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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttgtgatttctaactttctttattgttgttatatcttatttgcaagtgttttgaactgttgatctcatattttgctttagccttttaatattg...

Basic information

species Glycine max
transcript GLYMA10G28530.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G28530.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 5'ss of exon 9
CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttgtgatttctaactttctttattgttgttatatcttatttgcaagtgttttgaactgttgatctcatattttgctttagccttttaatattg--
||| |||| ||||| ||||||||||| ||||| ||||||||||||||||||||||      ||  ||  |   | | | ||      |||| ||   |||||     ||  |    |   |      |     |   |  | |   |      
CCTCTGTTTCCTGGAGAGAGTGGAGTCGATCAGCTTGTTGAGATTATCAAGgtaactacattgtatttcag--tacatcatgcaaaatatagctcgattgcattaaattaaatacatcttttctgagtggaattaccggatctaggtgggagg

upper sequence: GLYMA10G28530.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 5'ss of exon 8
CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatcttt--gtgatttctaactttctttattgttgttatat-cttatttgcaagtgttttgaactgttgatctcatattttgctttagccttttaatattg------------------------
||| ||||||| || ||||||||||| |||||| | || |||||||||||||||        | | |      | || | |      ||    | |||  ||||  ||  |      ||  |   |  |||  |||| | |  | | | |||                          
CCTCTGTTCCCCGGAGAGAGTGGAGTGGATCAATTGGTGGAGATTATCAAGgtagggcacaggcggtgcacggcgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggggtgttatgatgctgtggagtgtgagtatgttattgaggagtacttgtgtggcag

upper sequence: GLYMA10G28530.1 (Glycine max), 5'ss of exon 9
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 5'ss of exon 8
CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttgtgatttctaactttctt-tattgttgttatatcttatttgcaagtgttttgaac-tgttgatctcatattttgctttagcctttta-atattg-----------------------------------------------------------------------------------------
|||||||||||||| || || |||||||||||| | || ||||| |||||||||   | |      |  |         ||| |   | |  || | | | |   |||||      | | |||   |  | |||  |||   ||  | || ||                                                                                          
CCTTTGTTCCCTGGAGAAAGCGGAGTTGATCAATTGGTGGAGATCATCAAGgtatgttatacatggtagagtggaagcatatggagctgaagtcgtttgtactgatgtttgatgtgtatcgattaaaagtattgtattatatttaaagatgttagctgctcttgttgcttcgggtggtgttgcggtgatagcgcaagagtgatactgtagagcttatgagtaggcggatggtgatgttgacag

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|9983502|gb|BE657610.1|BE657610
EST:     GGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTNNGGGCANTCCAACAAGGGAAGAGATTAAGTGCATGNNNCCTAATTAT
genomic: GGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|151395928|gb|EV265805.1|EV265805
EST:     CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|21677182|gb|BQ629533.1|BQ629533
EST:     CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|27426035|gb|CA937555.1|CA937555
EST:     CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|9205358|gb|BE331582.1|BE331582
EST:     CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|6566727|gb|AW234359.1|AW234359
EST:     CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|151411363|gb|EV281174.1|EV281174
EST:     CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|16104780|gb|BI892520.1|BI892520
EST:     CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|19453358|gb|BM954768.1|BM954768
EST:     CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|10710608|gb|BF010326.1|BF010326
EST:     CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|5058458|gb|AI736869.1|AI736869
EST:     TTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGGAGAATATCAAG                         GTTCTGGGCACTCCCACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: TTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTG-AGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|31307101|gb|CD392304.1|CD392304
EST:     AGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: AGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|10843615|gb|BF066891.1|BF066891
EST:     CTGTGTTCCCTGGTGAGAGTGGAGTTGATCAACTAGTTGAGATTATCAAT                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATTGA-CCCTAATTA
genomic: CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCAT-GAACCCTAATTA
EST: gi|24206278|gb|BU965531.1|BU965531
EST:     CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTATTTAT
genomic: CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|6073128|gb|AW102515.1|AW102515
EST:     CTTTGTTCCCTGGTGAGAGTGGAGT-GATCAACTTGTTGAGATTATCAAG                         -TTCTGGGCACTTCAACAAGGGAAGAGAT-AAGTGCATGAACCCCTA-TTA
genomic: CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCC-TAATTA
EST: gi|7926372|gb|AW832398.1|AW832398
EST:     CTTTGTTCCCTGGAGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGATATTAAGTGCATGAACCCTAATTAT
genomic: CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|23729240|gb|BU762707.1|BU762707
EST:     CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: CTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
EST: gi|254344096|gb|GR851006.1|GR851006
EST:     TGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG                         GTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT
genomic: TGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttg ... gtgttaatagGTTCTGGGCACTCCAACAAGGGAAGAGATTAAGTGCATGAACCCTAATTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAGgtaatctttgtgatttctaactttctttattgttgttatatcttatttgcaagtgttttgaactgttgatctcatattttgctttagccttttaatattg

- - - - - - - - - AGTGGA
- - - - - - - - -  GTGGAG