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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttgtgttgtttctgaacgatttctctgttatctgtttcaattttgctggagtatttgaatatatagtcacttttaatggaagttttgctttttgcagTGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATGATGCTAAGATGAGTGAATT

Basic information

species Glycine max
transcript GLYMA08G20300.3
intron # 1
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|37997471|gb|CF809060.1|CF809060
EST:     CTCATTCTACTTAAAACTCCCACCAG                         TGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
genomic: CTCATTCTACTTAAAACTCCCACCAGgtatctctct ... ctttttgcagTGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
EST: gi|192296157|gb|FG989742.1|FG989742
EST:     CTCATTCTACTTAAAACTCCCACCAG                         TGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
genomic: CTCATTCTACTTAAAACTCCCACCAGgtatctctct ... ctttttgcagTGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
EST: gi|6719017|gb|AW306664.1|AW306664
EST:     CTCATTCTACTTAAAACTCCCACCAG                         TGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
genomic: CTCATTCTACTTAAAACTCCCACCAGgtatctctct ... ctttttgcagTGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
EST: gi|9820437|gb|BE555947.1|BE555947
EST:     CTCATTCTACTTAAAACTCCCACCAG                         TGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
genomic: CTCATTCTACTTAAAACTCCCACCAGgtatctctct ... ctttttgcagTGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
EST: gi|6134879|gb|AW133272.1|AW133272
EST:     CTCATTCTACTTAAAACTCCCACCAG                         TGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
genomic: CTCATTCTACTTAAAACTCCCACCAGgtatctctct ... ctttttgcagTGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
EST: gi|16347160|gb|BI972755.1|BI972755
EST:     CTCATTCTACTTAAAACTCCCACCAG                         TGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
genomic: CTCATTCTACTTAAAACTCCCACCAGgtatctctct ... ctttttgcagTGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
EST: gi|21995036|gb|BQ786564.1|BQ786564
EST:     CTCATTCTACTTAAAACTCCCACCAG                         TGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
genomic: CTCATTCTACTTAAAACTCCCACCAGgtatctctct ... ctttttgcagTGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
EST: gi|37994639|gb|CF806304.1|CF806304
EST:     CTCATTCTACTTAAAACTCCCACCAG                         TGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
genomic: CTCATTCTACTTAAAACTCCCACCAGgtatctctct ... ctttttgcagTGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
EST: gi|9986909|gb|BE661017.1|BE661017
EST:     CTCATTCTACTTAAAACTCCCACCAG                         TGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG
genomic: CTCATTCTACTTAAAACTCCCACCAGgtatctctct ... ctttttgcagTGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctggagtatttgaatatatagtcacttttaatggaagttttgctttttgcagTGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATGATGCTAAGATGAGTGAATT
                            ttttaat  putative branch site (score: 3)
                                        ttttgcttttt  putative PPT
       agtatttgaatatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttgtgttgtttctgaacgatttctctgttatctgtttcaattttgctggagtatttgaatatatagtcacttttaatggaagttttgctttttgcagTGATGGCAGGTTTGGCTCCAGAGGGAACACAATTCGATGGTCGCCAATATGATGCTAAGATGAGTGAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
-tcttgtg
- - - - - gtttctg
- - - - - - - - - - - - - - - - - ctgtttc
- - - - - - - - - - - - - - - - - - - - - - - tgctgga