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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGGACTATGCCTTTGAGTTCATTATCAACAATGGTGGCATTGACACTGAAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagttttacctttgattctttgataaattagtaaatgcttctaatagcttcattctaatacttataatagattttattcttcttatctatag

Basic information

species Glycine max
transcript GLYMA04G04400.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G04400.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os04g55650.1 (Oryza sativa), 5'ss of exon 2
TGTGGACTATGCCTTTGAGTTCATTATCAACAATGGTGGCATTGACACTGAAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagttttacctttgattctttgataaattagtaaatgcttctaatagcttcattctaatac-ttataatagattttattcttcttatctatag
  |||||||||| ||||| ||||| |||||||||||||| || ||||| || || || ||||| |   ||||    || |     |||||   | ||| |||   |||   |||   | ||    |   ||   |  |      | |||| | ||| | |||   |||     | ||         ||   | ||
GATGGACTATGCATTTGATTTCATCATCAACAATGGTGGAATCGACACCGAGGATGACTACCCTTACAAAGGCAAGGACGAACGGTGTGACGTAAACAGGgtatctttcgtcttctttgctcccttggtttttcaggt------agtagcataattttgatatgctattgctcacttgtgctgctatactcacag

upper sequence: GLYMA04G04400.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S285_10V6.1 (Physcomitrella patens), 5'ss of exon 2
TGTGGACTATGCCTTTGAGTTCATTATCAACAATGGTGGCATTGACACTGAAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagttttacctttgattctttgataaattagtaaatgcttctaatagcttcattctaatacttataatagattt---tattcttcttatc-tatag----------------------------------
| |||||||||| || ||||| |||||||| |||||||| |||||||||||  ||||||| || |   | |     ||||||   || ||| |    |  || ||| | | | | |     ||  |  |||   | |  || | | |  |||   |  |||| |||| | || ||     |||  ||  ||| ||  |                                  
TATGGACTATGCATTCGAGTTTATTATCAAGAATGGTGGTATTGACACTGAGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatcaacctag--cggttatttcattcacacaatctcccatttactttcattgaatatttatga-agtttcaagcatttatcacatcgtacggtcaccttacgtgcgtccttttgtgtttccttcag
















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|207785469|gb|GD756994.1|GD756994
EST:     AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATATAAG                         ATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
genomic: AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagtttta ... ttatctatagATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
EST: gi|58024799|gb|CX711540.1|CX711540
EST:     AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAG                         ATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
genomic: AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagtttta ... ttatctatagATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
EST: gi|192300770|gb|FG989697.1|FG989697
EST:     AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAG                         ATAAATGCTAGAGCTGT
genomic: AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagtttta ... ttatctatagATAAATGCTAGAGCTGT
EST: gi|7925963|gb|AW831989.1|AW831989
EST:     AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAG                         ATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
genomic: AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagtttta ... ttatctatagATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
EST: gi|58024179|gb|CX710920.1|CX710920
EST:     AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAG                         ATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
genomic: AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagtttta ... ttatctatagATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
EST: gi|207799338|gb|GD769177.1|GD769177
EST:     GCTGATGGTATCTGTGATCAATACAAG                         ATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
genomic: GCTGATGGTATCTGTGATCAATACAAGgttagtttta ... ttatctatagATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
EST: gi|208218021|gb|GE016109.1|GE016109
EST:     AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATATAAG                         ATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
genomic: AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagtttta ... ttatctatagATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
EST: gi|193698909|gb|FK635010.1|FK635010
EST:     AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAG                         ATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
genomic: AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagtttta ... ttatctatagATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
EST: gi|58016625|gb|CX703367.1|CX703367
EST:     GAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAG                         ATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
genomic: GAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagtttta ... ttatctatagATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
EST: gi|193393960|gb|FK358525.1|FK358525
EST:     AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAG                         ATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
genomic: AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagtttta ... ttatctatagATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
EST: gi|58014188|gb|CX700930.1|CX700930
EST:     AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAG                         ATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT
genomic: AAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagtttta ... ttatctatagATAAATGCTAGAGCTGTTACAATTGATGGTTACGAACGTGTTCCTGCTTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGGACTATGCCTTTGAGTTCATTATCAACAATGGTGGCATTGACACTGAAGAGGATTACCCCTTTCAAGGTGCTGATGGTATCTGTGATCAATACAAGgttagttttacctttgattctttgataaattagtaaatgcttctaatagcttcattctaatacttataatagattttattcttcttatctatag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT