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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaaaaaatcttgatattctttctggagttcttatttttgtaatggtacatgacatccatgtttaattaaactcccatcgttgcctgatttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAATGCTCGGATATGTGGGGCAGA

Basic information

species Glycine max
transcript GLYMA11G20840.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 2
gaaaaaaaatcttgatattctttctggagttcttatttttgtaatggtacatgacatccat---gtttaattaaact-cccatcgttgcctgatttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAATGCTCGGATATGTGGGGCAGA
     ||   |    | ||| | || |  ||    | ||     |  |  || | |||| |    |||| ||   |     ||  |||  |  ||| | |||||| || ||||| ||||| | ||| |||||||||||||| || |||||||| |||||||||||||| || ||||||||||||||||| |||||||| || ||
---ttaacggccgagtgttcatgcttggttttacttcttaactgttttgaattatatccttccaatttatttctgcaatttatatttgttttgttt-tctgcagCGGGGGTTCCATTGGAAAACATTCTTTATCTTGGAGGCCCTAACATTGCTTCAGAAATTTACAATAAAGAATATGCAAATGCTCGTATATGTGGAGCTGA

upper sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
gaaaaaaaatct---tgatattc-tttctggagttcttatttttgtaatggtacatgacatccatgtttaattaaactcccatcgttgcctgatttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAATGCTCGGATATGTGGGGCAGA
  | |   || |   |||||||   ||  |  |  |  |  | |    |      |   || ||  ||  |   || ||  | | ||     | |   |||||||||| |||||    || |  || || ||||||||||| || |||||||||||||| ||||| ||||| ||||||||||||||||| || |||||| |  |
-gacatgcatttatgtgatattaactttcgttgacccaacctattccttcccttgttttattcaaattacaactaattc--agcatt-ttaaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA

upper sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g41590.1 (Oryza sativa), 3'ss of exon 1
---------gaaaaaaaatcttgatattctttctggagttc-ttatttttgtaatggtacatgacatccatgtttaattaaactcccatcgttgcctgatttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAATGCTCGGATATGTGGGGCAGA
          | ||   || ||   || |   ||||  ||| |  ||  |   ||| |  | | | |  ||||||  ||    ||  ||  | | |  |||     |||||||| ||||| ||||| |  || || ||||||||||| || |||||||| || || || || ||||| ||||||||||||||||| |||||||| || ||
gtttcactgtataattgattttaccatcca--ctggtcttcatctttcctaccatgttgta-gcctttaatgttt--tttgtttcttatgatgggcctatt-----gcagCTGGAGTTCCATTGGAGAATATTCTATATCTTGGAGGTCCTAACATTGCATCTGAGATATATAACAAAGAATATGCAAATGCTCGCATATGTGGAGCTGA

upper sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G173195_T01 (Zea mays), 3'ss of exon 1
gaaaaaaaatcttgatattctttctggagttcttatttttgtaatggtacatgacatccatg-tttaattaaactcccatcgttgcctgatttct-ttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAATGCTCGGATATGTGGGGCAGA
     |      ||||| |    |     |  |||| |   |  || || |  | |    || |||  ||         | | |    ||||  |  ||||||||| ||||||||||| | ||| || ||||||||||| || |||||||| || || ||||| ||||| |||||||| |||||||| |||||||| || ||
-ttttaccgaactgatactaacaccctgctctttatctcaattctg-tatactatactgttggtttgcttttgtggttgttgatcatggattcttactgcagCTGGAGTTCCCTTGGAGAACATTCTATATCTTGGAGGCCCAAACATTGCTTCTGAGATTTATAACAAAGAATATGCGAATGCTCGCATATGTGGAGCTGA

upper sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 2
gaaaaaaaatcttgatattctttctggagttcttatttttgtaatggtacatgacatccatgtttaa--tta--aactcccatcgttgcct---gatttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAATGCTCGGATATGTGGGGCAGA
        |||| | |      | |  |    || ||| ||   |  | | || | | | | ||| |  | |  |   |  |  | |   |   || | | |||||||||| |||||    || |  || || |||||||||||||| ||||| ||||| |||||||| ||||| ||||||||||| ||||| || |||||  |  |
------gcatctggttgaaacgtataaacagtttttttctgct-taatgcttggcctgcttatttgagatcagcagtacagactgatttttaaggaatgcattgcagCTGGAGTTCCAACTGAAAATATACTCTATCTTGGAGGACCAAACATCGCCTCGGAAATTTATAACAAAGAATATGCAAACGCTCGAATCTGTGGATCCAA

