
transcript GRMZM2G082330_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082330_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os11g24540.2 (Oryza sativa), 5'ss of exon 11
TCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgt----------atgtgattttgccatatacattatttacttccttgtgatccattagttccactaaggcttcacgtatagaacaatatagttgtgcgctggttgtctat
|| |||| ||||| || |||||||||||||||||||| ||||| ||||||||||||||||||||||| |||||||||||||| |||| ||||||||| ||||          || |  |  ||| |||||  || |    |  ||| |||| | || ||| ||||      | | || | |     |       |   ||          
TCTTAAGAATACCTCGTTTCTTTGATCCATGGGGTGGCTATGACATGATAGGCTTTGGTGACATTATTTTCCCTGGATTGCTAGTTGCATTCAGCTACAGgtattatactatatatattgctgcaatataagttgtaacttctcttttgatgccttggtttcactggacgctaaagtgtcggtaggttggtaaatatact----------

upper sequence: GRMZM2G082330_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA10G44490.1 (Glycine max), 5'ss of exon 11
TCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgattttgccatatacattatttacttccttgt------gatccattagttccactaaggcttcacgtatagaacaatatagttgtgcgctggt-tgtctat------------------------------------------------------------
|  | ||  | || ||  | | |||||| |||||||| ||||||||||| || ||||| || ||| |||| ||||| |||||||||   || |    ||||||| ||| ||    || |     |   ||||   |        |||  || |  | | || | | |  ||   |      | ||| |||    |  || ||| | |                                                            
TTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTGGAGATATTCTCTTTCCTGGTTTGCTTGTTTCCTTTACTCGTAGgtat-tgaattccttatttggtcaaaaaacttgaataaatggaagattaataaacttctctgaagatatacacttgttttca-atatttgccttcgtgtgtgtgtgtttttcttctttttaatgtacatttgagaagatacattgttatggttttttattgtctcag

upper sequence: GRMZM2G082330_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA20G39260.1 (Glycine max), 5'ss of exon 10
TCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt---ttgccatatacattatttacttccttgtga---tccattagttccactaaggctt---cacgtatagaacaat-atagttgtgcgctggttgtctat----------------------------------------------------
|  | ||  | || ||  | | |||||| |||||||| ||||||||||| || ||||| || ||| |||| ||||| |||||||||   ||      |||||||   |||   ||       | |  | ||   |   ||  |   |  || |  | |  | | | |    |  || |  || | |     ||||| | |  |  |||                                                      
TTTTGAGATTTCCTCGTCTTTCTGATCCTTGGGGTGGCTATGATATGATTGGATTTGGAGATATTCTCTTTCCTGGTTTGCTTGTTTCCTTTGCTCGTAGgtattgaattccttttttggtcaaaaaacttgaataaatggaagattttataaacttctttgaagataacacttgttttcaatatttgcttttgtgtgtttttcttcttctttttaatgtacatttgagaagatgcattgttatggtttttgattgtctcag

upper sequence: GRMZM2G082330_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT2G43070.1 (Arabidopsis thaliana), 5'ss of exon 11
TCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgattttgccatatacattatttacttccttgtgatccatt---agttcca-ctaaggcttcacgtatagaacaatatagttgtgcgctggttgtctat----------------------------------------------
| |||||||| || || ||||||||||| |||||||||||||| ||||| || ||||| |||||  ||||||| || |||||  ||   ||    |  |||||  |   || | ||   ||||| ||           || | | |   | ||||| ||  | |   || |     | | | |  || |   |   |     ||                                              
TACTAAGGATTCCTCGGTTCTTTGATCCTTGGGGTGGTTATGACATGATTGGTTTTGGGGACATCCTCTTCCCCGGTTTGCTCATTTCCTTTGCTTCCAGgtactt---ttagtcagtgacattcttagagcttcaaagaacaacttggaattccatctttgcccatactttctccagagtgtctttctcaacgattctctcatccaatcctctcccacgattaatacttgctccactctttgatctcag

upper sequence: GRMZM2G082330_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv05s0062g01250.t01 (Vitis vinifera), 5'ss of exon 11
TCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgattttgccatatacattatttacttccttgtgatccatta---gttccactaaggcttcacgtatagaacaatatagttgtgcgctggttgtctat
|  | ||  | || || ||||||||||| |||||||||||||||||||| |||||||| |||||| |||||||||| |||||  ||  |||    |  |||||      ||| |  | |  | | |  | |   |       || |    |||    | | |  ||   |||    |  ||   || |    |     || | 
TGTTGAGAGTTCCTCGTTTCTTTGATCCTTGGGGTGGTTATGATATGATTGGCTTTGGGGACATTCTCTTCCCTGGTTTGCTCATTTCATTTGCTTTCAGgtactc---tttacactgtcaagtttccagtaagtgagataacagtgaaggttatgattatggatcctatattttcctttaagtttttttaataaaaatcaac

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|60342860|gb|DN209833.1|DN209833
EST:     GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
EST: gi|91053792|gb|EB164210.1|EB164210
EST:     GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATANNNNNNNNGGTT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
EST: gi|211115391|gb|FK954864.1|FK954864
EST:     GGCTTAG-TGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTT
EST: gi|78086708|gb|DV515101.1|DV515101
EST:     GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTTTCTGGCT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
EST: gi|211094546|gb|FL478908.1|FL478908
EST:     GGC-TTAGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
EST: gi|211115394|gb|FK954867.1|FK954867
EST:     GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
EST: gi|76932551|gb|DV173063.1|DV173063
EST:     GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTTTCTGGCT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
EST: gi|211116170|gb|FK954868.1|FK954868
EST:     GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTAACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
EST: gi|74246173|gb|DT654087.1|DT654087
EST:     GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTTTCTGGCT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
EST: gi|71313933|gb|DR793572.1|DR793572
EST:     GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
EST: gi|78086709|gb|DV515102.1|DV515102
EST:     GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
EST: gi|211115393|gb|FK954866.1|FK954866
EST:     GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTAACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
EST: gi|211115392|gb|FK954865.1|FK954865
EST:     GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
EST: gi|91049743|gb|EB160161.1|EB160161
EST:     GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
EST: gi|149015226|gb|EE045012.2|EE045012
EST:     GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
EST: gi|71771233|gb|DR969170.1|DR969170
EST:     GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAG                         ATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT
genomic: GGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCT

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 124

TCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCTAATTGTGGGATATGCAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

TCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCTAATTGTGGGATATGCAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 129

TCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCTAATTGTGGGATATGCAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 238

TCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgatt ... cgctgaacagATTTGACAGAGCAAACAGAAAGGGTGTCTTGAGTGGATATTTTCTCTGGCTAATTGTGGGATATGCAGTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTAAGGATACCCCGCTTCTTTGATCCATGGGGTGGTTATGATATGATAGGCTTTGGTGACATTATCTTCCCTGGATTGCTTGTTGGATTCAGCTATAGgtatgtgattttgccatatacattatttacttccttgtgatccattagttccactaaggcttcacgtatagaacaatatagttgtgcgctggttgtctat

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