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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACTGCTATGCCCCCAACAAAGCGCTTCCGTGATATGGAGCAGCTATCTGGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAGgtaggagttgtttgtactactacttggattagaacaagaatattttataactactctgaatttgtgttttaataacaaaaattcatctaagcaatatactgacacatctcacataagcctaaaactattttgctgatatcttatcttcttgttccattaatatggttccctacttacttcttgtttcag

Basic information

species Glycine max
transcript GLYMA10G04300.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G04300.1 (Glycine max), 5'ss of exon 17
lower sequence: AT3G54670.3 (Arabidopsis thaliana), 5'ss of exon 16
ACACTGCTATGCCCCCAACAAAGCGCTTCCGTGATATGGAGCAGCTATCTGGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAGgtaggagttgtttgtactactacttggattagaacaagaatattttataactactctgaatttgtgttttaataacaaaaattcatctaagcaatatactgacacatctcacataagcctaaaactattttgctgatatcttatcttcttgttccattaatatggttccctacttacttcttgtttcag
| ||| | ||||||||||||||||| || ||||| ||||| ||||| ||||| || || || |||||||| ||  | || ||||| |||||||| ||||||||         |   | || || | ||| |   ||    | ||  ||    |   ||| |||||   || |||      ||| ||||  |   | || |  |||   |   |                                                                            
ATACTACAATGCCCCCAACAAAGCGATTTCGTGACATGGAACAGCTCTCTGGAGGAGAGAAAACAGTTGCGGCCTTGGCGTTGCTCTTCTCCATACATAGgta---------tcctcaacgacctagat-atcccatttgt-ttcaatgttaaaagtgattttgtaggttcatattg---atttatctgtggtgtttagtttcactctttgaaa---------------------------------------------------------------------------

upper sequence: GLYMA10G04300.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv07s0005g03440.t01 (Vitis vinifera), 5'ss of exon 11
ACACTGCTATGCCCCCAACAAAGCGCTTCCGTGATATGGAGCAGCTATCTGGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAGgtaggagttgtttgtactactacttggattagaacaagaatattttataactactctgaatttgtgttttaataacaaaaattcatctaagcaatatactgacacatctcacataagcctaaaactattttgctgatatcttatcttcttgttccattaatatggttccctacttacttcttgtttcag
|||||||||||||||||||||||||||||||||||||||| ||||| |||||||| || || || ||||| |||||||||||||| ||||| |||||||||||     |||              ||| || || ||  || |||| |   |  | || |      ||    |       || ||   |    || |  ||| | || |    |||                                                                         
ACACTGCTATGCCCCCAACAAAGCGCTTCCGTGATATGGAACAGCTGTCTGGTGGTGAGAAAACTGTTGCAGCACTTGCATTGCTCTTCTCTATCCATAGgta-----tgtcaa-----------ggaatacaagaaacattttttctgtatgttttggacaaaccttactctgg-----atgcaggaataacatgtcttgaaatattttgtttaatttct--------------------------------------------------------------------
















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|192323291|gb|FK017052.1|FK017052
EST:     GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAG                         TTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
genomic: GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAGgtaggagttg ... cttgtttcagTTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
EST: gi|298174268|gb|HO017604.1|HO017604
EST:     GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAG                         TTATAAGCCTTCCCCATTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
genomic: GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAGgtaggagttg ... cttgtttcagTTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
EST: gi|214004496|gb|DB985080.1|DB985080
EST:     TCCATCCATAG                         TTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
genomic: TCCATCCATAGgtaggagttg ... cttgtttcagTTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
EST: gi|31472073|gb|CD414101.1|CD414101
EST:     GTTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAG                         TTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
genomic: GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAGgtaggagttg ... cttgtttcagTTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
EST: gi|254336329|gb|GR842508.1|GR842508
EST:     GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAG                         TTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
genomic: GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAGgtaggagttg ... cttgtttcagTTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
EST: gi|120493576|gb|EH221743.1|EH221743
EST:     GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAG                         TTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
genomic: GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAGgtaggagttg ... cttgtttcagTTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
EST: gi|31458556|gb|CD400584.1|CD400584
EST:     GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAG                         TTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
genomic: GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAGgtaggagttg ... cttgtttcagTTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
EST: gi|23063907|gb|BU578681.1|BU578681
EST:     GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAG                         TTATTTGTCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGG
genomic: GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAGgtaggagttg ... cttgtttcagTTACAAG-CCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGG
EST: gi|254336328|gb|GR842507.1|GR842507
EST:     GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAG                         TTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
genomic: GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAGgtaggagttg ... cttgtttcagTTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
EST: gi|22524955|gb|BU083766.1|BU083766
EST:     GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAG                         TTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
genomic: GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAGgtaggagttg ... cttgtttcagTTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
EST: gi|11687513|gb|BF595189.1|BF595189
EST:     GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAG                         TTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA
genomic: GGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAGgtaggagttg ... cttgtttcagTTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACTGCTATGCCCCCAACAAAGCGCTTCCGTGATATGGAGCAGCTATCTGGTGGGGAAAAGACAGTTGCTGCACTTGCATTGCTATTCTCCATCCATAGgtaggagttgtttgtactactacttggattagaacaagaatattttataactactctgaatttgtgttttaataacaaaaattcatctaagcaatatactgacacatctcacataagcctaaaactattttgctgatatcttatcttcttgttccattaatatggttccctacttacttcttgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC