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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctttcatcaaacattttggcttatatatatagagtttttatacaccctttctttggttcatttaacaccttctaatgttttattctttataacccttcatttggttagttgacttcatatgttttgatttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG

Basic information

species Glycine max
transcript GLYMA14G00760.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G00760.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 2
gtctttcatcaaacattttggcttatatatatagagtttttatacaccctttctttggttcatttaacaccttctaatgttttattctttataacccttcatttggttagttgacttcatatgttttgatttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG
                             || |   |||    | ||    || |        ||  ||  |   ||   || |   |  | |   || |  | ||||  |   |||  |  ||||     |  | |||||||||||| ||||||||||||||||| ||||||||||| ||| | ||||| || |||||| |||| || |||||||| || |||||||| |||||||
----------------------------gta-atgatttcgggatacggggtcatcaa---gctttgcatgtatcaaaaattaaaattccaaattgctcc--tgggtttctcagctttcttggttta----tgaacagATGTTTGCATTGTTGGTGTTGCACGTACGCCAATGGGTGGCTTTTTGGGTACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG
















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|16349042|gb|BI974637.1|BI974637
EST:     ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|7478350|gb|AW666230.1|AW666230
EST:     ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|9986217|gb|BE660325.1|BE660325
EST:     ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|209700566|gb|BW670310.1|BW670310
EST:     ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATTGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|19269211|gb|BM885467.1|BM885467
EST:     ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|16348094|gb|BI973689.1|BI973689
EST:     ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|19935544|gb|BQ080482.1|BQ080482
EST:     ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|120491397|gb|EH219564.1|EH219564
EST:     ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|192312109|gb|FK003872.1|FK003872
EST:     ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|37993878|gb|CF805624.1|CF805624
EST:     CAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: CAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|7926100|gb|AW832126.1|AW832126
EST:     TCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: TCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|192317815|gb|FK009407.1|FK009407
EST:     ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|192312110|gb|FK003873.1|FK003873
EST:     ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|7233754|gb|AW569097.1|AW569097
EST:     ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|13481409|gb|BG510752.1|BG510752
EST:     ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATTGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|192302972|gb|FG996988.1|FG996988
EST:     ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
EST: gi|19345910|gb|BM890790.1|BM890790
EST:     ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAG                         ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA
genomic: ATCAATGGCTCCAGTAGCAGCAGCATCTTCAGATTCAATCAAGCCAAGAGgtctttcatc ... atttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctttataacccttcatttggttagttgacttcatatgttttgatttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG
                                              tttctat  CT-rich tract
                                   atatgttttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctttcatcaaacattttggcttatatatatagagtttttatacaccctttctttggttcatttaacaccttctaatgttttattctttataacccttcatttggttagttgacttcatatgttttgatttctatagATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG