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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgctgcttgactcctacttgctaatatttcaaatcacatgcttatcgtttatctccggattctactcttgtcggtaattgatagactgctaagttttacatcttccgtctcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTTCAACCTTTTTCAGGGAAGAAGTATTCTTTACGGGGTTAATTTATACCAA

Basic information

species Glycine max
transcript GLYMA08G05030.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G05030.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv03s0038g00750.t01 (Vitis vinifera), 3'ss of exon 9
gtaatttgctgcttgactcctacttgctaatatttcaaatcacatgcttatcgtttatctccggattctactcttgtcggtaattgatagactgctaagttt---tacatcttccgtctcataagcagGCGAAAGAGTCA--AAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTTCAACCTTTTTCAGGGAAGAAGTATTCTTTACGGGGTTAATTTATACCAA
         | ||    |   |   ||    |||   ||  | |    | |  ||| | | |  |     ||  | | | ||    ||   ||||| | |||   |   ||||   ||    | | ||  | || || ||  ||||  |||   ||   | |||||||||||||||| || || |||||||||||||| ||||| |||||   ||| | | | |      
--------gtactgttgtttcatcagcc---attcagaactaaaatggtttttttttttttcaaaaaaagctgctattgata--caatt--ctgctcattttggatggttctttactcctgcagGAAGCTGCAAAAGCCACTAAACAGGAGGAGCC---AAAGAAAGAAGAGCCGAAGTTCCAGCCTTTTTCAGGGAAAAAGTACTCTTTGAAGGGATGAATGAATT---
















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|254318175|gb|GR832343.1|GR832343
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
EST: gi|151397988|gb|EV267861.1|EV267861
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
EST: gi|254318174|gb|GR832342.1|GR832342
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
EST: gi|214004575|gb|DB985590.1|DB985590
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
EST: gi|9563895|gb|BE473404.1|BE473404
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGANAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
EST: gi|254326847|gb|GR836456.1|GR836456
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
EST: gi|209716481|gb|BW657525.1|BW657525
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
EST: gi|254313715|gb|GR831344.1|GR831344
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
EST: gi|209716429|gb|BW653870.1|BW653870
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
EST: gi|192326508|gb|FK018815.1|FK018815
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
EST: gi|9439750|gb|BE440264.1|BE440264
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
EST: gi|209712047|gb|BW674192.1|BW674192
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
EST: gi|6667020|gb|AW278479.1|AW278479
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
EST: gi|9900177|gb|BE609145.1|BE609145
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATNT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
EST: gi|7028303|gb|AW458086.1|AW458086
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
EST: gi|58023681|gb|CX710422.1|CX710422
EST:     GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAG                         GCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT
genomic: GCAAGCTTGTGTTTGGGTCAAATGCAAACCGTACTAATGAGACAGGAAAGgtaatttgct ... tcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttgtcggtaattgatagactgctaagttttacatcttccgtctcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTTCAACCTTTTTCAGGGAAGAAGTATTCTTTACGGGGTTAATTTATACCAA
           aattgat  putative branch site (score: 4)
                                    tcttccgtctc  putative PPT
          taattgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgctgcttgactcctacttgctaatatttcaaatcacatgcttatcgtttatctccggattctactcttgtcggtaattgatagactgctaagttttacatcttccgtctcataagcagGCGAAAGAGTCAAAACCAGAGCCACCTAAAGAGAAAGAAGAGCCGAAATTTCAACCTTTTTCAGGGAAGAAGTATTCTTTACGGGGTTAATTTATACCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT