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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtactagcctctattgtttggggtgttaaggtgattagtgaaagcttgagataggtatatgctaatgagttttacttgttatccttgcttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAATGGCCCGCAGTTGTATCAG

Basic information

species Zea mays
transcript GRMZM2G115948_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824831_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 5
catgtactagcctctattgtttggggtgttaaggtgattagtgaaagcttgagataggtatatg-ctaatgagttttacttgttatccttgcttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAATGGCCCGCAGTTGTATCAG
    |  |     ||   ||   |     |      |    ||||    |||  ||     ||  || | |  |    |  |     |||| ||||  ||||||||| |||||||||||||||||| | |||||||| ||||| |||||||||||||| ||| ||||||||
-gattggtgaatcctgaagtacagttcactccttaaagatatgaatatatgatgtaaccgaatttctgaggcatgactcacggccaacttgtttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAATGGCCCACAGCTGTATCAG

upper sequence: GRMZM5G824831_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g42320.4 (Oryza sativa), 3'ss of exon 6
catgtactagcctctattgtttggggtgttaaggtgattagtgaaagcttgagataggtatatg-ctaatgagttttacttgttatccttgcttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAATGGCCCGCAGTTGTATCAG------------------------------
    |  |     ||   ||   |     |      |    ||||    |||  ||     ||  || | |  |    |  |     |||| ||||  ||||||||| |||||||||||||||||| | |||||||| ||||| |||||||||||||| ||| ||||||||                              
-gattggtgaatcctgaagtacagttcactccttaaagatatgaatatatgatgtaaccgaatttctgaggcatgactcacggccaacttgtttgttgcagTGGTGTAAGACCATTTGGAGTATCATTATTGATTGCCGGGTACGATGACAATGGCCCACAGCTGTATCAGGTATGCAGATAGCTGCGTGATAGGGGCTCT

upper sequence: GRMZM5G824831_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 3'ss of exon 6
--catgtactagcctctattgtttggggtgttaaggtgattagtgaaagcttgagataggtatatgctaatgagt-tttacttgttatccttgcttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAATGGCCCGCAGTTGTATCAG
    |   | |  |   |   | ||   |    | |    |||  ||||||  |  ||  || |||    |   | | |  |  || | |||  |  ||| |||||||| || || |||||||||||||||||| ||||||| | |||||||||||| || || ||||| |||
attttaagcaatgcataaacctctgaattacagaagcatatag-aaaagctcaat-tatttaaatgaagtttgatatcttttctttcttcttattcctat-agTGGTGTAAGGCCCTTTGGAGTATCACTGTTGGTTGCTGGTTTTGATGACAATGGTCCACAATTGTACCAG

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|60395022|gb|DN227891.1|DN227891
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|30087632|gb|CB885838.1|CB885838
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|5607822|gb|AI901489.1|AI901489
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|33092266|gb|CF052260.1|CF052260
EST:     GTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: GTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|18163469|gb|BM333308.1|BM333308
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|32934147|gb|CF038959.1|CF038959
EST:     GTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: GTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|211323462|gb|FL273341.1|FL273341
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|71445139|gb|DR826189.1|DR826189
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|149076955|gb|EE165612.2|EE165612
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|32830029|gb|CD969707.1|CD969707
EST:     GTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: GTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|78123839|gb|DV542223.1|DV542223
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|44901282|gb|CK827827.1|CK827827
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTGGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|32930013|gb|CF034825.1|CF034825
EST:     ACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: ACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|30306694|gb|CD001367.1|CD001367
EST:     CGAGAGACTGCTGCTGTCATGCAGGAGTTCAC-CAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCNCTGTTGATTGCTGGGTATGATGACAA
genomic: CGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|60350515|gb|DN217488.1|DN217488
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTCAGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|32931688|gb|CF036500.1|CF036500
EST:     GTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: GTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|74232754|gb|DT640668.1|DT640668
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|60346153|gb|DN213126.1|DN213126
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|32935134|gb|CF039946.1|CF039946
EST:     ACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: ACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|9951982|gb|BE638565.1|BE638565
EST:     CAGTTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|60356997|gb|DN223970.1|DN223970
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|60339671|gb|DN206644.1|DN206644
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|148987619|gb|EE031493.2|EE031493
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|89763964|gb|DY690939.1|DY690939
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|78118765|gb|DV537149.1|DV537149
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|30032061|gb|CB833912.1|CB833912
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATGGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|211258486|gb|FL474162.1|FL474162
EST:     TGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: TGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|5608197|gb|AI901864.1|AI901864
EST:     GCTGTCATGCAGGAGTTCCCCCAGTCAGG                         TGGTGTGAGNCCATTTGGAGTATCNCTGTTGATTGCTGGGTATGATGACAA
genomic: GCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|60339580|gb|DN206553.1|DN206553
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|50322577|gb|CO517703.1|CO517703
EST:     GTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: GTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
EST: gi|211323464|gb|FL273343.1|FL273343
EST:     CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGG                         TGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA
genomic: CAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAA

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), 47 (downstream exon)
Score: 561

GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAATGGCCCGCAGTTGTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 395

GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAATGGCCCGCAGTTGTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 438

GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAATGGCCCGCAGTTGTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 370

GAACATATACCTGTAACACAGCTTGTACGAGAGACTGCTGCTGTCATGCAGGAGTTCACACAGTCAGGgtatgtaact ... cttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAATGGCCCGCAGTTGTATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcttgagataggtatatgctaatgagttttacttgttatccttgcttgtatcagTGGTGTGAGACCATTTGGAGTATCACTGTTGATTGCTGGGTATGATGACAATGGCCCGCAGTTGTATCAG
                 tgctaat  putative branch site (score: 370)
                                       tccttgctt  putative PPT
                           ttttactt  TA-rich tract