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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAGgtacttgcacagctacaaaatctcagtagctgtttcttctattacttctatatgctgatgacaagcaatattgttag

Basic information

species Zea mays
transcript GRMZM2G133919_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133919_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 5'ss of exon 5
TGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAGgtacttgcac-agctacaaaatctcagtagctgtttcttctattacttctatatgctgatgacaagcaatattgttag
||| || |||||||| ||||| ||||||||||||||||| |||||||| || |||||||| ||||| ||||| |||||||| |||||||| | ||||||||||  |   | |   |||  ||    | ||||      |    |  |  |  ||     |||||||| || |||||||
TGCAACTAAGAAATTTGAGAAATTAATTACTGATAAGAATGAAATTGATGGGTTACCTGCCACAGCACTTGGCTTAGCAGCACAGACTGCCGCGTCAAAGgtatataagctataaacaccattattgaagcttaaaagttctctcttgattcatcacactgacaagccattttgttag
















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|149009256|gb|EE041351.2|EE041351
EST:     GTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAG                         GGCCATGAAAATGCTACAGC
genomic: GTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAGgtacttgcac ... atattgttagGGCCATGAAAATGCTACAGC
EST: gi|74240585|gb|DT648499.1|DT648499
EST:     GTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAG                         GGCCATGAAAATGCTACAGCTGAAAATGGACCTTGGGTTATCACGTTGGAT
genomic: GTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAGgtacttgcac ... atattgttagGGCCATGAAAATGCTACAGCTGAAAATGGACCTTGGGTTATCACGTTGGAT
EST: gi|148960061|gb|EE153304.2|EE153304
EST:     GTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAG                         GGCCATGAAAATGCTACAGCTGAAAATGGACCTTGGGTTATCACGTTGGAT
genomic: GTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAGgtacttgcac ... atattgttagGGCCATGAAAATGCTACAGCTGAAAATGGACCTTGGGTTATCACGTTGGAT
EST: gi|149072691|gb|EE160926.2|EE160926
EST:     GTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAA                         GGCCATGAAAATGCTA
genomic: GTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAGgtacttgcac ... atattgttagGGCCATGAAAATGCTA
EST: gi|148956895|gb|EC902819.2|EC902819
EST:     GTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAG                         GGCCATGAAAATGCTACAGCTGAAAATGGACCTTGGGTTATCACGTTGGAT
genomic: GTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAGgtacttgcac ... atattgttagGGCCATGAAAATGCTACAGCTGAAAATGGACCTTGGGTTATCACGTTGGAT
EST: gi|31354902|gb|CD439259.1|CD439259
EST:     GTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAG                         GGCCATGAAAATGCTACAGCTGAAAATGGACCTTGGGTTATCACGTTGGAT
genomic: GTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAGgtacttgcac ... atattgttagGGCCATGAAAATGCTACAGCTGAAAATGGACCTTGGGTTATCACGTTGGAT
EST: gi|148983362|gb|EE029348.2|EE029348
EST:     GTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAG                         GGCCATGAAAATGCTACAGCTGAAAATGGACCTTGGGGTTATCACGTTGGG
genomic: GTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAGgtacttgcac ... atattgttagGGCCATGAAAATGCTACAGCTGAAAATGGACCTTGGG-TTATCACGTTGG-

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: 49 (upstream exon), 48 (downstream exon)
Score: 265

TGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAGgtacttgcac ... atattgttagGGCCATGAAAATGCTACAGCTGAAAATGGACCTTGGGTTATCACGTTGGATGCACCAAGCTATATTCCTGTTATGCAACATGCTCGAAACAGAGAGCTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 326

TGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAGgtacttgcac ... atattgttagGGCCATGAAAATGCTACAGCTGAAAATGGACCTTGGGTTATCACGTTGGATGCACCAAGCTATATTCCTGTTATGCAACATGCTCGAAACAGAGAGCTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 316

TGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAGgtacttgcac ... atattgttagGGCCATGAAAATGCTACAGCTGAAAATGGACCTTGGGTTATCACGTTGGATGCACCAAGCTATATTCCTGTTATGCAACATGCTCGAAACAGAGAGCTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 221

TGCCACAAAGAAATTCGAGAAGTTAATTACTGATAAGAAAGAAATTGAGGGTTTACCTGCTACAGCCCTTGGTTTAGCAGCGCAGACTGCTGTGTCAAAGgtacttgcac ... atattgttagGGCCATGAAAATGCTACAGCTGAAAATGGACCTTGGGTTATCACGTTGGATGCACCAAGCTATATTCCTGTTATGCAACATGCTCGAAACAGAGAGCTCC