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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTAGCATTTGATGGCAAAACGCAAACCTTAAAGACTTCATCGGGGAAAGTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaactacacttatgcgaatgaggtgcatttaaatgtatgggaaaccatatttctgatgtcattatcatcatgtccatttttcttaaactttttct...

Basic information

species Zea mays
transcript GRMZM5G828229_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G828229_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os08g05570.3 (Oryza sativa), 5'ss of exon 6
TTGTAGCATTTGATGGCAAAACGCAAACCTTAAAGACTTCATCGGGGAAAGTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaactacacttatgcgaatgaggtgcatttaaa---tgtatgggaaaccat-atttctgatgtcattatcatcat-gtccatttttcttaaactttttct
||||||| |||||||||||||| || |||||||| |||||||| |||||| ||||||| || || |||||||||||||||||||| |||||||| || ||||| ||    | ||   ||  |||        |  ||      |||  |||  ||| |||   | | |||| ||  |  |    ||   |||||||  |      
TTGTAGCGTTTGATGGCAAAACACATACCTTAAAAACTTCATCAGGGAAAATTCTGAAGTATGGGTCACTTATTATTTCTACTGGCTGTGAAGCTTCAAGgta-accttcaaacagttgaaaatttatcttttgcaaggcccttatatgaattcatgattagaggtttcatgatttttttcactcagaattcttaagataa----
















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|149075601|gb|EE164139.2|EE164139
EST:     GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAG                         ATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
genomic: GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
EST: gi|148990927|gb|EE032350.2|EE032350
EST:     GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAG                         ATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
genomic: GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
EST: gi|21621068|gb|BQ619074.1|BQ619074
EST:     GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAG                         ATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
genomic: GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
EST: gi|87156678|gb|DY401467.1|DY401467
EST:     GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCAAG                         ATTACCTGAGAAAATTGGAAGGAAATTACCT
genomic: GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCT
EST: gi|148931379|gb|EC874296.2|EC874296
EST:     GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAG                         ATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
genomic: GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
EST: gi|148931941|gb|EC875173.2|EC875173
EST:     GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAG                         ATTACCTGAGAGAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
genomic: GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
EST: gi|148995891|gb|EE035131.2|EE035131
EST:     GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAG                         ATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
genomic: GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
EST: gi|78103956|gb|DV522374.1|DV522374
EST:     GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAG                         ATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
genomic: GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
EST: gi|211267804|gb|FL345561.1|FL345561
EST:     GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAG                         ATTACCNTGAGAAAATTGGAGGGGAAAT-ACCNTGGAGT-CACTACATACG
genomic: GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACC-TGAGAAAATTGGAGGG-AAATTACC-TGGAGTTCACTACATACG
EST: gi|148957061|gb|EC903025.2|EC903025
EST:     GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAG                         ATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
genomic: GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
EST: gi|19436377|gb|BM952787.1|BM952787
EST:     GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAG                         ATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
genomic: GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
EST: gi|18660451|gb|BM500869.1|BM500869
EST:     GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAG                         ATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
genomic: GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
EST: gi|88750901|gb|DY535042.1|DY535042
EST:     GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAG                         ATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
genomic: GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
EST: gi|213168062|gb|FM185604.1|FM185604
EST:     GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAG                         ATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
genomic: GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
EST: gi|7242278|gb|AW574464.1|AW574464
EST:     GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAG                         ATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
genomic: GTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
EST: gi|211294189|gb|FL028349.1|FL028349
EST:     TATTATTTCTACTGGATGTGAAGCATCGAG                         ATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA
genomic: TATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGA

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), 49 (downstream exon)
Score: 335

TTGTAGCATTTGATGGCAAAACGCAAACCTTAAAGACTTCATCGGGGAAAGTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGATGTTGCTGATGCTGATGCTCTAGTATCCTCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

TTGTAGCATTTGATGGCAAAACGCAAACCTTAAAGACTTCATCGGGGAAAGTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGATGTTGCTGATGCTGATGCTCTAGTATCCTCATTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 125

TTGTAGCATTTGATGGCAAAACGCAAACCTTAAAGACTTCATCGGGGAAAGTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGATGTTGCTGATGCTGATGCTCTAGTATCCTCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 233

TTGTAGCATTTGATGGCAAAACGCAAACCTTAAAGACTTCATCGGGGAAAGTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaact ... tttttttcagATTACCTGAGAAAATTGGAGGGAAATTACCTGGAGTTCACTACATACGGGATGTTGCTGATGCTGATGCTCTAGTATCCTCATTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTAGCATTTGATGGCAAAACGCAAACCTTAAAGACTTCATCGGGGAAAGTTCTGAAATACGGCTCACTTATTATTTCTACTGGATGTGAAGCATCGAGgtatacaactacacttatgcgaatgaggtgcatttaaatgtatgggaaaccatatttctgatgtcattatcatcatgtccatttttcttaaactttttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC