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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgatctacaccttctaatgctgatgtttcatggcttatatgtaatttgtggcattgtaggcctaatctgtttacattttttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG

Basic information

species Zea mays
transcript GRMZM2G158818_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158818_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g50970.1 (Oryza sativa), 3'ss of exon 7
gtaatttgatctacacct---tctaatgctgatgtttcatggcttatatgtaatttgtggc--attgt-aggcctaatctgtttacattttttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG
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gtaacatgagcagcacatatatataaatatggcaacacattgatcctctgtggcttatactttactatgaagtgtgaactcttcaactatttta---tcagGAACAAGAAATAGATGATGAATTGGAGTTTCTGATTTTAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG
















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|71770125|gb|DR968062.1|DR968062
EST:     TAAAACAATTTGTTATTGCAGACCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
genomic: TAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
EST: gi|20301082|gb|BQ164025.1|BQ164025
EST:     TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
genomic: TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
EST: gi|211312460|gb|FL459524.1|FL459524
EST:     TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
genomic: TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
EST: gi|149098862|gb|EE184875.2|EE184875
EST:     TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
genomic: TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
EST: gi|211050684|gb|FL481891.1|FL481891
EST:     TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
genomic: TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
EST: gi|211342700|gb|FL234317.1|FL234317
EST:     TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGAMCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCCTAGTGATGG
genomic: TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGC-TAGTGATGG
EST: gi|67022511|gb|CO451260.1|CO451260
EST:     AATTTGTTATTGCAGACCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
genomic: AATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
EST: gi|211331038|gb|FL445937.1|FL445937
EST:     TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
genomic: TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
EST: gi|32795938|gb|CD948174.1|CD948174
EST:     TAAAACAATTTGTTATTACAGACCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
genomic: TAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
EST: gi|9733204|gb|BE511956.1|BE511956
EST:     TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
genomic: TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
EST: gi|101388859|gb|EB816411.1|EB816411
EST:     TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
genomic: TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
EST: gi|19058198|gb|BM736865.1|BM736865
EST:     TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
genomic: TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
EST: gi|211345077|gb|FL234318.1|FL234318
EST:     TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
genomic: TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
EST: gi|20300882|gb|BQ163825.1|BQ163825
EST:     TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
genomic: TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
EST: gi|211342699|gb|FL234316.1|FL234316
EST:     TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
genomic: TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
EST: gi|61119350|gb|DN560311.1|DN560311
EST:     TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAG                         GAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG
genomic: TTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGG

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: 247

GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 97

GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 103

GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 139

GAACTTGGAGGGTAGGTGGTGTACTTGCAATGTCTCGGGCATTTGGCAACCGTCTCTTAAAACAATTTGTTATTGCAGACCCTGAGATTCAGgtaatttgat ... ttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatatgtaatttgtggcattgtaggcctaatctgtttacattttttggggtcagGAACAAGAAATAAATGATGAGTTGGAGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG
                         gcctaat  putative branch site (score: 139)
                                       catttttt  putative PPT
                                 tgtttacatttttt  TA-rich tract