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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGATCCTCCTCCCCTTCGCCGTCGCCATGGAGGGACCCAAGCTCTGGGCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagcttactctcacgttacgtagcgttaaactgtcacacacacacagtatgtgtgtgtgtgtgttagtgggtgtgtctattatcaggaattcca...

Basic information

species Zea mays
transcript GRMZM2G125850_T02
intron # 4
splice site 5'
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|211236186|gb|FL162466.1|FL162466
EST:     GCGGSGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTG                         GTGGGTGGCTGCGCAAAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
genomic: GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagc ... acgtacgcagGTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
EST: gi|89760567|gb|DY688924.1|DY688924
EST:     GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTG                         GTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
genomic: GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagc ... acgtacgcagGTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
EST: gi|37424457|gb|CF649961.1|CF649961
EST:     TCGGCCCCAACTTCGTCTG                         GTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
genomic: TCGGCCCCAACTTCGTCTGgtaattaagc ... acgtacgcagGTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
EST: gi|37422861|gb|CF649146.1|CF649146
EST:     CAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTG                         GTGGGTGGCTGCGCAAAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
genomic: CAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagc ... acgtacgcagGTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
EST: gi|27753886|gb|BM378078.1|BM378078
EST:     GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATTGGGCCCAACTTCGTCTG                         GTGGGTGGCTGCGCACAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
genomic: GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagc ... acgtacgcagGTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
EST: gi|149111560|gb|EE190694.2|EE190694
EST:     GCGGCGGGCGGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTG                         GTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
genomic: GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagc ... acgtacgcagGTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
EST: gi|24934556|gb|CA452774.1|CA452774
EST:     GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTG                         GTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGT
genomic: GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagc ... acgtacgcagGTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGT
EST: gi|37424641|gb|CF650053.1|CF650053
EST:     GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTG                         GTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
genomic: GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagc ... acgtacgcagGTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
EST: gi|78079571|gb|DV507983.1|DV507983
EST:     CGGCGGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTG                         GTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
genomic: CGGC-GGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagc ... acgtacgcagGTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
EST: gi|149086557|gb|EE176100.2|EE176100
EST:     GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTTTG                         GTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
genomic: GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagc ... acgtacgcagGTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
EST: gi|93282359|gb|EB674623.1|EB674623
EST:     GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTG                         GTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
genomic: GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagc ... acgtacgcagGTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
EST: gi|71770113|gb|DR968050.1|DR968050
EST:     GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTG                         GTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA
genomic: GCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagc ... acgtacgcagGTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

TGGTGATCCTCCTCCCCTTCGCCGTCGCCATGGAGGGACCCAAGCTCTGGGCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagc ... acgtacgcagGTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTACATGTCGCTGGACGAGATCTCGCCGCTCACGTTCTCCATCGGCAACACC


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 19

TGGTGATCCTCCTCCCCTTCGCCGTCGCCATGGAGGGACCCAAGCTCTGGGCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagc ... acgtacgcagGTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTACATGTCGCTGGACGAGATCTCGCCGCTCACGTTCTCCATCGGCAACACC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 117

TGGTGATCCTCCTCCCCTTCGCCGTCGCCATGGAGGGACCCAAGCTCTGGGCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagc ... acgtacgcagGTGGGTGGCTGCGCAGAGCGTGTTCTACCACCTGTACAACCAGGTGTCGTACATGTCGCTGGACGAGATCTCGCCGCTCACGTTCTCCATCGGCAACACC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGATCCTCCTCCCCTTCGCCGTCGCCATGGAGGGACCCAAGCTCTGGGCGGCGGGCTGGCAGCAAGCAGTCGCCGAGATCGGCCCCAACTTCGTCTGgtaattaagcttactctcacgttacgtagcgttaaactgtcacacacacacagtatgtgtgtgtgtgtgttagtgggtgtgtctattatcaggaattcca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC