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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACGATGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTACgtaagtttattgatatcaattgttttgtactctaattttacgagttagcttgggattgaaatttggggtgaaaagttcggtttgatcatcgtattgtgtt...

Basic information

species Glycine max
transcript GLYMA04G36420.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G36420.2 (Glycine max), 5'ss of exon 2
lower sequence: AT5G50250.1 (Arabidopsis thaliana), 5'ss of exon 2
TATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACGATGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTACgtaagtttattgatatcaattgttttgtactctaattttacgagttagcttgggattgaaatttggggtgaaaagttcggtttgatcatcgtattgtgtt
||| || |||||||| ||||| || ||||| || ||||||||||| || |||||||| ||||||||||| ||||| || || ||||| |||| | |||  |||||         |   ||| | ||||     ||| ||  | || |  || |||| |  |||   | ||   |  | | || |   ||   | |||   
TATATACAATAGGGACACTGATCAAAGTCGTGGATTTGGGTTTGTAACAATGAGTACAGTTGAAGAAGCAGAGAAAGCTGTTGAGAAGTTCAATAGTTTTgtaagc--------aatcattttcttgtttctcaatcttctgggtca--tttggatagtgattatagatgttgaagttgattgg--tatacaactgtag-

upper sequence: GLYMA04G36420.2 (Glycine max), 5'ss of exon 2
lower sequence: AT4G24770.1 (Arabidopsis thaliana), 5'ss of exon 2
TATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACGATGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTACgtaagtttattgatatcaattgttttgtactctaattttacgagttagcttgggattgaaatttggggtgaaaagttcggtttgatcatcgtattgtgtt----
||| || ||||||||||||||||||||||| || ||||| |||||||| |||||| | || || ||||||||||  || |||||||| ||||  ||||| ||||||||||     ||||   ||   |  | |   |||  ||||||  || | || | | | ||  | || |       ||||||  ||||  | | |     
TATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACAATGAGTTCTGTGGACGAAGCTGAGACAGCTGTGGAGAAGTTCAACCGTTATgtaagtttatatggttcaaactttcaatcatttctgtttctgagtta--ttagcat-gtattgtgatgggatattgctcctttgatt-tcgtcctttctgctct
















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|8403170|gb|BE058804.1|BE058804
EST:     TGAGTACCGTTGAAGAAGCTGAGAACGCC-TGGAGAAATTCAGTCGTTAC                         GATTTTGATGGAAGATTGTTGACTGTTAATAAGGCTTCTCCAAGAGGAACT
genomic: TGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTACgtaagtttat ... tctatgacagGATTTTGATGGAAGATTGTTGACTGTTAATAAGGCTTCTCCAAGAGGAACT
EST: gi|23058133|gb|BU578293.1|BU578293
EST:     TGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTAC                         GATTTTGATGGAAGATTGTTGACTGTTAATAAAGCTTCTCCAAGAGGAACT
genomic: TGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTACgtaagtttat ... tctatgacagGATTTTGATGGAAGATTGTTGACTGTTAATAAGGCTTCTCCAAGAGGAACT
EST: gi|17023176|gb|BM094210.1|BM094210
EST:     TGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTAC                         GATTTTGATGGAAGATTGTTGACTGTT
genomic: TGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTACgtaagtttat ... tctatgacagGATTTTGATGGAAGATTGTTGACTGTT
EST: gi|18848478|gb|BM567697.1|BM567697
EST:     TGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTAC                         GATTTTGATGGAAGATTGTTGACTGTTAATAAGGCTTCTCCAAGAGGAACT
genomic: TGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTACgtaagtttat ... tctatgacagGATTTTGATGGAAGATTGTTGACTGTTAATAAGGCTTCTCCAAGAGGAACT
EST: gi|15286229|gb|BI470120.1|BI470120
EST:     TGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTAC                         GATTTTGATGGAAGATTGTTGACTGTTAATAAGGCTTCTCCAAGAGGAACT
genomic: TGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTACgtaagtttat ... tctatgacagGATTTTGATGGAAGATTGTTGACTGTTAATAAGGCTTCTCCAAGAGGAACT
EST: gi|23728471|gb|BU762290.1|BU762290
EST:     TGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTAC                         GATTTTGATGGAAGATTGTTGACTGTTAATAAGGCTTCTCCAAGAGGAACT
genomic: TGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTACgtaagtttat ... tctatgacagGATTTTGATGGAAGATTGTTGACTGTTAATAAGGCTTCTCCAAGAGGAACT
EST: gi|298191349|gb|HO038828.1|HO038828
EST:     TGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTAC                         GATTTTGATGGAAGATTGTTGACTGTTAATAAGGCTTCTCCAAGAGGAACT
genomic: TGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTACgtaagtttat ... tctatgacagGATTTTGATGGAAGATTGTTGACTGTTAATAAGGCTTCTCCAAGAGGAACT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTTATAATAGGGAAACTGACCAGAGTCGCGGTTTTGGGTTTGTGACGATGAGTACCGTTGAAGAAGCTGAGAACGCCGTGGAGAAATTCAGTCGTTACgtaagtttattgatatcaattgttttgtactctaattttacgagttagcttgggattgaaatttggggtgaaaagttcggtttgatcatcgtattgtgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggtga