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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAGTCATGGATGATGCAGATATCAAATTGGCTGTACGATCTATTTTGTTTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTGgtattagaaccaatttaaaaaattgaatttcatagtttttaatgcaatcacatgtgatttttagaaggtatatttaatttttcatttagcttccttgtactgcag

Basic information

species Glycine max
transcript GLYMA15G19670.4
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G19670.2 (Glycine max), 5'ss of exon 9
lower sequence: PP1S237_29V6.1 (Physcomitrella patens), 5'ss of exon 10
AATAGTCATGGATGATGCAGATATCAAATTGGCTGTACGATCTATTTTGTTTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTGgtattagaaccaatttaaaaaattgaatttcatagtttttaatgcaatcacatgtgatttttagaaggtatatttaatttttcattt-agcttccttgtactgcag
||| || ||||| |||||||   |   | ||||||||||  || |||||||||||||||| |||||||| ||||| || ||||| || |||||  | ||||||    |||  |  | |  ||||   | |  |  |    | |   ||  ||| || || |      |||  |||   |   |||   || |    |  ||     
AATTGTGATGGACGATGCAGTCTTGCCACTGGCTGTACGTGCTGTTTTGTTTGCAGCTGTTGGTACTGCCGGTCAACGTTGTACCACCTGCCGGCGCCTGgta----aacatacgtcacgaatttcctctggtcttgcagagtagtataccatttgtttctctattagtagttttctgtgagcatcccaggtcatgtccacatt--
















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|193559875|gb|FK520512.1|FK520512
EST:     TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTG                         TTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
genomic: TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTGgtattagaac ... tgtactgcagTTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
EST: gi|9259105|gb|BE347252.1|BE347252
EST:     TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTG                         TTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
genomic: TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTGgtattagaac ... tgtactgcagTTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
EST: gi|16346239|gb|BI971834.1|BI971834
EST:     CAGCGGTGTACAACTTGCCGTAGACTG                         TTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
genomic: CAGCGGTGTACAACTTGCCGTAGACTGgtattagaac ... tgtactgcagTTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
EST: gi|8827562|gb|BE211292.1|BE211292
EST:     GGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTG                         TTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
genomic: GGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTGgtattagaac ... tgtactgcagTTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
EST: gi|20448705|gb|BQ252829.1|BQ252829
EST:     TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTG                         TTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
genomic: TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTGgtattagaac ... tgtactgcagTTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
EST: gi|193510918|gb|FK466772.1|FK466772
EST:     TGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTTG                         TTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGT
genomic: TGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACT-Ggtattagaac ... tgtactgcagTTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGT
EST: gi|19934585|gb|BQ079615.1|BQ079615
EST:     GGTCAGCGGTGTACAACTTGCCGTAGACTG                         TTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
genomic: GGTCAGCGGTGTACAACTTGCCGTAGACTGgtattagaac ... tgtactgcagTTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
EST: gi|193631080|gb|FK584549.1|FK584549
EST:     TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTG                         TTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
genomic: TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTGgtattagaac ... tgtactgcagTTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
EST: gi|254334456|gb|GR844241.1|GR844241
EST:     TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTG                         TTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
genomic: TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTGgtattagaac ... tgtactgcagTTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
EST: gi|20449046|gb|BQ253170.1|BQ253170
EST:     TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTG                         TTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
genomic: TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTGgtattagaac ... tgtactgcagTTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
EST: gi|254316180|gb|GR827717.1|GR827717
EST:     GCTGGTCAGCGGTGTACAACTTGCCGTAGACTG                         TTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
genomic: GCTGGTCAGCGGTGTACAACTTGCCGTAGACTGgtattagaac ... tgtactgcagTTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
EST: gi|192309267|gb|FG999144.1|FG999144
EST:     TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTG                         TTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
genomic: TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTGgtattagaac ... tgtactgcagTTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
EST: gi|15813675|gb|BI785950.1|BI785950
EST:     TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTG                         TTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
genomic: TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTGgtattagaac ... tgtactgcagTTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
EST: gi|19054093|gb|BM732760.1|BM732760
EST:     TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTG                         TTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC
genomic: TTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTGgtattagaac ... tgtactgcagTTTCTGCATGAAAGTATTTACGCAGATGTACTAGACCAACTTATTGGAGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATAGTCATGGATGATGCAGATATCAAATTGGCTGTACGATCTATTTTGTTTGCAGCTGTGGGTACTGCTGGTCAGCGGTGTACAACTTGCCGTAGACTGgtattagaaccaatttaaaaaattgaatttcatagtttttaatgcaatcacatgtgatttttagaaggtatatttaatttttcatttagcttccttgtactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG