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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGATGCGGAGGACAGAGACCTCCCCGAGATCTCCAATGGTGATGCAGGTGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccgtccgcctcttctctttcacgagcactggtgtctgggtttcgggtttctgattatctgataataggtgttgttgtgtcaaaatgcggcag

Basic information

species Zea mays
transcript GRMZM2G086052_T03
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|71326245|gb|DR799816.1|DR799816
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
EST: gi|32792113|gb|CD944349.1|CD944349
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
EST: gi|32826797|gb|CD966475.1|CD966475
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
EST: gi|93016466|gb|EB641986.1|EB641986
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
EST: gi|71297897|gb|DR784919.1|DR784919
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
EST: gi|93281358|gb|EB673622.1|EB673622
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
EST: gi|78108018|gb|DV526436.1|DV526436
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
EST: gi|71313522|gb|DR793329.1|DR793329
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
EST: gi|94478202|gb|EB707160.1|EB707160
EST:     TGCCCGGCTCATCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGACCCGTCGTCGGAATCCCGAGCTCGTCAAGCACATCAAG
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCC-GAGCTCGTCAAGCACATCAAG
EST: gi|71297664|gb|DR784782.1|DR784782
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
EST: gi|149097668|gb|EE183570.2|EE183570
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
EST: gi|93281137|gb|EB673401.1|EB673401
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
EST: gi|76293021|gb|DV032589.1|DV032589
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
EST: gi|32824168|gb|CD963890.1|CD963890
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
EST: gi|78090509|gb|DV518883.1|DV518883
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
EST: gi|89251237|gb|DY623023.1|DY623023
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
EST: gi|71772608|gb|DR970536.1|DR970536
EST:     TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAG                         AGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA
genomic: TGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGA

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: 33

GAGGATGCGGAGGACAGAGACCTCCCCGAGATCTCCAATGGTGATGCAGGTGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 29

GAGGATGCGGAGGACAGAGACCTCCCCGAGATCTCCAATGGTGATGCAGGTGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 18

GAGGATGCGGAGGACAGAGACCTCCCCGAGATCTCCAATGGTGATGCAGGTGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG


Block sizes: 46 (upstream exon), 41 (downstream exon)
Score: 8

GAGGATGCGGAGGACAGAGACCTCCCCGAGATCTCCAATGGTGATGCAGGTGCCCGGCTCAGCATCTCCGTCGACCGCTCCGGGCTCTACAACCCCACAGgtccgctccg ... aatgcggcagAGCACTCGCACGAGCCGTCGTCGGAATCCGAGCTCGTCAAGCACATCAAGAGCATCATAAAG