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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgccaatttccctcttgggttcgagttcgagggggtttgattctgatgtcagtggtttgcggcgtggctgcttgtgcagcagCGACGGGGGCGCGTTCGCAAACGCGGAGAACCTGGAGCACTGCGCCCGGTACCTGAACCAGACGCTCGTCACCTTCGGATTCCCGGCATCTCTCGACCTC

Basic information

species Zea mays
transcript GRMZM2G147500_T06
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147500_T06 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 1
----------------------------------------------gtgagcgccaatttccctcttgggttcgagttcgag----ggggtttgattctgatgtcagtggtttgcggcgtg-gctgcttgtgcagcagCGACGGGGGC---------------GCGTTCGCAAACGCGGAGAACCTGGAGCACTGCGCCCGGTACCTGAACCAGACGCTCGTCACCTTCGGATTCCCGGCATCTCTCGACCTC
                                               |  || ||        | |  |||| | ||| | |    || |  |||||  | ||   | | || | || ||| | || |||||  |||| ||||| |||               ||||||||  |||||| |||||| |||||||||||| ||||||| ||||||||||||||||||||||| ||||||               
gtgaggcgcgggcgatctcgtctcctccggggtttcggttttgtgcttttgcaccttggggtttttgaggttggggttggggtggcggtggctgatttggttggttg-gtttggtggtgtgtgatgtttgtgtcgcagTGACGGTGGCGGTGGCGCGGCGGCGGCGTTCGCGGACGCGGGGAACCTCGAGCACTGCGCCAGGTACCTCAACCAGACGCTCGTCACCTTCGGCTTCCCG---------------

upper sequence: GRMZM2G147500_T06 (Zea mays), 3'ss of exon 2
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 2
gtgagcgccaatttccctcttgggttcgagttcgagggggtttgattctgatgtcagtggtttgcggcgtggctgcttgtgcagcagCGACGGGGGCGCGTTCGCAAACGCGGAGAACCTGGAGCACTGCGCCCGGTACCTGAACCAGACGCTCGTCACCTTCGGATTCCCGGCATCTCTCGACCTC---
    |  |   || | || ||    | ||      ||  |  || |  ||    | ||| ||  |   | |  || |||||      |   | | |||| |||||  | ||||  ||| ||||||| || |||  |||  |||||||||||||||| || |||||||||||||| || ||||| ||    
----gtacgctttcctctgtttttgtggatgctagggttggctggtcttggaaactgtgtttctctaag-gtttggttgtgtt-tttcagGGAGTGCGCCTTCGCGGATGCGGGAAACTTGGAGCATTGTGCCAAGTATTTGAACCAGACGCTCGTGACGTTCGGATTCCCGGCCTCGCTCGATCTGTTC
















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|211122100|gb|FL004254.1|FL004254
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211124440|gb|FL004295.1|FL004295
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211123652|gb|FL004272.1|FL004272
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211123651|gb|FL004271.1|FL004271
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAG                         CAGCGACGGGGGCGCGTTCGCNAACGCGGAGAACCTGGAGCACTGCGCCCG
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGgtgagcgcca ... tgtgcagcagC-G--ACGGGGGCGCGTTCGCAAACGCGGAGAACCTGGAGCACTGCGCCCG
EST: gi|211122095|gb|FL004249.1|FL004249
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211124434|gb|FL004289.1|FL004289
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAG                         CAGCGACGGGGGCGCGTTCGCAAACGCGGAGAACCTGGAGCACTGCGCCCG
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGgtgagcgcca ... tgtgcagcagC-G--ACGGGGGCGCGTTCGCAAACGCGGAGAACCTGGAGCACTGCGCCCG
EST: gi|149081286|gb|EE170399.2|EE170399
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|22715261|gb|BU197668.1|BU197668
EST:     GCCTCGTCGCAGCAGTTGCAGCCGCCACCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211123661|gb|FL004281.1|FL004281
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAG                         CAGCGACGGGGGCGCGTTCGCAAACGCGGAGAACCTGGAGCACTGCGCCCG
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGgtgagcgcca ... tgtgcagcagC-G--ACGGGGGCGCGTTCGCAAACGCGGAGAACCTGGAGCACTGCGCCCG
EST: gi|211124431|gb|FL004286.1|FL004286
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|31611780|gb|CD568402.1|CD568402
EST:     CGGGCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: CGGGCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211122101|gb|FL004255.1|FL004255
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|26559425|gb|CA831660.1|CA831660
EST:     GCCTCGTCGCAGCAGTTGCAGCCGCCACCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211124438|gb|FL004293.1|FL004293
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|76923168|gb|DV169366.1|DV169366
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211123664|gb|FL004284.1|FL004284
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211122872|gb|FL004261.1|FL004261
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211122880|gb|FL004269.1|FL004269
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|87156724|gb|DY401513.1|DY401513
EST:     GCCTCGTCGCAGCAGTTGCAGCCGCCACCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211125213|gb|FL004301.1|FL004301
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211124442|gb|FL004297.1|FL004297
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211122098|gb|FL004252.1|FL004252
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211124441|gb|FL004296.1|FL004296
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|26558350|gb|CA830585.1|CA830585
EST:     GCCTCGTCGCAGCAGTTGCAGCCGCCACCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211122868|gb|FL004257.1|FL004257
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211124436|gb|FL004291.1|FL004291
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211122097|gb|FL004251.1|FL004251
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211122881|gb|FL004270.1|FL004270
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc
EST: gi|211124432|gb|FL004287.1|FL004287
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAG                         CAGCGACGGGGGCGCGTTCGCAAACGCGGAGAACCTGGAGCACTGCGCCCG
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGgtgagcgcca ... tgtgcagcagC-G--ACGGGGGCGCGTTCGCAAACGCGGAGAACCTGGAGCACTGCGCCCG
EST: gi|211123653|gb|FL004273.1|FL004273
EST:     GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGCAG                       
genomic: GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCAT--G-AGgtgagcgcca ... tgtgcagc

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: 47 (upstream exon), 49 (downstream exon)
Score: 305

GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGgtgagcgcca ... tgtgcagcagCGACGGGGGCGCGTTCGCAAACGCGGAGAACCTGGAGCACTGCGCCCGGTACCTGAACCAGACGCTCGTCACCTTCGGATTCCCGGCATCTCTCGACCTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 100

GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGgtgagcgcca ... tgtgcagcagCGACGGGGGCGCGTTCGCAAACGCGGAGAACCTGGAGCACTGCGCCCGGTACCTGAACCAGACGCTCGTCACCTTCGGATTCCCGGCATCTCTCGACCTC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 81

GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGgtgagcgcca ... tgtgcagcagCGACGGGGGCGCGTTCGCAAACGCGGAGAACCTGGAGCACTGCGCCCGGTACCTGAACCAGACGCTCGTCACCTTCGGATTCCCGGCATCTCTCGACCTC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 152

GCCTCGTCGCATCAGTTGCAGCCGCCGCCGTCGCACGCCAGCATGAGgtgagcgcca ... tgtgcagcagCGACGGGGGCGCGTTCGCAAACGCGGAGAACCTGGAGCACTGCGCCCGGTACCTGAACCAGACGCTCGTCACCTTCGGATTCCCGGCATCTCTCGACCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagggggtttgattctgatgtcagtggtttgcggcgtggctgcttgtgcagcagCGACGGGGGCGCGTTCGCAAACGCGGAGAACCTGGAGCACTGCGCCCGGTACCTGAACCAGACGCTCGTCACCTTCGGATTCCCGGCATCTCTCGACCTC
             ttctgat  putative branch site (score: 152)
        tttgatt  TA-rich tract