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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttatgagaatttttttcctaaaattttcccttgtaatgtatgaggtgttgatttatatgattgctttttctttccctttttcgttgtttagAATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCTGATATGATGTCT

Basic information

species Glycine max
transcript GLYMA10G40390.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G40390.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0091g00700.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------------gtaagtgttatgagaatttttttcctaaaattttccc-----ttgtaatgtatgaggtgttgatttatatgattgctttttctttccctttttcgttgtttagAATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCTGATATGATGTCT
                                            ||  ||  |    || |  ||| || |  ||  |       || | || |   | || |  ||        ||    |||  |||  |  | |  |  ||||||||||||||  ||||| || ||||| ||||||||||||||| | || ||||||   ||| | 
gttagctctggaatacattattttaataatactgttttcttcactatttgagacactaaataattttctgaggttgccttagtttttctcatcttcaaagtttgtatcccatctgttttaatttggttctatgatgcaattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG
















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|163921554|gb|EH039313.1|EH039313
EST:     ATAACCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTG                         AATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCT
genomic: ATAACCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTGgtaagtgtta ... cgttgtttagAATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCT
EST: gi|5760477|gb|AI965840.1|AI965840
EST:     CCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTG                         AATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCT
genomic: CCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTGgtaagtgtta ... cgttgtttagAATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCT
EST: gi|193521422|gb|FK481653.1|FK481653
EST:     TAACCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTG                         AATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCC
genomic: TAACCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTGgtaagtgtta ... cgttgtttagAATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCT
EST: gi|193547391|gb|FK501888.1|FK501888
EST:     ATAACCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTG                         AATGAGAAGAATGAGACCGTGGGATCAGAA-CTGAGGCATATTCCATAGCT
genomic: ATAACCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTGgtaagtgtta ... cgttgtttagAATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCT
EST: gi|209699127|gb|BW656167.1|BW656167
EST:     ATAACCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTG                         AATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCT
genomic: ATAACCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTGgtaagtgtta ... cgttgtttagAATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCT
EST: gi|208316513|gb|GE110185.1|GE110185
EST:     ATAACCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTG                         AATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCA
genomic: ATAACCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTGgtaagtgtta ... cgttgtttagAATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCA
EST: gi|22541066|gb|BU090909.1|BU090909
EST:     ATAACCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTG                         AATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCT
genomic: ATAACCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTGgtaagtgtta ... cgttgtttagAATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCT
EST: gi|193698567|gb|FK637146.1|FK637146
EST:     ATAACCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTG                         AATGAGAAGAATGAGACCG
genomic: ATAACCCTAGCAAACCTATTTACCTGTATATTAATTCATCTGGAACTCTGgtaagtgtta ... cgttgtttagAATGAGAAGAATGAGACCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatgaggtgttgatttatatgattgctttttctttccctttttcgttgtttagAATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCTGATATGATGTCT
         tgttgat  putative branch site (score: 4)
                        ttgctttttctttccc  putative PPT
           ttgatttatatgatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgttatgagaatttttttcctaaaattttcccttgtaatgtatgaggtgttgatttatatgattgctttttctttccctttttcgttgtttagAATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCTGATATGATGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT