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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAAgtatgttgagtggagaactttattgattttactagtcttatattttctgcgaaatactattttacatgcattttgacctgctttgtcag

Basic information

species Zea mays
transcript AC208327.4_FGT003
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC208327.4_FGT003 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os11g03990.1 (Oryza sativa), 5'ss of exon 9
TGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAAgtatgttgagtggagaactttattgattttactagtcttatattttctgcgaaatactattttacatgcattttgacctgctttgtcag
  ||  | || ||||| || ||||||||||| |||||||||||||||||||||||||| |  |||||  | || || |||||||| ||||||||||||  ||||| |  ||  |     ||    |||  | ||   | ||      | |    || ||||| |     ||  ||||   | ||  |||
CCGACAGAACAATATCTATCTGGGATATACGGACAGGGAAGAAACCTTGTATTTCTGTTAGGGCTCACAATGCTGACGTGAATGTCATCTCATGGAACCGgtatgatatgttca----cttgaaaattcgattatcttcatgaaaaattcttc-taatatttcatgaatatactgactaccgttaccag

upper sequence: AC208327.4_FGT003 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os12g03822.1 (Oryza sativa), 5'ss of exon 9
TGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAAgtatgttgagtggagaactttattgattttactagtcttatattttctgcgaaatactattttacatgcattttgacctgctttgtcag
  ||  | || ||||| || ||||||||||| |||||||||||||||||||||||||| |  |||||  | || || |||||||| ||||||||||||  ||||| |  ||  |     ||    |||  | ||   | |||     | |    || ||||| |     ||   |||   | ||  |||
CCGACAGAACAATATCTATCTGGGATATACGGACAGGGAAGAAACCTTGTATTTCTGTTAGGGCTCACAATGCTGACGTGAATGTCATCTCATGGAACCGgtatgatatgttca----cttgaaaattcgattatcttcataaaaaattcttc-taatatttcatgaatatacggactaccattaccag
















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|32866681|gb|CF006363.1|CF006363
EST:     ATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAA                         GCTTGCTAGCTGCATGATAGCTTCTGGGTGCGATGA
genomic: ATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAAgtatgttgag ... gctttgtcagGCTTGCTAGCTGCATGATAGCTTCTGGGTGCGATGA
EST: gi|211303562|gb|FL306499.1|FL306499
EST:     ATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAA                         GCTTGCTAGCTGNATGATAGCTTCTGGGTGCGATGATGGCAGTTTCTCAGT
genomic: ATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAAgtatgttgag ... gctttgtcagGCTTGCTAGCTGCATGATAGCTTCTGGGTGCGATGATGGCAGTTTCTCAGT
EST: gi|74242019|gb|DT649933.1|DT649933
EST:     ATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAA                         GCTTGCTAGCTGCATGATAGCTTCTGGGTGCGATGATGGCAGTTTCTCAGT
genomic: ATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAAgtatgttgag ... gctttgtcagGCTTGCTAGCTGCATGATAGCTTCTGGGTGCGATGATGGCAGTTTCTCAGT
EST: gi|31349324|gb|CD433681.1|CD433681
EST:     ATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAA                         GCTTGCTAGCTGCATGATAGCTTCTGGGTGCGATGATGGCAGTTTCTCAGT
genomic: ATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAAgtatgttgag ... gctttgtcagGCTTGCTAGCTGCATGATAGCTTCTGGGTGCGATGATGGCAGTTTCTCAGT
EST: gi|33091437|gb|CF051431.1|CF051431
EST:     ATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAA                         GCTTGCTAGCTGCATGATAGCTTCTGGGTGCGATGATGGCAGTTTCTCAGT
genomic: ATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAAgtatgttgag ... gctttgtcagGCTTGCTAGCTGCATGATAGCTTCTGGGTGCGATGATGGCAGTTTCTCAGT
EST: gi|31350283|gb|CD434640.1|CD434640
EST:     ATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAA                         GCTTGCTAGCTGCATGATAGCTTCTGGGTGCGATGATGGCAGTTTCTCAGT
genomic: ATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAAgtatgttgag ... gctttgtcagGCTTGCTAGCTGCATGATAGCTTCTGGGTGCGATGATGGCAGTTTCTCAGT

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: 237

TGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAAgtatgttgag ... gctttgtcagGCTTGCTAGCTGCATGATAGCTTCTGGGTGCGATGATGGCAGTTTCTCAGTTCGTGATCTTAGATCAATTGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 71

TGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAAgtatgttgag ... gctttgtcagGCTTGCTAGCTGCATGATAGCTTCTGGGTGCGATGATGGCAGTTTCTCAGTTCGTGATCTTAGATCAATTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

TGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAAgtatgttgag ... gctttgtcagGCTTGCTAGCTGCATGATAGCTTCTGGGTGCGATGATGGCAGTTTCTCAGTTCGTGATCTTAGATCAATTGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 108

TGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAAgtatgttgag ... gctttgtcagGCTTGCTAGCTGCATGATAGCTTCTGGGTGCGATGATGGCAGTTTCTCAGTTCGTGATCTTAGATCAATTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGATGGTACGATATCAATATGGGATATACGTACAGGGAAGAAACCTTGTATTTCTGTCAAAGCTCATGAAGCCGATGTGAATGTTATCTCATGGAACAAgtatgttgagtggagaactttattgattttactagtcttatattttctgcgaaatactattttacatgcattttgacctgctttgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA