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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgattttttttcttttcttccaattttttatttcgatgtggattcttcttgcccatgttcttatgtcacatacttgcgatgcag

Basic information

species Zea mays
transcript GRMZM2G070605_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070605_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g13770.3 (Oryza sativa), 5'ss of exon 4
AAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgattttttttcttttcttccaatttttta-tttcgatgtggattcttctt----gcccatgttcttatgtcacatacttgcgatgcag
||||| ||||||||||| ||  ||||||||| | |||||||  ||||||||||||| || || ||| |||||||||| |||||||||||||| || |||||||   |||||| |     |  |||| || | ||||||  |   ||  | ||    ||  ||||| || |||  |  | |||| ||||||
AAGCTGCTCTTTCCAGTTGCGTTGTGCCATGCTCTTGGTCATGTCACTAGCAATGTATCGTTTGCTACTGTTGCAGTTTCATTTGCCCACACCATTAAAGgtgccattttttgtgcatatttaattcttgaatttcgaccttcttttgttttatatgctaatgtttttgtgttgcccaattgcaatgcag
















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|149095141|gb|EE180755.2|EE180755
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGTAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|76914837|gb|DV165713.1|DV165713
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|149013546|gb|EE043037.2|EE043037
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|101394747|gb|EB819306.1|EB819306
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|32925288|gb|CF030100.1|CF030100
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|149075192|gb|EE163691.2|EE163691
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|148986357|gb|EE030094.2|EE030094
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|211519067|gb|FL311546.1|FL311546
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCTCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCGGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|116820056|gb|EC863241.1|EC863241
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|149075125|gb|EE163618.2|EE163618
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|149112153|gb|EE191267.2|EE191267
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|32925201|gb|CF030013.1|CF030013
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|91050012|gb|EB160430.1|EB160430
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|149026859|gb|EE046212.2|EE046212
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|149097452|gb|EE183315.2|EE183315
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|149015293|gb|EE045098.2|EE045098
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|71766326|gb|DR964263.1|DR964263
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|78077772|gb|DV506204.1|DV506204
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
EST: gi|32925598|gb|CF030410.1|CF030410
EST:     CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAG                         CTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC
genomic: CAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGC

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: 46 (upstream exon), 47 (downstream exon)
Score: 41

AAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGCAAGTTCCCTTCTCTCTGTGGCTTTCTCTTGCCCCTGTTGTCATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 431

AAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGCAAGTTCCCTTCTCTCTGTGGCTTTCTCTTGCCCCTGTTGTCATCG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 11

AAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGCAAGTTCCCTTCTCTCTGTGGCTTTCTCTTGCCCCTGTTGTCATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

AAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgatttttt ... tgcgatgcagCTCTGGAGCCCTTCTTCAGCGCAGCTGCTACTCAGTTTATCCTTGGACAGCAAGTTCCCTTCTCTCTGTGGCTTTCTCTTGCCCCTGTTGTCATCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCTCATTTGCCCACACTATCAAAGgtgattttttttcttttcttccaattttttatttcgatgtggattcttcttgcccatgttcttatgtcacatacttgcgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT