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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatttataggaatgaaaacatattttaacctttttttgaattcaaaaaaagggaatacagtgaaaattgttgacatccgacttttgttttatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAGGCATATCTTCATCTTGTGGACTTAGATCTAGCTGAGATGGATATTAAGA

Basic information

species Glycine max
transcript GLYMA05G28260.1
intron # 9
splice site 3'
intron type U2

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|19270890|gb|BM887146.1|BM887146
EST:     GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAG                         GTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
genomic: GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAGgtactttgtc ... tatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
EST: gi|57574566|gb|CX547541.1|CX547541
EST:     GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAG                         GTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
genomic: GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAGgtactttgtc ... tatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
EST: gi|7234543|gb|AW569879.1|AW569879
EST:     AGGACTACAAACAGGCAGAGAAGATGTGCACAAAG                         GTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
genomic: AGGACTACAAACAGGCAGAGAAGATGTGCACAAAGgtactttgtc ... tatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
EST: gi|10846141|gb|BF069114.1|BF069114
EST:     GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAG                         GTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
genomic: GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAGgtactttgtc ... tatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
EST: gi|9987554|gb|BE661662.1|BE661662
EST:     GTAAGTTGAAGCTAANGG-CTACAAACAGGCAGAGAAGATGTGCACAAAG                         GTTT-AGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGANGGCACAG
genomic: GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAGgtactttgtc ... tatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
EST: gi|58023136|gb|CX709877.1|CX709877
EST:     GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAG                         GTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
genomic: GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAGgtactttgtc ... tatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
EST: gi|10254106|gb|BE821872.1|BE821872
EST:     GTAAGTTGAAGCTAAAGGACTACAANNAGNNAGAGAAGATGTGCACAAAG                         GTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
genomic: GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAGgtactttgtc ... tatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
EST: gi|11412722|gb|BF424733.1|BF424733
EST:     GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAG                         GTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
genomic: GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAGgtactttgtc ... tatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
EST: gi|58022830|gb|CX709571.1|CX709571
EST:     GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAG                         GTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
genomic: GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAGgtactttgtc ... tatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
EST: gi|58019828|gb|CX706570.1|CX706570
EST:     GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAG                         GTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
genomic: GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAGgtactttgtc ... tatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
EST: gi|6455054|gb|AW185737.1|AW185737
EST:     GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAG                         GTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
genomic: GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAGgtactttgtc ... tatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
EST: gi|51334753|gb|CO978619.1|CO978619
EST:     GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAG                         GTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
genomic: GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAGgtactttgtc ... tatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
EST: gi|7234663|gb|AW569998.1|AW569998
EST:     GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAG                         GTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
genomic: GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAGgtactttgtc ... tatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
EST: gi|19346686|gb|BM891566.1|BM891566
EST:     GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAG                         GTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG
genomic: GTAAGTTGAAGCTAAAGGACTACAAACAGGCAGAGAAGATGTGCACAAAGgtactttgtc ... tatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaagggaatacagtgaaaattgttgacatccgacttttgttttatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAGGCATATCTTCATCTTGTGGACTTAGATCTAGCTGAGATGGATATTAAGA
                       tgttgac  putative branch site (score: 3)
                                    cttttgtttt  putative PPT
                                     ttttgttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatttataggaatgaaaacatattttaacctttttttgaattcaaaaaaagggaatacagtgaaaattgttgacatccgacttttgttttatcacgcagGTTTTAGAGCTTGATAGTAGAAATGTAAAAGCACTCTATCGGAGGGCACAGGCATATCTTCATCTTGTGGACTTAGATCTAGCTGAGATGGATATTAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - -ggaatga
- - - - - - - - - - - - - - - - - - -tgaattc
- - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tacagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgac