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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttttgtgacttattattgatggttttacctctctatgttgtaattaatttgagaagttgtcatctttcagtaatatctatttctcatcttcatgcagGAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGTTACAGGGATGGCCAAGAAACAAGGAAAGGAAAAGTCATCAGTTTCAAAT

Basic information

species Glycine max
transcript GLYMA14G11400.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G11400.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0008g01670.t01 (Vitis vinifera), 3'ss of exon 3
--ttcttttgtgacttattattgatggtt-ttacctctctatgttgtaattaatttgagaagttgtcatctttcagtaatatctatttctcatcttcat-gcagGAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGTTACAGGGATGGCCAAGAAACAAGGAAAGGAAAAGTCATCAGTTTCAAAT
  |    |||  | ||  |||  ||  || ||  || |  |||||||| |  ||    |   |  |   ||  | || || |||       ||  |  | ||||||| || || ||||| ||||||||||||||||| ||||||||||||||||| || || |  |||||||||||||  ||||||||||||||||| ||||||
ggtgtgcttgcaatttgctatgtatttttgttgtctattgatgttgtattatat----ggtttcatttactgactgtgatttcttgcgggtattcttgttgcagGAAACGCCTTTTTAACATGATAAATGATCTTCCAACAATATTTGAGGTTGTAACGGGAACAGCCAAGAAACAAGTTAAGGAAAAGTCATCAGTCTCAAAT
















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|208304277|gb|GE103882.1|GE103882
EST:     GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGACAG                         GAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
genomic: GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattt ... cttcatgcagGAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
EST: gi|58015897|gb|CX702639.1|CX702639
EST:     GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAG                         GAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
genomic: GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattt ... cttcatgcagGAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
EST: gi|6069841|gb|AW099441.1|AW099441
EST:     GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAG                         GAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
genomic: GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattt ... cttcatgcagGAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
EST: gi|208235418|gb|GE034210.1|GE034210
EST:     GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAG                         GAAGCGACTATTTAATATGATAAATGATCTTCCGACAATA
genomic: GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattt ... cttcatgcagGAAGCGACTATTTAATATGATAAATGATCTTCCGACAATA
EST: gi|208201268|gb|GD996625.1|GD996625
EST:     CTGTGGTCTTTT-ATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAG                         GAAGCGACTATTTAATATGATAAATTGATCTTCCGACAATATTTGAGGTTG
genomic: CTGTGG-CTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattt ... cttcatgcagGAAGCGACTATTTAATATGATAAAT-GATCTTCCGACAATATTTGAGGTTG
EST: gi|31462913|gb|CD404941.1|CD404941
EST:     TGGTGCTAGGTTTGGATTTGACAAGGCTGATAG                         GAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
genomic: TGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattt ... cttcatgcagGAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
EST: gi|193561661|gb|FK520670.1|FK520670
EST:     GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAG                         GAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
genomic: GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattt ... cttcatgcagGAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
EST: gi|193435906|gb|FK398894.1|FK398894
EST:     GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGACAG                         GAAGCGACTATTTAATATGGATAAATGATCTTCCGACAATATTTGAGGTTG
genomic: GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattt ... cttcatgcagGAAGCGACTATTTAATATG-ATAAATGATCTTCCGACAATATTTGAGGTTG
EST: gi|193692863|gb|FK628472.1|FK628472
EST:     GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAG                         GAAGCGACTATTTAANATGATAAATGATCTTCCGACAATATTTGAGGTTGT
genomic: GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattt ... cttcatgcagGAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
EST: gi|207775298|gb|GD750299.1|GD750299
EST:     GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAG                         GAAGCGACTATTTAATATGATAAA
genomic: GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattt ... cttcatgcagGAAGCGACTATTTAATATGATAAA
EST: gi|58016180|gb|CX702922.1|CX702922
EST:     GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAG                         GAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
genomic: GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattt ... cttcatgcagGAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
EST: gi|193461784|gb|FK426325.1|FK426325
EST:     GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAG                         GAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
genomic: GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattt ... cttcatgcagGAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
EST: gi|193607569|gb|FK557448.1|FK557448
EST:     GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAG                         GAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
genomic: GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattt ... cttcatgcagGAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
EST: gi|193497323|gb|FK461157.1|FK461157
EST:     GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAG                         GAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT
genomic: GCTGTGGCTTTTTATTTTGGTGCTAGGTTTGGATTTGACAAGGCTGATAGgtacatattt ... cttcatgcagGAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaatttgagaagttgtcatctttcagtaatatctatttctcatcttcatgcagGAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGTTACAGGGATGGCCAAGAAACAAGGAAAGGAAAAGTCATCAGTTTCAAAT
 aattaat  putative branch site (score: 3)
                                 tctatttctcatcttc  putative PPT
                          agtaatatctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttttgtgacttattattgatggttttacctctctatgttgtaattaatttgagaagttgtcatctttcagtaatatctatttctcatcttcatgcagGAAGCGACTATTTAATATGATAAATGATCTTCCGACAATATTTGAGGTTGTTACAGGGATGGCCAAGAAACAAGGAAAGGAAAAGTCATCAGTTTCAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- -ttttgtg
- - - - - - - - - - gatggtt
- - - - - - - - - - - - - - - cctctct
- - - - - - - - - - - - - - - - - - - tgttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtcatc