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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttgcatggttcaacattaatatgcattactaaagattatggaatgaaacctaaaatcatttgatttgttttacgctccattttttagtttactagaaccttaacacttcactttctcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG

Basic information

species Zea mays
transcript GRMZM2G150251_T02
intron # 6
splice site 3'
intron type U2

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|60353103|gb|DN220076.1|DN220076
EST:     AGAAGCATTGGCTTGCAAATAATGTTCTGGGATTGGCTTTCTGTATTCAG                         GGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG
genomic: AGAAGCATTGGCTTGCAAATAATGTTCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... actttctcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG
EST: gi|76020573|gb|DT947743.1|DT947743
EST:     AGAAGCATTGGCTTGCAAATAATGTTCTGGGATTGGCTTTCTGTATTCAG                         GGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG
genomic: AGAAGCATTGGCTTGCAAATAATGTTCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... actttctcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG
EST: gi|33092200|gb|CF052194.1|CF052194
EST:     AGAAGCATTGGCTTGCAAATAATGTTCTGGGTTTGGCTTTCTGTATTCAG                         GGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG
genomic: AGAAGCATTGGCTTGCAAATAATGTTCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... actttctcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG
EST: gi|33093608|gb|CF053602.1|CF053602
EST:     AGAAGCATTGGCTTGCAAATAATGTTCTGGGTTTGGCTTTCTGTATTCAG                         GGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG
genomic: AGAAGCATTGGCTTGCAAATAATGTTCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... actttctcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG
EST: gi|32837706|gb|CD977384.1|CD977384
EST:     AGAAGCATTGGCTTGCAAATAATGTTCTGGGTTTGGCTTTCTGTATTCAG                         GGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG
genomic: AGAAGCATTGGCTTGCAAATAATGTTCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... actttctcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG
EST: gi|78123104|gb|DV541488.1|DV541488
EST:     AGAAGCATTGGCTTGCAAATAATGTTCTGGGATTGGCTTTCTGTATTCAG                         GGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG
genomic: AGAAGCATTGGCTTGCAAATAATGTTCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... actttctcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG
EST: gi|93282675|gb|EB674939.1|EB674939
EST:     AGAAGCATTGGCTTGCAAATAATGTTCTGGGATTGGCTTTCTGTATTCAG                         GGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG
genomic: AGAAGCATTGGCTTGCAAATAATGTTCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... actttctcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG

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: 209

GATTGTTGCTTCAATACCTGGATTTTTCTTCTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAATAATGTTCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... actttctcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

GATTGTTGCTTCAATACCTGGATTTTTCTTCTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAATAATGTTCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... actttctcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

GATTGTTGCTTCAATACCTGGATTTTTCTTCTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAATAATGTTCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... actttctcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 246

GATTGTTGCTTCAATACCTGGATTTTTCTTCTGCTTGTGGTATGCGTCAAAGAAGCATTGGCTTGCAAATAATGTTCTGGGATTGGCTTTCTGTATTCAGgtttgtttgc ... actttctcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttttacgctccattttttagtttactagaaccttaacacttcactttctcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG
                                 ccttaac  putative branch site (score: 246)
                                       cacttcactttctc  CT-rich tract
              attttttagtttacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttgcatggttcaacattaatatgcattactaaagattatggaatgaaacctaaaatcatttgatttgttttacgctccattttttagtttactagaaccttaacacttcactttctcagGGGATTGAGATGCTGTCATTGGGATCATTTAAAACCGGAGCCATTCTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG