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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAAAGGGTCATCATGCTTGAAAATGACTTGAAATGCTACTACCAAACTGAGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAGgtatagatgtcttatgtccttctgtgcagtaagggcctgttgctttgtgaactgaacctgtctggtgcaggcagctctcccaggtggggctggatgaagc...

Basic information

species Zea mays
transcript GRMZM2G054905_T01
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054905_T01 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os01g57073.1 (Oryza sativa), 5'ss of exon 21
TAAAAGGGTCATCATGCTTGAAAATGACTTGAAATGCTACTACCAAACTGAGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAGgtatagatgtcttatgtccttctgtgcagtaagggcctgttgctttgtgaactgaacctgtctggtgcaggcagctctcccaggtggggctggatgaagc----
||||||||| ||||||||||||||||| || ||||||||| |||||| |||||| ||||| ||||||||||| |||||||||||  ||||||||||||||||| |  |  | | || | |  | |  |||    |   | |||  ||  ||||     |  |    |||   |    |||  | |  |         | |    
TAAAAGGGTTATCATGCTTGAAAATGAGTTAAAATGCTACCACCAAATTGAGGGCTTAAATCAGAAGAATGAAAATTCATCAGTGGTCCAATATATTCAGgtaaatgt-ccctgtggcttgatctttagtgcaagg--gatgcaatgc-aactactattaacgaaagcaactactgatccatgatcagtaacttcagaactaat

upper sequence: GRMZM2G054905_T01 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os01g57082.1 (Oryza sativa), 5'ss of exon 21
TAAAAGGGTCATCATGCTTGAAAATGACTTGAAATGCTACTACCAAACTGAGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAGgtatagatgtcttatgtc-cttctgtgcagtaagggc--ctgttgctttgtgaactgaacctgtctggtgcaggcagctctcccaggtggggctggatgaagc
|| |||||| ||||  ||||||||||| || || |||||| |||||| |||||| ||||| |||||||||||||||||||||||  ||||| ||||||||||| |  |  || | | | | ||| |   | |||||   |   | || |    |    || |  ||| | || | | | ||  |   ||        |  |  
TAGAAGGGTTATCACCCTTGAAAATGAGTTAAAGTGCTACCACCAAATTGAGGGCTTAAATCAGAAGAATGAGAATTCATCAGTAGTCCAACATATTCAGgtaaatgtccctgaggcctcatctttcgtgcaagggatgcaactactattaacaaaagacattactgatccatg-atcgctaacttctgaactaatgttca--
















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|87153301|gb|DY398090.1|DY398090
EST:     AGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAG                         GTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTA
genomic: AGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAGgtatagatgt ... atattttcagGTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTA
EST: gi|22490447|gb|BU050370.1|BU050370
EST:     GAAGAATGAGAATTCATCAGTTATCCAATATATTCAG                         GTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTA
genomic: GAAGAATGAGAATTCATCAGTTATCCAATATATTCAGgtatagatgt ... atattttcagGTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTA
EST: gi|33091207|gb|CF051201.1|CF051201
EST:     AGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAG                         GTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTA
genomic: AGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAGgtatagatgt ... atattttcagGTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTA
EST: gi|6031436|gb|AW076338.1|AW076338
EST:     AGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAG                         GTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTA
genomic: AGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAGgtatagatgt ... atattttcagGTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTA
EST: gi|18384145|gb|BM417345.1|BM417345
EST:     AGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAG                         GTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTA
genomic: AGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAGgtatagatgt ... atattttcagGTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTA
EST: gi|67020141|gb|CO448890.1|CO448890
EST:     AGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAG                         GTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTA
genomic: AGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAGgtatagatgt ... atattttcagGTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTA
EST: gi|87153758|gb|DY398547.1|DY398547
EST:     AGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAG                         GTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTA
genomic: AGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAGgtatagatgt ... atattttcagGTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTA

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: 46 (upstream exon), 48 (downstream exon)
Score: 59

TAAAAGGGTCATCATGCTTGAAAATGACTTGAAATGCTACTACCAAACTGAGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAGgtatagatgt ... atattttcagGTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTAATAGCAAAACAGCCAGCCTTCAACCAGCTACGAACTGTTGAACAACTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

TAAAAGGGTCATCATGCTTGAAAATGACTTGAAATGCTACTACCAAACTGAGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAGgtatagatgt ... atattttcagGTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTAATAGCAAAACAGCCAGCCTTCAACCAGCTACGAACTGTTGAACAACTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

TAAAAGGGTCATCATGCTTGAAAATGACTTGAAATGCTACTACCAAACTGAGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAGgtatagatgt ... atattttcagGTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTAATAGCAAAACAGCCAGCCTTCAACCAGCTACGAACTGTTGAACAACTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

TAAAAGGGTCATCATGCTTGAAAATGACTTGAAATGCTACTACCAAACTGAGGGATTAAACCAGAAGAATGAGAATTCATCAGTTATCCAATATATTCAGgtatagatgt ... atattttcagGTGCATCAAGATGACGCCATTTTGAATATCAAACTTGAGCTGTTCTCTCTAATAGCAAAACAGCCAGCCTTCAACCAGCTACGAACTGTTGAACAACTTG