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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccaggacccaaaaattcagcttggcatgcacggttacaagtaggcatacatgaaactatatacggcaacgtaacatttccgtcccactgcaaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGCCATCAAACTTGTCTGGTCCTGCCACAGGGAAGTCATATATGACGTCGGG

Basic information

species Zea mays
transcript GRMZM2G090087_T03
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090087_T03 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 14
gtgagccaggacccaaaaattcagcttggcatgcacggttacaagtaggcatacatgaaactatatacggcaacgtaacatttccgtcccactgcaaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGCCATCAAACTTGTCTGGTCCTGCCACAGGGAAGTCATATATGACGTCGGG
|||||| | |||   ||| |  | | || |||   |  ||               | || | | ||| |  ||| |  |||||   |   | |    ||| ||||||||| || || ||||||||  |||| ||||||||||| ||||| |||||||| ||||| || ||||| |||||||||||  ||||||||||| | || 
gtgagctaagactagaaactggaacctgccatcttcctttt--------------ttaaccaaaataggttaacatgtcattt---tattatt-tgtaattcagGTTTGGGCCTGCTGGTGATCCAAGAGGTGCAGGGATCGGAACTCCAGAAGCCATTAAACTCGTTTGGTCTTGCCACAGGGAGATCATATATGACATTGGC
















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|31997860|gb|CD661809.1|CD661809
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|32845913|gb|CD985594.1|CD985594
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|18383619|gb|BM416819.1|BM416819
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|28984490|gb|BQ539097.2|BQ539097
EST:     ACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|211120257|gb|FL200678.1|FL200678
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGT
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGT
EST: gi|67020094|gb|CO448843.1|CO448843
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|27769727|gb|CB042906.1|CB042906
EST:     ACCTACGCCGGAATTCGAGCGAGGACCCCGGGCGCTCCACAGAACCCCTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|28361615|gb|CB239971.1|CB239971
EST:     CCTACGCCGGAATTCGTAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: CCTACGCCGGAATTCG-AGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|6827469|gb|AW331112.1|AW331112
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|29576986|gb|CB617098.1|CB617098
EST:     GCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: GCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|27576018|gb|CA998712.1|CA998712
EST:     ACCTACGCCGGAATTCGAGCGAGGACCCCGGGCGCTCCCCAGAACCCCTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|30088118|gb|CB886323.1|CB886323
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|29544968|gb|CB605146.1|CB605146
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|18181309|gb|BM382519.1|BM382519
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|28361799|gb|CB240155.1|CB240155
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|28422820|gb|CB251998.1|CB251998
EST:     ACCTACGCCGGAATTCGAGCGAGGACCCCGGGCGCTCCCCAGAACCCCTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|31997861|gb|CD661810.1|CD661810
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|4966653|gb|AI691509.1|AI691509
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|29946900|gb|CB816380.1|CB816380
EST:     ACCTACGCCGGAATTCTAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGG-CGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|67025872|gb|CO454621.1|CO454621
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|29544562|gb|CB604942.1|CB604942
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|67023454|gb|CO452203.1|CO452203
EST:     ACCTACGCCG-AATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|37380563|gb|CF627102.1|CF627102
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|27521928|gb|CA989034.1|CA989034
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCCCTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|30306480|gb|CD001153.1|CD001153
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|60340281|gb|DN207254.1|DN207254
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|67018698|gb|CO447447.1|CO447447
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|211507628|gb|FL212141.1|FL212141
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|67014372|gb|CO443121.1|CO443121
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|211301793|gb|FL438947.1|FL438947
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|31558187|gb|CD527399.1|CD527399
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|60349947|gb|DN216920.1|DN216920
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|211342162|gb|FL434432.1|FL434432
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|71440457|gb|DR821507.1|DR821507
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
EST: gi|211507626|gb|FL212139.1|FL212139
EST:     ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG                         GTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC
genomic: ACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGC

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: 229

GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGCCATCAAACTTGTCTGGTCCTGCCACAGGGAAGTCATATATGACGTCGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGCCATCAAACTTGTCTGGTCCTGCCACAGGGAAGTCATATATGACGTCGGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 37

GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGCCATCAAACTTGTCTGGTCCTGCCACAGGGAAGTCATATATGACGTCGGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 95

GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTGgtgagccagg ... caaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGCCATCAAACTTGTCTGGTCCTGCCACAGGGAAGTCATATATGACGTCGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catacatgaaactatatacggcaacgtaacatttccgtcccactgcaaaatccagGTTTGGCCCGGCCGGTGATCCGCGAGGCGCAGGGATCGGGACTCCGGAAGCCATCAAACTTGTCTGGTCCTGCCACAGGGAAGTCATATATGACGTCGGG
                       acgtaac  putative branch site (score: 95)
        aaactatata  TA-rich tract