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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAGATCCAGATGCTGAAGAACAAGTAGAGATGATACAGTGCTGTCTATGTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAGgttggtattttggaatttgatgttttagcttctcttaacctttttattttgtgttatcaacttcttgtacttcagtcttcaatgatgagatttttatgca...

Basic information

species Glycine max
transcript GLYMA11G01960.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G01960.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G129431_T01 (Zea mays), 5'ss of exon 3
TCCAGATCCAGATGCTGAAGAACAAGTAGAGATGATACAGTGCTGTCTATGTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAGgt-tggtattttggaatttgatgttttagcttctcttaacctttttattttgtgttatcaacttcttgtacttcagtcttcaatgatgagatttttatgca
||| || ||||| ||| | || ||||| || |||||||| |||| | ||||||||||||||||||||| ||| ||| |||||||| | |||  ||  ||||| |  ||||||  | |    |   |  | |  | | |   |   |  ||| |||  ||   ||| |||   |  | ||      || |  | | | ||||
TCCTGACCCAGAAGCTAAGGAGCAAGTTGAAATGATACAATGCTCTATATGTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatattttccagtaccttaaatgcgatcatat-atgttaggtgctttttgtgttctgattcctgtgtgtttgcctagttgcatcacctgtatctgca

upper sequence: GLYMA11G01960.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G23860.1 (Arabidopsis thaliana), 5'ss of exon 4
TCCAGATCCAGATGCTGAAGAACAAGTAGAGATGATACAGTGCTGTCTATGTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAGgttggtattttggaatttgatgttttagcttc-tcttaacctttttattttgtgttatcaacttcttgtacttca-gtcttcaatgatgagatttttatgca
            ||  |||||||||||||||||||| ||||| ||||| |||||||| |||||||||||||||||||| |||||     |||| |     |||||||    ||  ||||  |     ||||  ||||    |||    ||  | || |    |  | |  |||   |   |   | ||| ||| || |    
------------TGTGGAAGAACAAGTAGAGATGATTCAGTGTTGTCTCTGTGAGGATTGGTTTCATGAGGAGCATCTCGGTCTCACACCTTCAGACAGTGTTGGTAGCCAGg--tttgtggccagtgcttaatcttgttgtttacgattgattttttttgttgttggcgcttagtgcaatttgttatgtgatgttaacag-

upper sequence: GLYMA11G01960.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv02s0025g01440.t01 (Vitis vinifera), 5'ss of exon 3
TCCAGATCCAGATGCTGAAGAACAAGTAGAGATGATACAGTGCTGTCTATGTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAGgttggtattttggaatttgatgttttagcttctcttaacctttttattt--tgtgttatcaacttcttgtacttcagtcttcaatgatgagatttttatgca--
||| ||||||||   ||||||||||| ||||||||||||||||||| | |||||||||||||| ||||||||||||||||| |||||||||||||  |||||| || | || || ||      ||| |||  |       || | ||||    |||| |     | ||||| |   ||  |  ||| | |   |||     |  
TCCTGATCCAGACATTGAAGAACAAGAAGAGATGATACAGTGCTGTATCTGTGAGGACTGGTTCCATGAGGAGCATCTTGGCCTTGAGTCTTCTGATGAGgttagtttctttgacttctcctatttggctgttgcctgggttctcatttgtcatgtttttggtatattgtatt---gttattcatg-tcatgctttggcataaa

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|208056031|gb|GD855460.1|GD855460
EST:     GTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAG                         ATTCCTAAAGATGATGAGGGAGAGCCAATGTATGAAGAATTCATATGTAAG
genomic: GTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAGgttggtattt ... ctgaactcagATTCCTAAAGATGATGAGGGAGAGCCAATGTATGAAGAATTCATATGTAAG
EST: gi|16106233|gb|BI893973.1|BI893973
EST:     GTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAG                         ATTCCTAAAGATGATGAGGGAGAGCCAATGTATGAAGAATTCATATGTAAG
genomic: GTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAGgttggtattt ... ctgaactcagATTCCTAAAGATGATGAGGGAGAGCCAATGTATGAAGAATTCATATGTAAG
EST: gi|192295390|gb|FG987004.1|FG987004
EST:     GTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAG                         ATTCCTAAAGATGATGAGGGAGAGCCAATGTATGAAGAATTCATATGTA-G
genomic: GTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAGgttggtattt ... ctgaactcagATTCCTAAAGATGATGAGGGAGAGCCAATGTATGAAGAATTCATATGTAAG
EST: gi|193487292|gb|FK452273.1|FK452273
EST:     GTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAG                         ATTCCTAAAGATGATGAGGGAGAGCCAATGTATGAAGAATTCATATGTAAG
genomic: GTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAGgttggtattt ... ctgaactcagATTCCTAAAGATGATGAGGGAGAGCCAATGTATGAAGAATTCATATGTAAG
EST: gi|208214613|gb|GE012902.1|GE012902
EST:     GTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAG                         ATTCCTGAAGATGATGAGGGAGAGCCAATGTATGAAGAATTCATATGTAAG
genomic: GTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAGgttggtattt ... ctgaactcagATTCCTAAAGATGATGAGGGAGAGCCAATGTATGAAGAATTCATATGTAAG
EST: gi|192305248|gb|FG997528.1|FG997528
EST:     GTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAG                         ATTCCTAAAGATGATGAGGGAGAGCCAATGTATGAAGAATTCATATGTAAG
genomic: GTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAGgttggtattt ... ctgaactcagATTCCTAAAGATGATGAGGGAGAGCCAATGTATGAAGAATTCATATGTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCAGATCCAGATGCTGAAGAACAAGTAGAGATGATACAGTGCTGTCTATGTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAGgttggtattttggaatttgatgttttagcttctcttaacctttttattttgtgttatcaacttcttgtacttcagtcttcaatgatgagatttttatgca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA