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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcattttttttcttttattctgtgagcagtcctctatgcttattgcagttatgtaatgatggaataagttgtacaaatggtcttttttcgaattggcagGCTAGCTCTATGGTTGAAGAGGAGATTCAATACCTTCGAGTGGCCATGGGTCATGAAAATGAATCTTTTGAGGACTTCGTGAAAGCACATGATGCATGCC

Basic information

species Zea mays
transcript AC203535.4_FGT001
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC203535.4_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g28090.1 (Oryza sativa), 3'ss of exon 2
--ttcattttttttcttttattctgtgagcagtcctctatgcttattgcagttatgtaatgatggaataagttgtacaaatggtcttttttcgaattggcagGCTAGCTCTATGGTTGAAGAGGAGATTCAATACCTTCGAGTGGCCATGGGTCATGAAAATGAATCTTTTGAGGACTTCGTGAAAGCACATGATGCATGCC
  | ||   | |  |||  ||  | |   ||||| | |   | || |  | |||||||||| || ||     |  | |    ||| ||| |    ||  ||||| |  |||||| |||| |||||| ||||||||||||| || |||||||| ||||||| ||||||||| || || || ||||||||||||||||||||||
tctgcaagatatgacttc-atattatttccagtcttgtgcccctaatttatttatgtaatggtgcaagttaatccatattgcgtcatttatttg-ttcacagGCCAATTCTATGCTTGAGGAGGAGGTTCAATACCTTCGTGTCGCCATGGGACATGAAAGTGAATCTTTGGAAGATTTTGTGAAAGCACATGATGCATGCC
















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|211209236|gb|FL379058.1|FL379058
EST:     GACCTCTTGTCCCTGAAATTGATGATTTTGATGAAGATGAACTAAAAGAG                         GCTAGCTCTATGGTTGAAGAGGAGATTCAATACCTTCGAGTGGCCATGGGT
genomic: GACCTCTTGTCCCTGAAATTGATGATTTTGATGAAGATGAACTAAAAGAGgtgctattct ... gaattggcagGCTAGCTCTATGGTTGAAGAGGAGATTCAATACCTTCGAGTGGCCATGGGT
EST: gi|32934502|gb|CF039314.1|CF039314
EST:     GTCCCTGAAATTGATGATTTTGATGAAGATGAACTAAAAGAG                         GCTAGCTCTATGGTTGAAGAGGAGATTCAATACCTTCGAGTGGCCATGGGT
genomic: GTCCCTGAAATTGATGATTTTGATGAAGATGAACTAAAAGAGgtgctattct ... gaattggcagGCTAGCTCTATGGTTGAAGAGGAGATTCAATACCTTCGAGTGGCCATGGGT
EST: gi|32931520|gb|CF036332.1|CF036332
EST:     GAAATTGATGATTTTGATGAAGATGAACTAAAAGAG                         GCTAGCTCTATGGTTGAAGAGGAGATTCAATACCTTCGAGTGGCCATGGGT
genomic: GAAATTGATGATTTTGATGAAGATGAACTAAAAGAGgtgctattct ... gaattggcagGCTAGCTCTATGGTTGAAGAGGAGATTCAATACCTTCGAGTGGCCATGGGT

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: 48 (upstream exon), 45 (downstream exon)
Score: 183

AAAAACTCAAAAAGAGAAAAAGAAAGGAAGCAAGCGTCAGCAAAATGGAGGACCTCTTGTCCCTGAAATTGATGATTTTGATGAAGATGAACTAAAAGAGgtgctattct ... gaattggcagGCTAGCTCTATGGTTGAAGAGGAGATTCAATACCTTCGAGTGGCCATGGGTCATGAAAATGAATCTTTTGAGGACTTCGTGAAAGCACATGATGCATGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

AAAAACTCAAAAAGAGAAAAAGAAAGGAAGCAAGCGTCAGCAAAATGGAGGACCTCTTGTCCCTGAAATTGATGATTTTGATGAAGATGAACTAAAAGAGgtgctattct ... gaattggcagGCTAGCTCTATGGTTGAAGAGGAGATTCAATACCTTCGAGTGGCCATGGGTCATGAAAATGAATCTTTTGAGGACTTCGTGAAAGCACATGATGCATGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 170

AAAAACTCAAAAAGAGAAAAAGAAAGGAAGCAAGCGTCAGCAAAATGGAGGACCTCTTGTCCCTGAAATTGATGATTTTGATGAAGATGAACTAAAAGAGgtgctattct ... gaattggcagGCTAGCTCTATGGTTGAAGAGGAGATTCAATACCTTCGAGTGGCCATGGGTCATGAAAATGAATCTTTTGAGGACTTCGTGAAAGCACATGATGCATGCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 121

AAAAACTCAAAAAGAGAAAAAGAAAGGAAGCAAGCGTCAGCAAAATGGAGGACCTCTTGTCCCTGAAATTGATGATTTTGATGAAGATGAACTAAAAGAGgtgctattct ... gaattggcagGCTAGCTCTATGGTTGAAGAGGAGATTCAATACCTTCGAGTGGCCATGGGTCATGAAAATGAATCTTTTGAGGACTTCGTGAAAGCACATGATGCATGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagttatgtaatgatggaataagttgtacaaatggtcttttttcgaattggcagGCTAGCTCTATGGTTGAAGAGGAGATTCAATACCTTCGAGTGGCCATGGGTCATGAAAATGAATCTTTTGAGGACTTCGTGAAAGCACATGATGCATGCC
                                    tcttttttcg  CT-rich tract
     tatgtaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcattttttttcttttattctgtgagcagtcctctatgcttattgcagttatgtaatgatggaataagttgtacaaatggtcttttttcgaattggcagGCTAGCTCTATGGTTGAAGAGGAGATTCAATACCTTCGAGTGGCCATGGGTCATGAAAATGAATCTTTTGAGGACTTCGTGAAAGCACATGATGCATGCC

ttcattt
- - - - - - - - - ttctgtg
- - - - - - - - - - - - - - - - - - atgctta
- - - - - - - - - - - - - - - - - - - - - - tgcagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtacaaa