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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCCCACCACCCGACGCCGGAGGCCCGGAGGAGGAGGCGGCGATGGCGGGGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttccttccgtcatccgcactaccttgtcccttcggcggccttcgacttgtctagatctcggggggagttggcgcgcttctccgatccgatcac...

Basic information

species Zea mays
transcript GRMZM2G174730_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174730_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g42330.2 (Oryza sativa), 5'ss of exon 1
-CAGCCCACCACCCGACGCCGGAGGCCCGGAGGAGG-AGGCGGCGATGGCGGGGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtg-----ttccttccgtcatccgcactaccttgtcccttcggcggccttcg--acttgtctagatctcggggggagttggcgcgcttctccgatccgatcac
 |  |    |   || |||||  |||  |||| ||| ||||||| ||||||||||||||||| |||||||||||||| |||||| ||||||| || |||||||||||||     | ||   |||    | | |   || ||   ||||      ||||    | |  |||||||||||| | |||  |   ||  || ||||       
TCGTCGTTGCCGTCGTCGCCGTCGGC--GGAGTAGGCAGGCGGCCATGGCGGGGAAGCACGGCCGCAACGGCTTCGAGGACGACGACGTCAATCCCTTCGCGgtgagtgctcgctccccctcgttccacccccgcgctagtatattcgagaaggttcgctgttcgcgtagatctcggggtgggttctc---ctgatctgatctac----
















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|149076952|gb|EE165608.2|EE165608
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211455821|gb|FL370764.1|FL370764
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211251918|gb|FL397021.1|FL397021
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|31353834|gb|CD438191.1|CD438191
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCCCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211137749|gb|FL292364.1|FL292364
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211138691|gb|FL292374.1|FL292374
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211137750|gb|FL292365.1|FL292365
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211039428|gb|FL384648.1|FL384648
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|91876331|gb|EB406288.1|EB406288
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211501973|gb|FL392126.1|FL392126
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|149069546|gb|EE157919.2|EE157919
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|76927277|gb|DV171213.1|DV171213
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211138685|gb|FL292368.1|FL292368
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACNACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211138688|gb|FL292371.1|FL292371
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211341624|gb|FL411903.1|FL411903
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCA
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCA
EST: gi|211122269|gb|FL373644.1|FL373644
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211138687|gb|FL292370.1|FL292370
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|76289053|gb|DV028621.1|DV028621
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|91872788|gb|EB402745.1|EB402745
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|71322127|gb|DR797759.1|DR797759
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211228158|gb|FL414420.1|FL414420
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|149079646|gb|EE168643.2|EE168643
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211137751|gb|FL292366.1|FL292366
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACNACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|78081465|gb|DV509877.1|DV509877
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211138689|gb|FL292372.1|FL292372
EST:     GGAAGCACGTGCGCAACGGCTTCGACGACGACNACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211138692|gb|FL292375.1|FL292375
EST:     GAAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: G-AAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211130112|gb|FL389065.1|FL389065
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211138694|gb|FL292377.1|FL292377
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|78112246|gb|DV530640.1|DV530640
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|37417263|gb|CF646284.1|CF646284
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211035296|gb|FL425638.1|FL425638
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211138693|gb|FL292376.1|FL292376
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211137579|gb|FL389525.1|FL389525
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|149104177|gb|EE289611.2|EE289611
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT

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), 49 (downstream exon)
Score: 222

CAGCCCACCACCCGACGCCGGAGGCCCGGAGGAGGAGGCGGCGATGGCGGGGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

CAGCCCACCACCCGACGCCGGAGGCCCGGAGGAGGAGGCGGCGATGGCGGGGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

CAGCCCACCACCCGACGCCGGAGGCCCGGAGGAGGAGGCGGCGATGGCGGGGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 309

CAGCCCACCACCCGACGCCGGAGGCCCGGAGGAGGAGGCGGCGATGGCGGGGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG