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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCGCAACTGCCCCATTTGAGCATTCCAGAGACTGAAGCTGGAAAAACACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgtatgcacccttgtgtttgtgaatggttgatttaacactatacctatactgaacatagaacagagactacatgtgcattgattagagatctacctgtctgctgatgctagtatatagtttctgtaaatattcagtcaatgtggaagttctaggaggtctgacttatgctgatactgcattaataatttgcag

Basic information

species Zea mays
transcript GRMZM2G071071_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071071_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os03g59590.1 (Oryza sativa), 5'ss of exon 13
GCTGCGCAACTGCCCCATTTGAGCATTCCAGAGACTGAAGCTGGAAAAACACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtga-gttgtatgcacccttg-tgtttgtgaatggttgatttaacactatacctatactgaacatagaacagag-actacatgtgcattgattagagatctacctgtctgctgatgctagtatatagtttctgtaaatattcagtcaatgtggaagttctaggaggtctgacttatgctgatactgcattaataatttgcag
|||||||| | ||| ||| ||||||||||||||||||||||||| ||||||||| | ||||| || |||||||| |||||||| || ||||||||||| ||| | |     | ||| || |    |  ||    ||| | |   |     |  ||  ||    |||   ||  | | |  |     ||    || | |||||                                                                                                    
GCTGCGCAGCAGCCTCATCTGAGCATTCCAGAGACTGAAGCTGGGAAAACACGCAGACAATACCGTCAACTTCTGAACCGTTCCCTTATGGTTGTCTCAGgtaaagccagttccacactcgacagtcctgttgtgtttactct-cgtcgcatttacgctct-tatactgcattgtattgtacaaatatattctataaatcta----------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G071071_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os01g62570.1 (Oryza sativa), 5'ss of exon 14
GCTGCGCAACTGCCCCATTTGAGCATTCCAGAGACTGAAGCTGGAAAAACACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgtatgcacccttgtgtttgtgaatggttgatttaacactatacctatactgaacatagaacagagactacatgtgcattgattagagatctacctgtctgctgatgctagtatatagtttctgtaaatattcagtcaatgtggaagttctaggaggtctgacttatgctgatactgcattaataatttgcag
|| ||||| | ||| ||||||||||| ||||||||||||||||| ||||||| | ||||||| || |||||||| |||||||| || | ||||||||| ||| ||||     ||  ||| ||  | | ||  ||   | |     |     ||| ||     | | ||| |     ||||   ||| | || |||       |                                                                                                
GCGGCGCAGCAGCCTCATTTGAGCATCCCAGAGACTGAAGCTGGGAAAACACACAGGCAATACCGTCAACTTCTGAACCGTTCCCTCACGGTTGTCTCAGgtaagttagtgtcaagcttctgcctctaaagtgtgtttctgtatttgcctttatgctc----tggcacaaatcgatcatgccaatt-actacagaatagtaagag----------------------------------------------------------------------------------------------
















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|166562131|gb|EG126367.1|EG126367
EST:     GGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTAGGACTAGCTGCTTACCGGGTTTATGCA
genomic: GGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTT-GGACTAGCTGCTTACCGGGTTTATGCA
EST: gi|148971579|gb|EE022294.2|EE022294
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|67012174|gb|CO440923.1|CO440923
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|113666134|gb|DW829520.1|DW829520
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTAGGAGCTGCTGTTGCAGTTG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTT-GGAGCTGCTGTTGCAGTTG
EST: gi|32943481|gb|CF048300.1|CF048300
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGTTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|32923193|gb|CF028005.1|CF028005
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|148933976|gb|EC877974.2|EC877974
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|71443064|gb|DR824114.1|DR824114
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|60345129|gb|DN212102.1|DN212102
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|31356495|gb|CD440852.1|CD440852
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGCCTCTG                         TTGGAGCTGCTGTTGCAATTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|24768382|gb|CA403511.1|CA403511
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|166607247|gb|EG311972.1|EG311972
EST:     GGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: GGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|31357304|gb|CD441661.1|CD441661
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|211424544|gb|FL433274.1|FL433274
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|32942774|gb|CF047593.1|CF047593
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|87152121|gb|DY396910.1|DY396910
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAACTGCTGTTGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAG
EST: gi|149010210|gb|EE042028.2|EE042028
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|5816321|gb|AI987237.1|AI987237
EST:     NCGCAGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|5928681|gb|AW055898.1|AW055898
EST:     ACGCAGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|60350823|gb|DN217796.1|DN217796
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|76011272|gb|DT938442.1|DT938442
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|32943845|gb|CF048664.1|CF048664
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|37379192|gb|CF626328.1|CF626328
EST:     ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
genomic: ACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG
EST: gi|45846851|gb|CN070794.1|CN070794
EST:     ACTTCTAAACCGTTCGCTAATGGTTGTCTCTG                         TTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCCTACCGGGTTTATGCAG
genomic: ACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAG

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: 259

GCTGCGCAACTGCCCCATTTGAGCATTCCAGAGACTGAAGCTGGAAAAACACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAGCTCGGAAAAACTCTTCCTCTTGAAGCCTCCTGGACAAGTGGGAAAATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 162

GCTGCGCAACTGCCCCATTTGAGCATTCCAGAGACTGAAGCTGGAAAAACACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAGCTCGGAAAAACTCTTCCTCTTGAAGCCTCCTGGACAAGTGGGAAAATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264

GCTGCGCAACTGCCCCATTTGAGCATTCCAGAGACTGAAGCTGGAAAAACACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAGCTCGGAAAAACTCTTCCTCTTGAAGCCTCCTGGACAAGTGGGAAAATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

GCTGCGCAACTGCCCCATTTGAGCATTCCAGAGACTGAAGCTGGAAAAACACGCCGGCAATATCGGCAACTTCTAAACCGTTCGCTAATGGTTGTCTCTGgtgagttgta ... taatttgcagTTGGAGCTGCTGTTGCAGTTGTTGGACTAGCTGCTTACCGGGTTTATGCAGCTCGGAAAAACTCTTCCTCTTGAAGCCTCCTGGACAAGTGGGAAAATAA