upper sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G090747_T02 (Zea mays), 3'ss of exon 2
gaaaaaaaatcttgatattctttctggagttcttatttttgtaatggtacatgacatcca-tgtttaattaaac---tcccatcgttgcctgatttctt--tgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAATGCTCGGATATGTGGGGCAGA
      | ||    ||||    ||     ||| |  |  | |    |||  ||   |||  | ||| |||           ||  | | ||  |    |  ||||||||| ||||| |  || |  || ||||||||||| ||||| || ||||| || |||||||||||||| |||||||||||||| || || ||||| || ||
------agatacatatatatgctcaatgcttcctcctaatctccaagtatttgttgtcccctctttgattttgtatgatttattatggactattggtataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTTCTGAAATTTACAACAAAGAATATGCAAATGCACGTATTTGTGGAGCTGA

upper sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 1
gaaaaaaaatcttgatattctttctggagttcttattt-ttgtaatggtacatgacatccatgtttaattaaactcccatcgttgcctgattt----------ctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAATGCTCGGATATGTGGGGCAGA
           |    |   | |||| |||| |||||| |  |||| |       | |   | ||| | |     | | || |||||| |||           |||||||||||| |||||| |||| |  || || |||||||| |||||||| ||||||||||||||||||||||||||||| || |||||||| |||||||| || ||
-----------tcaccacattctctgtagtttttatttgtcctaattgatgccaccttttttattttactttctccacttctttgcctcattattatattgtgctttgcagCTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCTCAGAAATTTACAACAAGGAATACGCTAATGCTCGCATATGTGGAGCTGA

upper sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S114_190V6.1 (Physcomitrella patens), 3'ss of exon 3
gaaaaaaaatcttgatattctttctgg--agttcttattt--ttgtaatggtacatgacatccatgtttaattaaactcccatcgttgcctgatttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAATGCTCGGATATGTGGGGCAGA
         | |  || |    ||  |   | |||| |    ||| ||||||  |||| ||  || |     |     |  |   |||  | |||    | |||| ||||| || |  || |   |  | || || ||||| ||||||||||| || ||| ||||||||||||| ||||| ||||| ||||| || ||| | ||
-tgtgtgtgtgtaaatgtgtcctccagctggctcttgtcaggttgaaatggt--atga-attaatatgagggttgggactgaatattgtgtaattgtgattcagCCGGCGTGCCTTCTGAAAATGTTTTGTACCTGGGAGGTCCGAACATTGCTTCTGAAGTTTACAACAAGGAGTATGCTAATGCACGGATCTGCGGGTCTGA

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|193523287|gb|FK479128.1|FK479128
EST:     GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAA                         CTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
genomic: GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAAgtaagatgca ... ttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
EST: gi|193346231|gb|FK309723.1|FK309723
EST:     GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAA                         CTGGCGTTCCCTTGGACA
genomic: GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAAgtaagatgca ... ttctttgcagCTGGCGTTCCCTTGGACA
EST: gi|193719572|gb|FK650880.1|FK650880
EST:     GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAA                         CTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
genomic: GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAAgtaagatgca ... ttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
EST: gi|15812784|gb|BI785059.1|BI785059
EST:     GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAAT----CAA                         CTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
genomic: GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAAgtaagatgca ... ttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
EST: gi|208262748|gb|GE058892.1|GE058892
EST:     GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAA                         CTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
genomic: GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAAgtaagatgca ... ttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
EST: gi|208126836|gb|GD920718.1|GD920718
EST:     GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAA                         CTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
genomic: GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAAgtaagatgca ... ttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
EST: gi|193659430|gb|FK605537.1|FK605537
EST:     GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAA                         CTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAA
genomic: GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAAgtaagatgca ... ttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAA
EST: gi|208328772|gb|GE127970.1|GE127970
EST:     GCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAA                         CTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
genomic: GCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAAgtaagatgca ... ttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
EST: gi|208086692|gb|GD884220.1|GD884220
EST:     GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAA                         CTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
genomic: GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAAgtaagatgca ... ttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
EST: gi|193406506|gb|FK371811.1|FK371811
EST:     GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAA                         CTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
genomic: GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAAgtaagatgca ... ttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
EST: gi|193366530|gb|FK332896.1|FK332896
EST:     TCTAATGATCAATCAAGCAA                         CTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
genomic: TCTAATGATCAATCAAGCAAgtaagatgca ... ttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
EST: gi|193479778|gb|FK445459.1|FK445459
EST:     GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAA                         CTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT
genomic: GGGCACTGAGCCACGGATAATAACACCAACTCTAATGATCAATCAAGCAAgtaagatgca ... ttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtacatgacatccatgtttaattaaactcccatcgttgcctgatttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAATGCTCGGATATGTGGGGCAGA
                                      gcctgat  putative branch site (score: 4)
                                            tttctttgc  CT-rich tract
              atgtttaattaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaaaaaatcttgatattctttctggagttcttatttttgtaatggtacatgacatccatgtttaattaaactcccatcgttgcctgatttctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAATGCTCGGATATGTGGGGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
-aaaaaaa
- - - - - - - - - -ctttctg
- - - - - - - - - - - - - - - - - - - - - - - - acatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgcct