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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAATACATTTTGCCCAAGTTTTTCAAAGGGGCACATCTTCAAGATTTAGATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGTgtaagttttcaattctttcgctctgaattagagtccttatgcacttttggtttctcttccttcatcatattttcacgttaaaatctgggaaaagaaaagaacttacacccagtggcttatttcagtttataaattttctgtacttgctgtgttcttagcag

Basic information

species Vitis vinifera
transcript Vv05s0020g00440.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g00440.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA09G03600.1 (Glycine max), 5'ss of exon 14
ACAATACATTTTGCCCAAGTTTTTCAAAGGGGCACATCTTCAAGATTTAGATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGTgtaagttttcaattctttcgctctgaattagagtccttatgcacttttggtttctcttccttcatcatattttcacgttaaaatctgggaaaagaaaagaacttacacccagtggcttatttcagtttataaattttctgtacttgctgtgttcttagcag
 ||||||||| ||||||||||||| ||||| ||||| ||||||||||||||||| |||||||||||||| || ||||||||| |||||||| |   || ||||||| ||||||             | ||||| ||   | |||||||     || ||     | |||| |     |        ||| ||||  |||  |  || ||  | |   ||||                                         
GCAATACATTCTGCCCAAGTTTTTTAAAGGAGCACACCTTCAAGATTTAGATGCTGCAGAATATGAAGAAGTACCTGCTTTACCATTCAACTTAGTGACTgtaagtattcaat-------------actagag-ccaagttcactttt-----ctatttagcta-catactagggggggttctcttggtaaaaagaaactatctatactta-tatgttatg----------------------------------------
















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|110692037|gb|EE070827.1|EE070827
EST:     ATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGT                         GAGAGGGAGCTGAGTAGGAGAAGTTCATTTGTAGACCATGGAGAGGTTTTA
genomic: ATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGTgtaagttttc ... ttcttagcagGAGAGGGAGCTGAGTAGGAGAAGTTCATTTGCAGACCATGGAGAGGTTTTA
EST: gi|110362963|gb|EC926527.1|EC926527
EST:     ATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGT                         GAGAGGGAGCTGAGTAGGAGAAGTTCATTTGCAGACCATGGAGAGGTTTTA
genomic: ATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGTgtaagttttc ... ttcttagcagGAGAGGGAGCTGAGTAGGAGAAGTTCATTTGCAGACCATGGAGAGGTTTTA
EST: gi|22014079|gb|BQ799113.1|BQ799113
EST:     ATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGT                         GAGAGGGAGCTGAGTAGGAGAAGTTCATTTGCAGACCATGGAGAGGTTTTA
genomic: ATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGTgtaagttttc ... ttcttagcagGAGAGGGAGCTGAGTAGGAGAAGTTCATTTGCAGACCATGGAGAGGTTTTA
EST: gi|110717152|gb|EE092758.1|EE092758
EST:     ATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGT                         GAGAGGGAGCTGAGTAGGAGAAGTTCATTTGTAGACCATGGAGAGGTTTTA
genomic: ATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGTgtaagttttc ... ttcttagcagGAGAGGGAGCTGAGTAGGAGAAGTTCATTTGCAGACCATGGAGAGGTTTTA
EST: gi|110726434|gb|EE102210.1|EE102210
EST:     ATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGT                         GAGAGGGAGCTGAGTAGGAGAAGTTCATTTGTAGACCATGGAGAGGTTTTA
genomic: ATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGTgtaagttttc ... ttcttagcagGAGAGGGAGCTGAGTAGGAGAAGTTCATTTGCAGACCATGGAGAGGTTTTA
EST: gi|110422205|gb|EC988520.1|EC988520
EST:     ATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGT                         GAGAGGGAGCTGAGTAGGAGAAGTTCATTTGCAGACCATGGAGAGGTTTTA
genomic: ATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGTgtaagttttc ... ttcttagcagGAGAGGGAGCTGAGTAGGAGAAGTTCATTTGCAGACCATGGAGAGGTTTTA
EST: gi|110424761|gb|EC991132.1|EC991132
EST:     ATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGT                         GAGAGGGAGCTGAGTAGGAGAAGTTCATTTGCAGACCATGGAGAGGTTTTA
genomic: ATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGTgtaagttttc ... ttcttagcagGAGAGGGAGCTGAGTAGGAGAAGTTCATTTGCAGACCATGGAGAGGTTTTA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAATACATTTTGCCCAAGTTTTTCAAAGGGGCACATCTTCAAGATTTAGATGCCGCAGAATATGAAGAGGTTCCTGCTTTATCATTCAACCTCACGAGTgtaagttttcaattctttcgctctgaattagagtccttatgcacttttggtttctcttccttcatcatattttcacgttaaaatctgggaaaagaaaagaacttacacccagtggcttatttcagtttataaattttctgtacttgctgtgttcttagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG