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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATATCCGGGATGATGATGGGGGTCATTGTTGGCGTCGCCATCATGGCCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggttagggttgtgccgctgcgagcagactgtaataagcctcgccccgttctcgctacaccgtggagttggatcgttcaattcaggactaactgtgaggcttggtctttgtcggatttgagtttcgttgcgtgtctctctcttccttgctgtag

Basic information

species Zea mays
transcript GRMZM2G092129_T02
intron # 1
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|211212135|gb|FL050029.1|FL050029
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|211212127|gb|FL050021.1|FL050021
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCGGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|211214697|gb|FL050035.1|FL050035
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCGGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|211162012|gb|FL219539.1|FL219539
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|211212138|gb|FL050032.1|FL050032
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCGGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|148971559|gb|EE022272.2|EE022272
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|211212134|gb|FL050028.1|FL050028
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCGGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|211162015|gb|FL219542.1|FL219542
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|211212131|gb|FL050025.1|FL050025
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCGGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|74241137|gb|DT649051.1|DT649051
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|211212129|gb|FL050023.1|FL050023
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|211212132|gb|FL050026.1|FL050026
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGNGCTTGGGTCTCTCAGCGGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|86467094|gb|DY233464.1|DY233464
EST:     CCGGGTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAGGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|211162016|gb|FL219543.1|FL219543
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|211212136|gb|FL050030.1|FL050030
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGGATATCAAAGGTGCTTGGGTCTCTCAGCGGGGACGACCTCAGGA
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGG-ATATCAA-GGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGA
EST: gi|71331353|gb|DR802511.1|DR802511
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|211162018|gb|FL219545.1|FL219545
EST:     CCGGCTCGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|211212128|gb|FL050022.1|FL050022
EST:     CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
EST: gi|211162017|gb|FL219544.1|FL219544
EST:     CCGGCTCGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAG                         GCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG
genomic: CCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAG

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), 49 (downstream exon)
Score: 147

GTTGATATCCGGGATGATGATGGGGGTCATTGTTGGCGTCGCCATCATGGCCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAGCTGTGCGGTGATAACTTCCCGGAGTGGATATCCTTCCCGCAGTTTGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 280

GTTGATATCCGGGATGATGATGGGGGTCATTGTTGGCGTCGCCATCATGGCCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAGCTGTGCGGTGATAACTTCCCGGAGTGGATATCCTTCCCGCAGTTTGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

GTTGATATCCGGGATGATGATGGGGGTCATTGTTGGCGTCGCCATCATGGCCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAGCTGTGCGGTGATAACTTCCCGGAGTGGATATCCTTCCCGCAGTTTGAGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 160

GTTGATATCCGGGATGATGATGGGGGTCATTGTTGGCGTCGCCATCATGGCCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggt ... cttgctgtagGCTGCGGATATCAAGGTGCTTGGGTCTCTCAGCAGGGACGACCTCAGGAAGCTGTGCGGTGATAACTTCCCGGAGTGGATATCCTTCCCGCAGTTTGAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATATCCGGGATGATGATGGGGGTCATTGTTGGCGTCGCCATCATGGCCGGCTGGAGCCGCGTCATGCGCCGACGCAGCACGAAGCGCATCGCCAAGgtgagttggttagggttgtgccgctgcgagcagactgtaataagcctcgccccgttctcgctacaccgtggagttggatcgttcaattcaggactaactgtgaggcttggtctttgtcggatttgagtttcgttgcgtgtctctctcttccttgctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA