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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatcaccagttatgacaattgcatgtgttcttgttgtgtttctcagcaaatattgatggaactcaatctgaattgtcactcttaag

Basic information

species Zea mays
transcript GRMZM2G104294_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104294_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 15
GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatcaccagttatgaca-attgcatgtgttcttgttgtgtttctcagcaaatattgatggaactcaatctgaattgtcactcttaag
||||| ||||| || |||||||||||||  |||||||||| |||| | || ||||||||||||||||||||||||||||||   ||||  || ||   ||      |  | || |  |  |||| |||        ||  |||| |||| |||||||   ||  ||  ||
GAAAGATTAGCTCTAAAACAATCTGGAGTTGAACTGGGCAATTCAGTTCTCTTCTTTGGATGCAGGAACCGTAATATGgtatgcatcaaaagatagttcatgagatacatattatgatcatgttgctc--------ttactggacctca-tctgaatgaccaacctgcag
















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|211061849|gb|FL232858.1|FL232858
EST:     TTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: TTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|32928790|gb|CF033602.1|CF033602
EST:     CAGAACTGGGCACTTCAGTCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|113701122|gb|EE678626.1|EE678626
EST:     CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|194716812|gb|FK933971.1|FK933971
EST:     CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|60353207|gb|DN220180.1|DN220180
EST:     CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|60398924|gb|DN231740.1|DN231740
EST:     TGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: TGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|60340539|gb|DN207512.1|DN207512
EST:     GCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: GCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|60344210|gb|DN211183.1|DN211183
EST:     CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|67024128|gb|CO452877.1|CO452877
EST:     AGAACTGGGCACTTCAATCCTTTTCTTTGGATGCANNGAACCGTA-TATG                         GACTACATATATGAAGATGAGCTGCANACTTTCCTTTGAG-AGGGGGCGCT
genomic: AGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAG-GAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTT-GAGGAGGGGGCGCT
EST: gi|211021947|gb|FL480535.1|FL480535
EST:     GGATGCGGGACCCGTAATAGG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: GGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|60398791|gb|DN231607.1|DN231607
EST:     CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|32835489|gb|CD975167.1|CD975167
EST:     CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|32929541|gb|CF034353.1|CF034353
EST:     CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|32835138|gb|CD974816.1|CD974816
EST:     CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|211061847|gb|FL232856.1|FL232856
EST:     ATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: ATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|61119293|gb|DN560254.1|DN560254
EST:     CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|60399770|gb|DN232580.1|DN232580
EST:     GGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: GGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|32921780|gb|CF026592.1|CF026592
EST:     CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGACCCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
EST: gi|32920698|gb|CF025510.1|CF025510
EST:     CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATG                         GACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT
genomic: CAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTT

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: 451

GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACTAAAGAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 482

GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACTAAAGAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 616

GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACTAAAGAATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 769

GAAAGGTTAGCACTGAAACAATCTGGAGCAGAACTGGGCACTTCAATCCTTTTCTTTGGATGCAGGAACCGTAATATGgtaaagatca ... cactcttaagGACTACATATATGAAGATGAGCTGCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACTAAAGAATATG