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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAAATTCCCAGAAGAATTACCTCTATAAATGTGACCAGTTAAAGTCTATTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAGgtactcatttgtttgacatattctgacggatagcattctatcattggttctgcttattcttaatatttttcaatttaatagttccccacttcccctactt...

Basic information

species Glycine max
transcript GLYMA20G38620.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38620.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os01g61930.1 (Oryza sativa), 5'ss of exon 8
TCAAAATTCCCAGAAGAATTACCTCTATAAATGTGACCAGTTAAAGTCTATTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAGgtactcatttgtttgacatattctgacggata-gcattctatcattggttctgcttattc--ttaatatttttcaatttaatagttccccacttcccctactt
| |||  || ||||||||||| || ||||||||||||||  |||| || ||||| ||||| || ||||||||  | || |  ||  |  | || |||| ||||  | ||   ||  |  | | ||   | ||   | |  || ||   | ||| | | |   ||| |   |||  |    | |  ||    |      ||   
TGAAACATCTCAGAAGAATTATCTGTATAAATGTGACCAACTAAAATCAATTCGGCAAGATCTTACTGTTCAGAGGATTCAGAACGAGCTGACTGTCATGgtagcctttc--ttagcccactttgtgtgttatatactgcattat-actcctgttcactatgttagtccattttcacgggaaatatcatttcacaatgtatcc

upper sequence: GLYMA20G38620.1 (Glycine max), 5'ss of exon 12
lower sequence: AT2G39340.1 (Arabidopsis thaliana), 5'ss of exon 9
TCAAAATTCCCAGAAGAATTACCTCTATAAATGTGACCAGTTAAAGTCTATTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAGgtactcatttgtttgacatattctgacggatagcattctatcattggttctgcttattcttaatatttttcaatttaatagttccccacttcccctactt-------------------------------
|||  |||| || |||||||| || | ||||||||| ||  |||||||||||||||||||||| || || ||||| |||| |||||| |||||||  |||||||  |  ||  |  || ||  || ||  |   |||  ||  | || |    ||  | ||   |  |||  || | ||     |||| ||  | |  ||                               
TCAGGATTCTCAAAAGAATTATCTTTTTAAATGTGATCAACTAAAGTCTATTCGCCAAGACCTCACAGTACAACGGATACACAATCATTTAACAGCTAAGgtacataactgacttcca-ataatgtcgagtgttattgcat-gtaggattcatttcctgttggaacgttt--atcttatttacacccaattagcatgtttataatggttccatgtgcaatctcaatttcag

upper sequence: GLYMA20G38620.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv13s0067g03720.t01 (Vitis vinifera), 5'ss of exon 3
TCAAAATTCCCAGAAGAATTACCTCTATAAATGTGACCAGTTAAAGTCTATTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAGgtactcatt-tgtttgacatattctgacggatagcattctatcattggttctgct-tattcttaatatttttcaatttaatagttccccacttcccctactt----
||| ||||| || ||||| ||||| ||||||||||| || || || || ||||||||||| || ||||| ||||| |||| |||| |  ||||||| ||||||   ||  |  |||| ||    ||    ||   ||||| | || |||  ||   |  || |  |  |  ||||||  ||  |   | | |     |        
TCAGAATTCTCACAAGAACTACCTTTATAAATGTGATCAATTGAAATCGATTCGCCAAGATCTTACTGTGCAACGGATACACAATGAGCTAACAGTTAAGgtatatatcattcttgatat----tgctatatgttattctctgat-ggtcatgtaatgatcctcctcctcatcaatt-gatgatgtacaaatgaggatgaaaatgt

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|193563810|gb|FK517933.1|FK517933
EST:     TTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAG                         GTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG
genomic: TTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAGgtactcattt ... aatgcttcagGTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG
EST: gi|193682710|gb|FK621764.1|FK621764
EST:     TTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAG                         GTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG
genomic: TTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAGgtactcattt ... aatgcttcagGTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG
EST: gi|193690224|gb|FK627997.1|FK627997
EST:     TTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAG                         GTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG
genomic: TTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAGgtactcattt ... aatgcttcagGTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG
EST: gi|207822545|gb|GD795208.1|GD795208
EST:     TTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAG                         GTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG
genomic: TTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAGgtactcattt ... aatgcttcagGTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG
EST: gi|193532296|gb|FK491976.1|FK491976
EST:     CGCCAAGACCTAACTGTTCTAACGTAATACGCAATCAATTAACAGTCAAG                         GTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG
genomic: CGCCAAGACCTAACTGTTC-AACG-AATACGCAATCAATTAACAGTCAAGgtactcattt ... aatgcttcagGTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG
EST: gi|193694976|gb|FK634348.1|FK634348
EST:     TTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAG                         GTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG
genomic: TTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAGgtactcattt ... aatgcttcagGTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG
EST: gi|193670598|gb|FK612720.1|FK612720
EST:     TTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAG                         GTGTATGAAACACATGCCCGATTGGCAACTAGGAATTTGGGGACCTGTTT
genomic: TTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAGgtactcattt ... aatgcttcagGTGTATGAAACACATGCCCGATTGGCA-CT-GGAATTTGGGGACCTGTTT
EST: gi|208319804|gb|GE110829.1|GE110829
EST:     CGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAAACAAGTCAAG                         GTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGA
genomic: CGCCAAGACCTAACTGTTCAACGAATACGCAATCAATT-AAC-AGTCAAGgtactcattt ... aatgcttcagGTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGA
EST: gi|193454256|gb|FK420823.1|FK420823
EST:     TTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAG                         GTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG
genomic: TTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAGgtactcattt ... aatgcttcagGTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG
EST: gi|208284795|gb|GE085609.1|GE085609
EST:     CGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAG                         GTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG
genomic: CGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAGgtactcattt ... aatgcttcagGTGTATGAAACACATGCCCGATTGGCACTGGAATTTGGGGACCTGTTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAAATTCCCAGAAGAATTACCTCTATAAATGTGACCAGTTAAAGTCTATTCGCCAAGACCTAACTGTTCAACGAATACGCAATCAATTAACAGTCAAGgtactcatttgtttgacatattctgacggatagcattctatcattggttctgcttattcttaatatttttcaatttaatagttccccacttcccctactt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcccc