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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTATATCATCTTTGAGGACGAAATTCATCAAACTATTGTCCAGAATTCTCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccagatttggacatgccatcagttggtaaagaagtagaagatagtactatttatggcaatgcacatcttactcgttagttctgcacattttaat...

Basic information

species Zea mays
transcript GRMZM2G402242_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G402242_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g52470.2 (Oryza sativa), 5'ss of exon 3
TTCTATATCATCTTTGAGGACGAAATTCATCAAACTATTGTCCAGAATTCTCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccagatttggacatgccatcagttggtaaagaagtagaagatagtactatttatggcaatgcacatcttactcgttagttctgcaca-ttttaat----------------------------------------------------------------------------
|||||| |  |||||||||| || || ||||| ||||||||  | |||  | |||||||| ||||||| |||||||| || ||||||||||||||||||||||  |||| |  || |  |||||||| |   ||| ||| ||| |    ||  | |||||  |||  |  |      || ||| |  || |||  | ||||                                                                            
TTCTATGTTGTCTTTGAGGATGAGATCCATCAGACTATTGTTGACAATAATTTGTTTAAACCTGGTGATCGTGTGGCCATTGGAGCTTCTGGTGGAAAAGgtatttccacacctgtatgtgccatcactaactaatgaaatagcat---gtgttctttata-caactctgactactttctttattcatgtacagctataatctgcatgcttctttctttattctgctcttgatattccaacagactcaaatattttcacgccatgactgttatgcag

upper sequence: GRMZM2G402242_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g41565.1 (Oryza sativa), 5'ss of exon 2
TTCTATATCATCTTTGAGGACGAAATTCATCAAACTATTGTCCAGAATTCTCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccagatttggacatgccatcagttggtaaagaagtagaagatagtactatttatggcaatgcacatcttactcgttagttctgcacattt-taat-------------------------------------------------------------------------------
||||| ||  |||||||||| || || ||||| ||||||||  |||||  | |||||||| ||||||| |||||||| || |||||||||||||| |||||||  |||| |  || | ||||||||| |   ||| ||| ||| |    ||  | ||||||  | |    |   |  || ||  |  || | |  | ||||                                                                               
TTCTACATTGTCTTTGAGGATGAGATCCATCAGACTATTGTTGAGAATAATTTGTTTAAACCTGGTGATCGTGTGGCCATTGGAGCTTCTGGTGGTAAAGgtatttccacacctgtatatgccatcactaactaatgaaatagcat---gtgttctttatgcaactattgactattttctttcttcatgtatagctataatctgcatgcttctttctttattctgctcttgatcttccaacagactcaaatattttcatgtcatgactgctattatgcag
















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|74232164|gb|DT640078.1|DT640078
EST:     TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAG                         ATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
genomic: TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
EST: gi|71774415|gb|DR972293.1|DR972293
EST:     TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAG                         ATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
genomic: TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
EST: gi|37419554|gb|CF647460.1|CF647460
EST:     TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAG                         ATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
genomic: TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
EST: gi|37416521|gb|CF645910.1|CF645910
EST:     TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAG                         ATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTGAGCACAACT
genomic: TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
EST: gi|50323940|gb|CO519066.1|CO519066
EST:     TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAG                         ATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
genomic: TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
EST: gi|26558362|gb|CA830597.1|CA830597
EST:     TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAG                         ATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCATAACT
genomic: TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
EST: gi|87157289|gb|DY402078.1|DY402078
EST:     TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAG                         ATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCATAACT
genomic: TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
EST: gi|71770543|gb|DR968480.1|DR968480
EST:     TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAG                         ATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
genomic: TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
EST: gi|91872707|gb|EB402664.1|EB402664
EST:     TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAG                         ATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
genomic: TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
EST: gi|22472216|gb|BU036696.1|BU036696
EST:     TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAG                         ATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCATAACT
genomic: TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
EST: gi|91877955|gb|EB407912.1|EB407912
EST:     TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAG                         ATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
genomic: TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
EST: gi|50337086|gb|CO532212.1|CO532212
EST:     TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAG                         ATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT
genomic: TCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACT

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: 45 (upstream exon), 49 (downstream exon)
Score: 75

TTCTATATCATCTTTGAGGACGAAATTCATCAAACTATTGTCCAGAATTCTCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACTATGGTCTTGATTTGTTCCTTTTATCTGTCGATGAAGGAATCACAGGATA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 43

TTCTATATCATCTTTGAGGACGAAATTCATCAAACTATTGTCCAGAATTCTCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACTATGGTCTTGATTTGTTCCTTTTATCTGTCGATGAAGGAATCACAGGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

TTCTATATCATCTTTGAGGACGAAATTCATCAAACTATTGTCCAGAATTCTCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACTATGGTCTTGATTTGTTCCTTTTATCTGTCGATGAAGGAATCACAGGATA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 54

TTCTATATCATCTTTGAGGACGAAATTCATCAAACTATTGTCCAGAATTCTCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccag ... tgtaatgcagATTCAACCGTGCTTGCATATGTGTTATCGGAGTTAAACCGTCAGCACAACTATGGTCTTGATTTGTTCCTTTTATCTGTCGATGAAGGAATCACAGGATA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTATATCATCTTTGAGGACGAAATTCATCAAACTATTGTCCAGAATTCTCTGTTTAAAGCTGGTGAGCGTGTGGCAATCGGAGCTTCTGGTGGAAAAGgtaagtccagatttggacatgccatcagttggtaaagaagtagaagatagtactatttatggcaatgcacatcttactcgttagttctgcacattttaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA