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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataccagctctcagtttatttgtgtacatacatatatagcattacaaaatttcttggaaagaaccagaacacctgaaatttctgaatgtgaacttgtctgcttggacaagttattacactaccttggtgaagtatgtgtgttgcaacttattatgggagttctttcctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGAACGAATCCTGTCTTCAAAGGGATGTACTGACTCAGAGCGGTTCCCTGTG

Basic information

species Zea mays
transcript AC205703.4_FGT002
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC205703.4_FGT002 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g38340.1 (Oryza sativa), 3'ss of exon 9
----------------------gtataccagctctcagtttatttgtgtacatacatatatagcattacaaaatttcttggaaagaaccagaacacctgaaatttctgaatgtgaacttgtctgcttggacaagttattacactaccttggtgaagtatgtgtgttgcaacttattatgggagttctttcctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGAACGAATCCTGTCTTCAAAGGGATGTACTGACTCAGAGCGGTTCCCTGTG
                      ||| |  ||   | |       | |  || |  |  ||  ||||  |      | ||| ||         | | || |||||| |   |  |||  | ||  | |   |  | | ||    | ||||  |  | | |     ||  | || ||| ||| |||| |  |      | |||||||||||||||| |||||||| || ||||| || || ||||||||||| ||||||||||| |||||||||||||||| |  ||  |||     ||   
gtattcaaacttctatttctatgtacagtagtaatgaacactcatat-cacttgaaactagtgcatagcgtttacttttgcaagttgtttccaaagcttaaatttttttgttggaatatatccccatattcggggt-ttctttttcctttttccattttagaaattaaagctaattctggtagttttccc----aaccagGCTTGCCACACAAAAGCAGAGTATGAAGAGTATGGCGCAAGCATCTGCCGGACGAATCCTGTTTTCAAAGGGATGTACTAAACCACGGCGCAAAGCTTCT

upper sequence: AC205703.4_FGT002 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 8
gtataccagctctcagtttatttgtgtacatacatatatagcattacaaaatttcttggaaagaaccagaacacctgaaatttctgaatgtgaacttgtctgcttggacaagttattacactaccttggtgaagtatgtgtgttgcaacttattatgggagttctttcctg-tgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGAACGAATCCTGTCTTCAAAGGGATGTACTGACTCA--GAGCGGTTCCCTGTG
                                                                     ||   |     |   ||   |||  | |   | |||    | |||  |  | | | |     || | |    | |||||    || |   | |||    ||  ||   ||||||| || ||||||||||| || |||||||| || || ||||| ||||| || |||||||| ||||| || ||||| | | |||  ||    ||   ||  
---------------------------------------------------------------------aatgtc-attctccttgggagtgcccataatttctta---atgtttctttaatccttccaataaatct---cgatgcaa---gttttaaaatttcgggtctaatgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACGACAAATTAGTTG--

upper sequence: AC205703.4_FGT002 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 8
gtataccagctctcagtttatttgtgtacatacatatatagcattacaaaatttcttggaaagaaccagaacacctgaaatttctgaatgtgaacttgtctgcttggacaagttattacactaccttggtgaagtatgtgtgttgcaacttattatgggagttctttcctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGAACGAATCCTGTCTTCAAAGGGATGTACTGACTCAG--AGCGGTTCCCTGTG
                                                                           ||  ||| ||   || ||   |   |  || |  ||    |      | | |    |   || |  | ||||| || |||    | |    |||  ||   ||||||| || ||||||||||| || |||||||| || || ||||| ||||| || |||||||| ||||| || ||||| | | |||   |    ||   ||  
--------------------------------------------------------------------------atgccatt-ctccttgggagtgtccataatttgttaatgcttcttttaatccttccaataaatct-cgatgcaagtt-ttacaata-tctggtccattgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACAACAAATTAGTTG--

upper sequence: AC205703.4_FGT002 (Zea mays), 3'ss of exon 9
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 3'ss of exon 8
gtataccagctctcagtttatttgtgtacatacatatatagcattacaaaatttcttggaaagaaccagaacacctgaaatttctgaatgtgaacttgtctgcttggacaagttattacactaccttggtgaagtatgtgtgttgcaacttattatgggagttctt--tcctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGAACGAATCCTGTCTTCAAAGGGATGTACTGACTCAGAGCGGTTCCCTGTG-
                                                                          ||| | | |       |  || ||          ||  |||| | | ||| |  ||  |  ||   | ||| |  | | ||||  | ||| |  | ||||||  ||||||| || ||||| || ||||| ||||| ||||| || ||||| |||||||| |||||||||||||| |||||||| |||     ||   |    || | 
--------------------------------------------------------------------------ctgcattgttgttgattccacatggtattccatgcatattatcatattacatgagtcga-cat---tcttgta--tgactatgaaaattcatggttctgtgcacagGCTTGTCATACAAAAGCTGAGTATGAGGAATACGGGGCAAGCATATGCCGAACAAATCCTGTCTTCAAGGGGATGTATTGATGTGAAG-ATTCTTTTGGGC

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|84969374|gb|DW467812.1|DW467812
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGTTTCAACCGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|89249037|gb|DY620823.1|DY620823
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTTTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|4621597|gb|AI612430.1|AI612430
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|6449711|gb|AW181251.1|AW181251
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACTGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|32920418|gb|CF025230.1|CF025230
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACTGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGT
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGT
EST: gi|74240911|gb|DT648825.1|DT648825
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTTTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|30032185|gb|CB834036.1|CB834036
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|32921953|gb|CF026765.1|CF026765
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACTGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTA
EST: gi|110210892|gb|EC892789.1|EC892789
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|149099376|gb|EE185415.2|EE185415
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|67032896|gb|CO461645.1|CO461645
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACTGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|50336873|gb|CO531999.1|CO531999
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|28390221|gb|CB250106.1|CB250106
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|24769340|gb|CA404469.1|CA404469
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACTGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|71759494|gb|DR957431.1|DR957431
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|32920457|gb|CF025269.1|CF025269
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACTGCCGAATTCTACGAG                         GCTTGCCGCACAAAGGCAGAGTA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTA
EST: gi|32922282|gb|CF027094.1|CF027094
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACTGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTA
EST: gi|5804491|gb|AI979461.1|AI979461
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|24769945|gb|CA405074.1|CA405074
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACTGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|37382936|gb|CF628439.1|CF628439
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACTGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|32846117|gb|CD985798.1|CD985798
EST:     CGGTATGGTTTGGCGGCTCTGTTCTTGCTTCAACCGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTA
EST: gi|67042751|gb|CO469006.1|CO469006
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACTGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|148957989|gb|EC904154.2|EC904154
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTTTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|91872833|gb|EB402790.1|EB402790
EST:     CGGTATGGTTTGGTGGTTCTGTGCTTGCTTCAACCGCCGAATTTTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCTTCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|166607189|gb|EG234060.1|EG234060
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACTGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAG
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAG
EST: gi|10191671|gb|BE761747.1|BE761747
EST:     CGGTATGGTTTGGTGGCGCTGTGCTTGCTTCAACCGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
EST: gi|109637254|gb|EC590799.1|EC590799
EST:     CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAG                         GCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA
genomic: CGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGA

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: 45 (upstream exon), 49 (downstream exon)
Score: 93

GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGAACGAATCCTGTCTTCAAAGGGATGTACTGACTCAGAGCGGTTCCCTGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 116

GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGAACGAATCCTGTCTTCAAAGGGATGTACTGACTCAGAGCGGTTCCCTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGAACGAATCCTGTCTTCAAAGGGATGTACTGACTCAGAGCGGTTCCCTGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 128

GCCCAGCCTATAGAAGTGAACGTGGTCAGTCATCCGATCCAGAGATATGCGGTATGGTTTGGTGGCTCTGTGCTTGCTTCAACCGCCGAATTCTACGAGgtataccagc ... ctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGAACGAATCCTGTCTTCAAAGGGATGTACTGACTCAGAGCGGTTCCCTGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttggtgaagtatgtgtgttgcaacttattatgggagttctttcctgtgcctagGCTTGCCACACAAAGGCAGAGTACGAGGAGTACGGTGCCAGCATCTGCCGAACGAATCCTGTCTTCAAAGGGATGTACTGACTCAGAGCGGTTCCCTGTG
                                      ttctttcctgtgcct  CT-rich tract
                       aacttattat  TA-rich tract