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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtaatgttggaataaacttagcccctattccacgctctattattattactacatttatgatttcttaatagaatcacctttttcttgtccttgcaGCATCCCTATGTGTATGGCGTGTTGGTCTTTGAGGCAATGGCCACATTTATAGGCCAAGTTTCTGTCCTCTCCCTCATTGCTATCTTTGGTGCTGCCACC

Basic information

species Glycine max
transcript GLYMA18G46240.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G46240.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G12600.1 (Arabidopsis thaliana), 3'ss of exon 5
ggtaatgttggaataaacttagcccctattccacgctctattattattact-acatttatgatttcttaatagaatcaccttt--ttcttgtccttgcaGCATCCCTATGTGTATGGCGTGTTGGTCTTTGAGGCAATGGCCACATTTATAGGCCAAGTTTCTGTCCTCTCCCTCATTGCTATCTTTGGTGCTGCCACC-
    ||       | ||||||      |    ||  | ||| || ||   | ||   | |  ||  |||||   ||     ||  ||    |  | | ||||||| ||||||||||| |||||||| || || || ||||| |||||||| || ||||| || || || |||||||||||  ||||||| || |||||  
ttcgatcaccaccttaacttatatgacaagagacattatatgatgatcgttgactaatgtagttgattaattacatttttcttaattgacattttggtagCATCCATATGTGTATGGAGTGTTGGTGTTCGAAGCCATGGCTACATTTATCGGACAAGTCTCCGTTCTATCCCTCATTGCACTCTTTGGCGCAGCCACAA

upper sequence: GLYMA18G46240.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G23010.3 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------------------------------------------------------------------ggtaatgttggaataaacttagcccctattccacgctctatta--ttattactacatttatg---atttcttaatagaatcacctttttcttgtccttgcaGCATCCCTATGTGTATGGCGTGTTGGTCTTTGAGGCAATGGCCACATTTATAGGCCAAGTTTCTGTCCTCTCCCTCATTGCTATCTTTGGTGCTGCCACC-
                                                                                                  |||  |  | |  ||| | |    ||||  |   || |     ||| |  | ||||  |    || | | ||   |||     |||  || |  ||||||||||| ||||||||||| ||| | || ||||| || |||||||||||||| || ||||| || || ||||| || |||||| ||||||| || |||||  
gtaccacgaaatgagagagatcattgaccgacgacgtgcctctgaatctgccaaactttttaaaagccaaattgtctcttttaaattcattgattccataacttaagtaccaacgtggaa--tattttatagtcaaacggtttaatgattcattggttgacatatttaaaaccaattgtgctttgtttatatttgcagCATCCGTATGTGTATGGAGTGCTTGTATTTGAAGCCATGGCCACATTTATCGGTCAAGTCTCCGTTCTCTCGCTTATTGCTCTCTTTGGAGCCGCCACAA

upper sequence: GLYMA18G46240.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G23010.2 (Arabidopsis thaliana), 3'ss of exon 5
ggtaatgttggaataaacttagcccctattccacgctctatta--ttattactacatttatg---atttcttaatagaatcacctttttcttgtccttgcaGCATCCCTATGTGTATGGCGTGTTGGTCTTTGAGGCAATGGCCACATTTATAGGCCAAGTTTCTGTCCTCTCCCTCATTGCTATCTTTGGTGCTGCCACC-
  |||  |  | |  ||| | |    ||||  |   || |     ||| |  | ||||  |    || | | ||   |||     |||  || |  ||||||||||| ||||||||||| ||| | || ||||| || |||||||||||||| || ||||| || || ||||| || |||||| ||||||| || |||||  
cataacttaagtaccaacgtggaa--tattttatagtcaaacggtttaatgattcattggttgacatatttaaaaccaattgtgctttgtttatatttgcagCATCCGTATGTGTATGGAGTGCTTGTATTTGAAGCCATGGCCACATTTATCGGTCAAGTCTCCGTTCTCTCGCTTATTGCTCTCTTTGGAGCCGCCACAA

upper sequence: GLYMA18G46240.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0048g01060.t01 (Vitis vinifera), 3'ss of exon 5
ggtaatgttggaataaacttagcccctattccacgctctattattattactacatttatgatttcttaatagaatcacctttttcttgtccttgcaGCATCCCTATGTGTATGGCGTGTTGGTCTTTGAGGCAATGGCCACATTTATAGGCCAAGTTTCTGTCCTCTCCCTCATTGCTATCTTTGGTGCTGCCACC-
      ||    | ||  | |     || | |   || || |   || || | | |    |||||| |||||  ||   || ||  | ||| |||||||||  || |||||||| |||||||| ||||| || |||||||| || || |||||||| || |||||||||||||| || ||||| |||||||||||  
------gtgaccaaaagatgattatttaattccttctgtaatcagatcaccaaagtagaaatttct-aatag--tctttttattaatttccatgcagCATCTGTACGTGTATGGGGTGTTGGTGTTTGAAGCCATGGCCACCTTCATCGGCCAAGTCTCGGTCCTCTCCCTCATAGCCATCTTCGGTGCTGCCACAA

upper sequence: GLYMA18G46240.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ20197 (Selaginella moellendorffii), 3'ss of exon 5
ggtaatgttggaataaacttagcccctattccacgctctattattattacta-catttatgatttcttaatagaatcacctttttcttgtccttgcaGCATCCCTATGTGTATGGCGTGTTGGTCTTTGAGGCAATGGCCACATTTATAGGCCAAGTTTCTGTCCTCTCCCTCATTGCTATCTTTGGTGCTGCCACC-
                                           | |  ||||  |  |  | |||||  | |     |    ||| ||      ||||||||| ||||| ||    ||  | || ||||| || ||||| || |||||||||||| | || |||||||||||||||||  ||||||| ||||||||| 
------------------------------------------gtaagcactagtaactgcg-tttctccaaaactctaaagctttgttacttgcgcagCATCCATATGTCTACCTGGTCCTCGTGTTTGAAGCGATGGCAACGTTTATAGGCCAACTCTCCGTCCTCTCCCTCATTGCCCTCTTTGGAGCTGCCACCA

upper sequence: GLYMA18G46240.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ14308 (Selaginella moellendorffii), 3'ss of exon 5
ggtaatgttggaataaacttagcccctattccacgctctattattattacta-catttatgatttcttaatagaatcacctttttcttgtccttgcaGCATCCCTATGTGTATGGCGTGTTGGTCTTTGAGGCAATGGCCACATTTATAGGCCAAGTTTCTGTCCTCTCCCTCATTGCTATCTTTGGTGCTGCCACC-
                                           | |  ||||  |  | || || ||  | |     |    ||| ||      ||||||||| ||||| ||    ||  | || ||||| || ||||| || |||||||||||| | || |||||||||||||||||  ||||||| ||||||||| 
------------------------------------------gtaagcactagtaactgtg-ttcctccaaaactctaaagctttgttacttgggcagCATCCATATGTTTACCTGGTCCTTGTGTTTGAAGCGATGGCAACGTTTATAGGCCAACTCTCCGTCCTCTCCCTCATTGCCCTCTTTGGAGCTGCCACCA

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|193625499|gb|FK577487.1|FK577487
EST:     CCCATGCTTTTCACAGGAGAATTATTCAAAGCATGGACTTCATGTTCACA                         GCATCCCTATGTGTATGGCGTGT
genomic: CCCATGCTTTTCACAGGAGAATTATTCAAAGCATGGACTTCATGTTCACAggtaatgttg ... tgtccttgcaGCATCCCTATGTGTATGGCGTGT
EST: gi|193515393|gb|FK477169.1|FK477169
EST:     CCTATGCTTTTCACAGGAGAATTATTCAAAGCATGGACTTCATGTTCACA                         GCATCCCTATGTGTATGG
genomic: CCCATGCTTTTCACAGGAGAATTATTCAAAGCATGGACTTCATGTTCACAggtaatgttg ... tgtccttgcaGCATCCCTATGTGTATGG
EST: gi|208102074|gb|GD897375.1|GD897375
EST:     ATGCTTTTCACAGGAGAATTATTCAAAGCATGGACTTCATGTTCACA                         GCATCCCTATGTGTATGGCGTGTTGGTCTTTGAGGCAATGGCCACATTTAT
genomic: ATGCTTTTCACAGGAGAATTATTCAAAGCATGGACTTCATGTTCACAggtaatgttg ... tgtccttgcaGCATCCCTATGTGTATGGCGTGTTGGTCTTTGAGGCAATGGCCACATTTAT
EST: gi|207844712|gb|GD816633.1|GD816633
EST:     ATGCTTTTCACAGGAGAATTATTCAAAGCATGGACTTCATGTTCACA                         GCATCCCTATGTGTATGGCGTGTTGGTCTTTGAGGCAATGGCCACATTTAT
genomic: ATGCTTTTCACAGGAGAATTATTCAAAGCATGGACTTCATGTTCACAggtaatgttg ... tgtccttgcaGCATCCCTATGTGTATGGCGTGTTGGTCTTTGAGGCAATGGCCACATTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattattactacatttatgatttcttaatagaatcacctttttcttgtccttgcaGCATCCCTATGTGTATGGCGTGTTGGTCTTTGAGGCAATGGCCACATTTATAGGCCAAGTTTCTGTCCTCTCCCTCATTGCTATCTTTGGTGCTGCCACC
                      tcttaat  putative branch site (score: 3)
                                 tcacctttttcttgtc  putative PPT
            atttatgatttcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtaatgttggaataaacttagcccctattccacgctctattattattactacatttatgatttcttaatagaatcacctttttcttgtccttgcaGCATCCCTATGTGTATGGCGTGTTGGTCTTTGAGGCAATGGCCACATTTATAGGCCAAGTTTCTGTCCTCTCCCTCATTGCTATCTTTGGTGCTGCCACC

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