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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttctcaattttattgcatgttgcataatgcatagttacgagttataatgtttttggtccttgcatggcatgcagcctaattcatcagtggaggaagttatgactagtttcattttacgtggcag

Basic information

species Zea mays
transcript GRMZM2G073054_T01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA03G35020.1 (Glycine max), 5'ss of exon 17
GATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttctcaattttattgcatgttgcataatgcatagttacgagttataatgtttttggtccttgcatggcatgcagcctaattcatcagtggaggaagttatgactagtttcattttacgtggcag
|||||||| ||||| || || ||||||||||||||| | || |||||| | || |||||||| ||| ||||||| ||||| ||||| ||||| ||||||||| |   |  |  | ||| |  |||||  ||| |   | || | | | | || || |     ||  ||  ||   |||    | | || |    | |      | ||   | ||| |  | | |       
GATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGTCTTGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTTGGCCATCCTGgtaatcatatttgacttt-tgtcatgt--cattacttagagattcaa-taatgatatgaccagttgttagattttatgttatcaagttaagtt-tagcattgctcattcattgttgctctcttcag-----

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 17
lower sequence: GLYMA19G37750.2 (Glycine max), 5'ss of exon 17
GATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttctcaattttattgcatgttgcataatgcatagttacg-agttataatgtttttggtcc--ttgcatggcatgcagcctaattcatcagtggaggaa-gttatgactagtttcattttacgtggcag
|||||||| ||||| || || ||||||||||||||| | || |||||  | || |||||||| ||| ||||||| ||||| ||||| || || ||||||||| | || | |     || |  |||||       | | |||  |   | | || || |     ||    ||  ||   ||  ||   | || | || ||        || |  ||   ||||             
GATCGTGGTATAGCGTTGCACAAAATGATTAGGCTTATTACCATGGGCCTTGGTGGTGAAGGGTATTTAAATTTTATGGGGAATGAATTCGGCCATCCTGgt-aatcatatttgacttgtgtcatgtcattacttacgtagagattcaataatgatatgaccagttagattttatattatcaagttaagtttagcattgctcattcattgttgctcacttcag------------

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 17
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 5'ss of exon 17
GATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttctcaattttattgcatgttgcataatgcatagttacgagttataatgtttttggtccttgcatggcatgcagcctaattcatcagtggaggaagttatgactagtttcattttacgtggcag
||| | || ||||| || || ||||||||||||||| | || ||||| ||||| |||||||| ||  ||||||| |||||||| || || || ||||| |||        || |||| |     | |    || |   |    |  | || | | || |    |   | |||    | | ||   |||||                                         
GATAGAGGAATAGCTTTGCACAAAATGATTAGGCTTATAACTATGGGATTAGGCGGTGAAGGTTACTTAAATTTTATGGGAAACGAATTCGGACATCCAGgt--actaaatcgatttaagcttgtttcatttactttctgtgcaaaaattttga-gtgtacaatttcttcatctactcctgcaatattcag----------------------------------------

upper sequence: GRMZM2G073054_T02 (Zea mays), 5'ss of exon 17
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 5'ss of exon 17
GATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttctcaatt--ttattgcatgttgcataatgcatagttacgagttataatgtttttggtccttgcatggcatgcagcctaattcatcagtggaggaagttatgactagtttcattttacgtggcag
|||||||| ||||||||||| |||||||| || ||| | || ||||| ||||| || ||||| || || |||||||||||||| || ||||| ||||||||| |        | |   |||||  || ||||||    || ||| | || |  |  |  | ||  |  |     |  ||  |   |  |  |||||| | |    || |  |     | ||||    |  |||
GATCGTGGAATAGCATTACACAAAATGATCAGACTTATTACCATGGGCTTAGGGGGAGAAGGATACCTGAATTTCATGGGAAACGAATTTGGACATCCTGgtaaaagaataaagtcaattattttat-ttgcatt-cccaaagtaatgattcttgctagtgtttata-tcattcgaaatatatttt--tgaatcagttgtgattatt-tatcctacgttatttcttttatcag

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|32836879|gb|CD976557.1|CD976557
EST:     AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTG                         AATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
genomic: AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
EST: gi|32934500|gb|CF039312.1|CF039312
EST:     AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTG                         AATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCC
genomic: AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTC-
EST: gi|60338294|gb|DN205267.1|DN205267
EST:     AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTG                         AATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
genomic: AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
EST: gi|32837113|gb|CD976791.1|CD976791
EST:     AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTG                         AATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
genomic: AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
EST: gi|32920624|gb|CF025436.1|CF025436
EST:     AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTG                         AATGGATAGATTTTCCAAGAGGTCCTCAAAAGTCTTCCAAATGGCTCCGTC
genomic: AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTC-AAAGTCTTCCAAATGGCTCCGTC
EST: gi|60394366|gb|DN227236.1|DN227236
EST:     AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTG                         AATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
genomic: AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
EST: gi|60345781|gb|DN212754.1|DN212754
EST:     AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTG                         AATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
genomic: AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
EST: gi|211026372|gb|FL004586.1|FL004586
EST:     AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAATTTGGGCATCCTG                         AATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
genomic: AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
EST: gi|32864974|gb|CF004656.1|CF004656
EST:     AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTG                         AATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
genomic: AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
EST: gi|32930900|gb|CF035712.1|CF035712
EST:     AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTG                         AATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCC
genomic: AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGT-C
EST: gi|32837751|gb|CD977429.1|CD977429
EST:     AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTG                         AATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
genomic: AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
EST: gi|32921787|gb|CF026599.1|CF026599
EST:     AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTG                         AATGGATAGATTTTCCAAGAGGTCCTCAAAAGTCTTCCAAATGGCTCCGTC
genomic: AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTC-AAAGTCTTCCAAATGGCTCCGTC
EST: gi|32931179|gb|CF035991.1|CF035991
EST:     AGCAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTG                         AATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
genomic: AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCA
EST: gi|32933816|gb|CF038628.1|CF038628
EST:     AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTG                         AATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCC
genomic: AGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGT-C

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: 48 (upstream exon), 48 (downstream exon)
Score: 695

GATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCATTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

GATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCATTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCT


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 27

GATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCATTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 257

GATCGTGGGATAGCATTACATAAAATGATTAGGCTTGTCACAATGGGTTTAGGAGGTGAAGGCTATCTAAATTTCATGGGAAATGAGTTTGGGCATCCTGgttagtcttc ... tacgtggcagAATGGATAGATTTTCCAAGAGGTCCTCAAAGTCTTCCAAATGGCTCCGTCATTCCTGGGAATAACAATAGCTTTGATAAATGCCGCCGTAGATTTGACCT