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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttctctctctctctcaatttctaaattttctatttctttttctctcttaattgtttagtttttatgataagagattagaatattgcggtgtttcacgattattttggtttctgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGCTGCCTATGGCAATTCGGCAAGACACGATCGTGGCGATTCGGAAAAATGA

Basic information

species Glycine max
transcript GLYMA17G03990.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 1
------------------------------gttcttctctctctctctca----------------atttctaaattttctatttctttttctctctta---attgt--ttagtttttatgataagagattagaatattgcggtgtttc--acgatt--attttggtttctgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGCTGCCTATGGCAATTCGGCAAGACACGATCGTGGCGATTCGGAAAAATGA
                              |||  ||      | | | |                |||| |  | ||| | |   |   | | |  |    |||||  |  ||||  |||||       | || ||| | |  ||||   | | ||  |||||   || |  |||||||| || ||||| ||||| || |||||||||||||||||||| ||||||||| |||| |||||||| ||||| |||||||||||||||||||||||  ||||
gtcggtaacacgcgtgttcatagtttttctgttggtcgtgtattgtatgacgaggaaaaggaggagatttttggagtttttgtgagtgggtgtgtggtggggattgtggtgggtttggatgattgattgatggagtatcgggaggtttttgatggttttattttttatttttgggtgcagGGAGGGTGAATTTGATAGGAGAGCACATTGATTATGAAGGCTATTCGGTGTTGCCGATGGCAATACGGCAGGACACGATCGTGGCGATTCGGAAGCATGA

upper sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S89_154V6.3 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------gttcttctctctctctctcaatttctaaattttctatttctttttctctcttaattgtttagtttttatgataagagattagaatattgcggtgtttcacgattattttggtttctgcg----gtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGCTGCCTATGGCAATTCGGCAAGACACGATCGTGGCGATTCGGAAAAATGA
                                                                       |     | | | | ||     ||   | || | ||| | |||||||   |  | |   | | ||   |  |||||   |  |    |||         | |   |||||  |||    ||| ||| ||||||||  | || || |||||||| ||||| || |||||||| ||||| || ||||||||||| ||||||||| | || || ||  | |     ||
gtttgattttacaaatgcaaccccatcatttttctctgtttagataattatgtgttcataattaaacagagttcgagttttttttaacaggaaagcatactctctctctctctctctctctc-tctctctctcattgaagcagattgttacttacttgtgaagattctgtctgagggttttcgcgatttgtgtagGGAGAGTGAATCTAATAGGAGAGCACATCGATTACGAGGGTTATTCCGTGCTTCCAATGGCAATTCGCCAAGACACGGTGGTTGCTATCGGTAGGCGAGA

upper sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ17214 (Selaginella moellendorffii), 3'ss of exon 1
gttcttctctctctctctcaatttctaaattttctatttctttttctctcttaattgtttagtttttatgataagagattagaatattgcggtgt-ttcacgattattttggtttctgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGCTGCCTATGGCAATTCGGCAAGACACGATCGTGGCGATTCGGAAAAATGA
                                                             |||||  |||||      | || |  ||   ||  ||  |||||     | |  | |   ||||||  |||||||  | || || |||||||| ||||| ||||| || ||||||||||| ||||||||||| || ||||| || || |||||| ||| |     
-------------------------------------------------------------gttttcttgatatttcgctcgatttgtggattggattggcgattggcg-gctcccgggaatgcagGTCGAGTGAATCTTATCGGCGAGCACATCGATTACGAAGGCTACTCGGTGCTGCCAATGGCAATTCGCCAGGACACAATTGTCGCGATTGGGAGATCCTC

upper sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ30960 (Selaginella moellendorffii), 3'ss of exon 1
gttcttctctctctctctcaatttctaaattttctatttctttttctctcttaattgtttagtttttatgataagagattagaatattgcggtgt-ttcacgattattttggtttctgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGCTGCCTATGGCAATTCGGCAAGACACGATCGTGGCGATTCGGAAAAATGA
                                                             |||||  |||||      | || |  ||   ||  ||  |||||     | |  | |   ||||||  |||||||  | || || |||||||| ||||| ||||| || ||||||||||| |||||||| || || |||||||| || |||||| ||| |     
-------------------------------------------------------------gttttcttgatattttgctcgatttgtggattggattggcgattggcg-gctcccgggaatgcagGTCGAGTGAATCTTATCGGCGAGCACATCGATTACGAAGGCTACTCGGTGCTGCCAATGGCAATCCGCCAGGACACGATTGTCGCGATTGGGAGATCCTC

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|298199023|gb|HO042386.1|HO042386
EST:     ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTG                         GAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
genomic: ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTGgttcttctct ... tgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
EST: gi|209699970|gb|BW661199.1|BW661199
EST:     ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTG                         GAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
genomic: ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTGgttcttctct ... tgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
EST: gi|193577947|gb|FK537027.1|FK537027
EST:     ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTG                         GAAGAGTGAACTTGATTGGGGAGCACA
genomic: ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTGgttcttctct ... tgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACA
EST: gi|213611707|gb|DB969095.1|DB969095
EST:     ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTG                         GAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
genomic: ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTGgttcttctct ... tgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
EST: gi|298190390|gb|HO032511.1|HO032511
EST:     ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTG                         GAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
genomic: ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTGgttcttctct ... tgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
EST: gi|192321624|gb|FK013968.1|FK013968
EST:     ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTG                         GAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
genomic: ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTGgttcttctct ... tgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
EST: gi|208192805|gb|GD989240.1|GD989240
EST:     ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTG                         GAAGAGTGAACTTGATTGGG
genomic: ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTGgttcttctct ... tgcggtgcagGAAGAGTGAACTTGATTGGG
EST: gi|13481495|gb|BG510838.1|BG510838
EST:     GTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTG                         GAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
genomic: GTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTGgttcttctct ... tgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
EST: gi|19453433|gb|BM954843.1|BM954843
EST:     ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTG                         GAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
genomic: ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTGgttcttctct ... tgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
EST: gi|213597925|gb|DB958306.1|DB958306
EST:     ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTG                         GAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
genomic: ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTGgttcttctct ... tgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
EST: gi|209712397|gb|BW671249.1|BW671249
EST:     ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTG                         GAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC
genomic: ATTCGTCGAAATCTTCGGTCATCATCCTCAAATCTTCGCTCGCTCACCTGgttcttctct ... tgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagagattagaatattgcggtgtttcacgattattttggtttctgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGCTGCCTATGGCAATTCGGCAAGACACGATCGTGGCGATTCGGAAAAATGA
                                         tttctgc  CT-rich tract
       attagaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttctctctctctctcaatttctaaattttctatttctttttctctcttaattgtttagtttttatgataagagattagaatattgcggtgtttcacgattattttggtttctgcggtgcagGAAGAGTGAACTTGATTGGGGAGCACATTGATTATGAAGGTTATTCGGTGCTGCCTATGGCAATTCGGCAAGACACGATCGTGGCGATTCGGAAAAATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA