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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGTATTCCTGTTGCGACTGTTGCTATCGGGATTGCAGAAAATGCAGGTTTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAGgtatggttctttgctagtgttacttttgcattcaaattcttagttctgaacggggcaagagtaactgtttgccatattaatttctcccttagatcttgtt...

Basic information

species Zea mays
transcript GRMZM2G133121_T02
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133121_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g10280.2 (Oryza sativa), 5'ss of exon 15
AAGGTATTCCTGTTGCGACTGTTGCTATCGGGATTGCAGAAAATGCAGGTTTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAGgtatggttctttgctagtgttacttttgcattcaaattcttagttctgaacggggcaagagtaa--ctgtttgccat-attaatttctcccttagatcttgtt
|||||||||||||||| |||||||| || || | ||| ||||||||||||||  |||||| |||||| |||||  |||||||||||||| |   ||||| ||||| ||  ||  |      | || | | | |||||| | |  | ||    | | ||  |||   |||| ||| ||   ||||     |||   | |  || 
AAGGTATTCCTGTTGCTACTGTTGCAATTGGAAATGCGGAAAATGCAGGTTTATTGGCAGTTAGGATGCTGGCCTCAAGAGATCCTGAGTTGGGGGACAAgtatgatttcttcttttctgcaattgtcc-tgcaaattttgaagtttggttagtgtaactgtatgtctgtatgcaattgataatagacacctcccagca-gt-
















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|33091539|gb|CF051533.1|CF051533
EST:     TTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAG                         GGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGA
genomic: TTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAGgtatggttct ... attcttgcagGGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGA
EST: gi|32797336|gb|CD949572.1|CD949572
EST:     GATCCTGAGCTCCAGGACAG                         GGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGA
genomic: GATCCTGAGCTCCAGGACAGgtatggttct ... attcttgcagGGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGA
EST: gi|9566321|gb|BE475830.1|BE475830
EST:     TTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAG                         GGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGA
genomic: TTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAGgtatggttct ... attcttgcagGGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGA
EST: gi|211118596|gb|FL071336.1|FL071336
EST:     TTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAG                         GGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGA
genomic: TTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAGgtatggttct ... attcttgcagGGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGA
EST: gi|32796854|gb|CD949090.1|CD949090
EST:     GATCCCGAGCTCCAGGACAG                         GGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGA
genomic: GATCCTGAGCTCCAGGACAGgtatggttct ... attcttgcagGGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGA
EST: gi|6538950|gb|AW225089.1|AW225089
EST:     TTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGCCAG                         GGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGA
genomic: TTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAGgtatggttct ... attcttgcagGGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGA
EST: gi|29544764|gb|CB605372.1|CB605372
EST:     TTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAG                         GGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGA
genomic: TTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAGgtatggttct ... attcttgcagGGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGA

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: 40 (upstream exon), 49 (downstream exon)
Score: 87

AAGGTATTCCTGTTGCGACTGTTGCTATCGGGATTGCAGAAAATGCAGGTTTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAGgtatggttct ... attcttgcagGGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGAAAGGCTGGAGGACCAAGGCCCGGAGGAATTTCTGAAGGGAATGGATTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 85

AAGGTATTCCTGTTGCGACTGTTGCTATCGGGATTGCAGAAAATGCAGGTTTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAGgtatggttct ... attcttgcagGGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGAAAGGCTGGAGGACCAAGGCCCGGAGGAATTTCTGAAGGGAATGGATTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 127

AAGGTATTCCTGTTGCGACTGTTGCTATCGGGATTGCAGAAAATGCAGGTTTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAGgtatggttct ... attcttgcagGGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGAAAGGCTGGAGGACCAAGGCCCGGAGGAATTTCTGAAGGGAATGGATTGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 81

AAGGTATTCCTGTTGCGACTGTTGCTATCGGGATTGCAGAAAATGCAGGTTTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAGgtatggttct ... attcttgcagGGTAACTAAGTACCAGGATGATCTGAGGGACATGGTTTTGGAGACGGCAGAAAGGCTGGAGGACCAAGGCCCGGAGGAATTTCTGAAGGGAATGGATTGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGTATTCCTGTTGCGACTGTTGCTATCGGGATTGCAGAAAATGCAGGTTTGCTGGCAGCTAGGATTCTGGCTGCAAGAGATCCTGAGCTCCAGGACAGgtatggttctttgctagtgttacttttgcattcaaattcttagttctgaacggggcaagagtaactgtttgccatattaatttctcccttagatcttgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC