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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCGGGGTGGAGGTTCTCGACTTCCCCGCCGGGGAGGGCCTCCCTGCCGTCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacactagcactttttccgccgtatgccttcttcaacgcccctgcccccttctgagatgctctgctctgctgcgtgccgcag

Basic information

species Zea mays
transcript GRMZM2G011456_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011456_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g04660.1 (Oryza sativa), 5'ss of exon 1
CTGCGGGGTGGAGGTTCTCGACTTCCCCGCCGGGGAGGGCCTCCCTGCCGTCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacactagcactttttccgccgtatgccttcttcaacgcccctgcccccttctgagatgctctgctctgctgcgtgccgcag-----------
||||||||||||||| ||||||||||||||||| ||||  ||||| |||||||||   ||||||||| ||||| ||||||||||| |||||||||| || ||| | ||     ||||    || |||    ||||  || |  || |  | ||  |||||||      ||||   ||   |  |  |           
CTGCGGGGTGGAGGTGCTCGACTTCCCCGCCGGCGAGGAGCTCCCCGCCGTCCTCTCCCACTCCCTCTCCTCCTCCTTCGACTTCCTCCTCGCCCCCCTCgtgagtactactccactagcgcctccgc---ccttactcgattccgc--ctcctctctgagactactagctcacttggtggtggtggcgctgctgcag
















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|211230909|gb|FL222478.1|FL222478
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|211230907|gb|FL222476.1|FL222476
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|211230912|gb|FL222481.1|FL222481
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|71311078|gb|DR791853.1|DR791853
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|71300983|gb|DR786520.1|DR786520
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|211230911|gb|FL222480.1|FL222480
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|89762829|gb|DY690269.1|DY690269
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|91876145|gb|EB406102.1|EB406102
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|74233408|gb|DT641322.1|DT641322
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|37419121|gb|CF647236.1|CF647236
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|211230918|gb|FL222487.1|FL222487
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|211230908|gb|FL222477.1|FL222477
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|149109143|gb|EE190035.2|EE190035
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|37418481|gb|CF646909.1|CF646909
EST:     CCTCAATCACTCCCTCGCCTCCGCGCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCG
genomic: CCTCAATCACTCCCTCGCCTCCGC-CTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCG
EST: gi|211228853|gb|FL222474.1|FL222474
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACT-CATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|89251153|gb|DY622939.1|DY622939
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|211230914|gb|FL222483.1|FL222483
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACT-CATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|71434207|gb|DR815257.1|DR815257
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|78117239|gb|DV535626.1|DV535626
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
EST: gi|211230910|gb|FL222479.1|FL222479
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCC-AACTACCGGCCGGCGCCCGGTCGC-GTTCTGCCAGTGTCAGC
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGG-CGCCGTTCTGCCAGTGTCAGC
EST: gi|211230917|gb|FL222486.1|FL222486
EST:     TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTG                         GTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG
genomic: TCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCG

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 31

CTGCGGGGTGGAGGTTCTCGACTTCCCCGCCGGGGAGGGCCTCCCTGCCGTCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCGTCGGACCTCGTCCTCGGCCCGTCCCAGTGGAGCAACCACGTCGTCGGGA


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 15

CTGCGGGGTGGAGGTTCTCGACTTCCCCGCCGGGGAGGGCCTCCCTGCCGTCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCGTCGGACCTCGTCCTCGGCCCGTCCCAGTGGAGCAACCACGTCGTCGGGA


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 21

CTGCGGGGTGGAGGTTCTCGACTTCCCCGCCGGGGAGGGCCTCCCTGCCGTCCTCAATCACTCCCTCGCCTCCGCCTTCGACTTCATCCTCGCCCCTCTGgtgggcacac ... cgtgccgcagGTTGATCCCAACTACCGGCCGGCGCCCGGCGCCGTTCTGCCAGTGTCAGCGTCGGACCTCGTCCTCGGCCCGTCCCAGTGGAGCAACCACGTCGTCGGGA