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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCAATGTGGAGAGGCAGAGCTTGAAAAGAAAATAGATGAGAAGATTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatgtgatgaaaatggtgctagtaggttttttgtctttggtttttgttttactgtaaataatttttttgatagggttgtgaattggatggtgcag

Basic information

species Glycine max
transcript GLYMA17G21590.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G21590.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G66930.2 (Arabidopsis thaliana), 5'ss of exon 4
GTGCAATGTGGAGAGGCAGAGCTTGAAAAGAAAATAGATGAGAAGATTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcg-atgtgatgaaaat--------------ggtgctagtaggttttttgtctttggtttttgttttactgtaaataatttttttgatagggttgtgaattggatggtgcag---------------------------------------------------------------------
|| ||||| || ||    ||  | || |||||||| ||||| ||||||||||||||  ||   ||| | ||||| ||||||||||| |||||||||||      |  | |  ||                   ||  |||        | |        ||  |    |    | | |   |||    ||  |   |  ||| ||  || ||                                                                     
GTACAATGCGGTGAAATTGAAGTGGAGAAGAAAATCGATGAAAAGATTGAGCAGTTCATTAACTGGATTGAGAAACACCCAAACAAAAAGAGTCAGgtatatacagataacaaatgcttgatttccatttcattgacagtgaaccacatattccataccttgctcaagcaaggattgaacgtttctgcagcatatagggttgtataatgaagtaatgatctcatccttttcattgtctcatcctttgtggctgttaatgatctctttttctttttgccaag

upper sequence: GLYMA17G21590.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv00s0253g00070.t01 (Vitis vinifera), 5'ss of exon 4
GTGCAATGTGGAGAGGCAGAGCTTGAAAAGAAAATAGATGAGAAGATTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatgtga--tgaaaatggtgctagtaggttttttgtctttggtttttgttttactgtaaat--aatttttttgatagggttgtgaattgg-atggtgcag
|| ||||||||||| |||||  |||||| ||| ||  ||||||||||||| |||||  |  ||||||| ||||| |||||||||||||| ||||||||    ||| |    |   | |     | |   |   || || | ||| | |  ||||| |  |  |   |  |  | |||     | |  |||   ||       
GTACAATGTGGAGATGCAGAAGTTGAAAGGAAGATCAATGAGAAGATTGACCAGTTCATCAGTTGGGTAGAGAAACACCCAAACAAGAAAAGTCAGgttcatgattttcctttggattttcatttgcctggaattggtttgtggatataattttaatccatcttagagctcctagatgttaatttacatttatata------
















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|7589649|gb|AW705419.1|AW705419
EST:     TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAG                         ATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
genomic: TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatg ... gatggtgcagATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
EST: gi|15204778|gb|BI427546.1|BI427546
EST:     TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAG                         ATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
genomic: TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatg ... gatggtgcagATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
EST: gi|213596239|gb|DB960171.1|DB960171
EST:     TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAG                         ATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
genomic: TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatg ... gatggtgcagATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
EST: gi|33387938|gb|CA851145.1|CA851145
EST:     TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAG                         ATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
genomic: TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatg ... gatggtgcagATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
EST: gi|42722958|gb|CK768857.1|CK768857
EST:     TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAG                         ATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
genomic: TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatg ... gatggtgcagATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
EST: gi|151412937|gb|EV282749.1|EV282749
EST:     TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAG                         ATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
genomic: TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatg ... gatggtgcagATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
EST: gi|9564745|gb|BE474254.1|BE474254
EST:     TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAG                         ATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
genomic: TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatg ... gatggtgcagATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
EST: gi|15284740|gb|BI468631.1|BI468631
EST:     TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAG                         ATATGTTTATCTTTCTATGAG
genomic: TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatg ... gatggtgcagATATGTTTATCTTTCTATGAG
EST: gi|298184471|gb|HO029684.1|HO029684
EST:     TTGAGCAGTCTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAG                         ATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
genomic: TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatg ... gatggtgcagATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
EST: gi|13563309|gb|BG551529.1|BG551529
EST:     CCCAAACAAGAAGAGTCAG                         ATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
genomic: CCCAAACAAGAAGAGTCAGgtcagcgatg ... gatggtgcagATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
EST: gi|298180729|gb|HO022168.1|HO022168
EST:     TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACGAGAAGAGTCAG                         ATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
genomic: TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatg ... gatggtgcagATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
EST: gi|14125643|gb|BG790081.1|BG790081
EST:     TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAG                         ATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
genomic: TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatg ... gatggtgcagATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
EST: gi|298171918|gb|HO021510.1|HO021510
EST:     TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAG                         ATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
genomic: TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatg ... gatggtgcagATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
EST: gi|16347736|gb|BI973331.1|BI973331
EST:     TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAG                         ATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT
genomic: TTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatg ... gatggtgcagATATGTTTATCTTTCTATGAGGTGAAGAACAAACAGGCGTCTTGGTTCAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCAATGTGGAGAGGCAGAGCTTGAAAAGAAAATAGATGAGAAGATTGAGCAGTTTGTTTGTTGGGTGGAGAAGCACCCAAACAAGAAGAGTCAGgtcagcgatgtgatgaaaatggtgctagtaggttttttgtctttggtttttgttttactgtaaataatttttttgatagggttgtgaattggatggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG