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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcgcgaatccttccgtgtttttcagggttcccccgcttcgatttcgggtcagcagttgttgtctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTACTGCGGCCAG

Basic information

species Zea mays
transcript AC194389.3_FGT001
intron # 1
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|50326933|gb|CO522059.1|CO522059
EST:     GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGAC                         ATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC
genomic: GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGACgtacgcgcga ... ctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC
EST: gi|149014811|gb|EE044512.2|EE044512
EST:     GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGAC                         ATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC
genomic: GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGACgtacgcgcga ... ctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC
EST: gi|211516107|gb|FL391741.1|FL391741
EST:     GCGGGCTCAACACTCCGCTACACTTCGNCGCCGCCAAGGGGCATCTCGAC                         ATTGTCACGATGCTGCTGGAGAAAGGNGCTGACGTTAACGCGCGCAACTAC
genomic: GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGACgtacgcgcga ... ctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC
EST: gi|148961455|gb|EE012203.2|EE012203
EST:     GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGAC                         ATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC
genomic: GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGACgtacgcgcga ... ctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC
EST: gi|211065139|gb|FL368215.1|FL368215
EST:     GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGAC                         ATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC
genomic: GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGACgtacgcgcga ... ctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC
EST: gi|148942318|gb|EC887337.2|EC887337
EST:     GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGAC                         ATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC
genomic: GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGACgtacgcgcga ... ctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC
EST: gi|211243066|gb|FL400453.1|FL400453
EST:     GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGAC                         ATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC
genomic: GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGACgtacgcgcga ... ctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC
EST: gi|211516673|gb|FL422113.1|FL422113
EST:     GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGAC                         ATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTNACGCGCGCAACTAC
genomic: GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGACgtacgcgcga ... ctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC
EST: gi|74238026|gb|DT645940.1|DT645940
EST:     GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGAC                         ATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC
genomic: GCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGACgtacgcgcga ... ctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTAC

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: 407

GCGGATGCTGCTGGAGCTCAGCCCCGCGCTCGCGCGCTACTCCACCTTCGGCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGACgtacgcgcga ... ctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTACTGCGGCCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 298

GCGGATGCTGCTGGAGCTCAGCCCCGCGCTCGCGCGCTACTCCACCTTCGGCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGACgtacgcgcga ... ctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTACTGCGGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 418

GCGGATGCTGCTGGAGCTCAGCCCCGCGCTCGCGCGCTACTCCACCTTCGGCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGACgtacgcgcga ... ctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTACTGCGGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 447

GCGGATGCTGCTGGAGCTCAGCCCCGCGCTCGCGCGCTACTCCACCTTCGGCGGCCTCAACACTCCGCTACACTTCGCCGCCGCCAAGGGCCATCTCGACgtacgcgcga ... ctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTACTGCGGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcagggttcccccgcttcgatttcgggtcagcagttgttgtctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTACTGCGGCCAG
                                         ttgtctcc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcgcgaatccttccgtgtttttcagggttcccccgcttcgatttcgggtcagcagttgttgtctccgtgtagATTGTCACGATGCTGCTGGAGAAAGGCGCTGACGTTAACGCGCGCAACTACTGCGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA