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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaaatgtctattacatcaaatttaaatcatgattcttgtttcttgatttatgtgaatttaaacttatatgccttggttcttgagtgcagGTAAAAAAGTCATGGCTTGATGTTCAGCTCTGTAAAGAAGGAACCCAAGATTGTGATGCATCAGCATCAAATGATACCAATGTTGGAGGAGGAGTACTTA

Basic information

species Glycine max
transcript GLYMA16G20730.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G20730.1 (Glycine max), 3'ss of exon 11
lower sequence: AT2G35610.1 (Arabidopsis thaliana), 3'ss of exon 10
gtactaaatgtctattacatcaaatttaaatcatgattcttgtttcttgatttatgtgaatttaaacttatatgccttggttcttgagtgcagGTAAAAAAGTCATGGCTTGATGTTCAGCTCTGTAAAGAAGGAACCCAAGATTGTGATGCATCAGCATCAAATGATACCAATGTTGGAGGAGGAGTACTTA-
            || || | |       |   ||  ||||  ||  |   || ||   ||   ||  | |   |      |  ||   | ||||| ||| |||||||||||||||||||||| ||| |||||||||   |||  || || ||||||  || | |  |  ||      ||      ||| |  | 
-----------gtaatatagccgcccagatatatttttctaattaatcatttcatagaaaa--aatgtcaggagtgaaaatattt---ttcagGTGAAAGAGTCATGGCTTGATGTTCAGCTTTGTCAAGAAGGAAAAGAAGGATGCGAGGCATCAA-ATAACACTAGCCCCTCTCGGGTTCTTAAGTTCCCAA
















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|58021216|gb|CX707958.1|CX707958
EST:     TAGATTTTCGAGAGTACTCAATACTTGATAATCCCTCTCTGCCGTCAGAG                         GTAAAAAAGTCATGGCTTGATGTTCAGCTCTGTAAAGAAGGAACCCAAGAT
genomic: TAGATTTTCGAGAGTACTCAATACTTGATAATCCCTCTCTGCCGTCAGAGgtactaaatg ... ttgagtgcagGTAAAAAAGTCATGGCTTGATGTTCAGCTCTGTAAAGAAGGAACCCAAGAT
EST: gi|58024281|gb|CX711022.1|CX711022
EST:     AGATTTTCGAGAGTACTCAATAC-TGNATAATCCCTCTCTGCCGTCAGAG                         GTAAAAAAGTCATGGCTTGATGTTCAGCTCTGTAAAGAAGGAACCCAAGAT
genomic: AGATTTTCGAGAGTACTCAATACTTG-ATAATCCCTCTCTGCCGTCAGAGgtactaaatg ... ttgagtgcagGTAAAAAAGTCATGGCTTGATGTTCAGCTCTGTAAAGAAGGAACCCAAGAT
EST: gi|58016055|gb|CX702797.1|CX702797
EST:     TAGATTTTCGAGAGTACTCAATACTTGATAATCCCTCTCTGCCGTCAGAG                         GTAAAAAAGTCATGGCTTGATGTTCAGCTCTGTAAAGAAGGAACCCAAGAT
genomic: TAGATTTTCGAGAGTACTCAATACTTGATAATCCCTCTCTGCCGTCAGAGgtactaaatg ... ttgagtgcagGTAAAAAAGTCATGGCTTGATGTTCAGCTCTGTAAAGAAGGAACCCAAGAT
EST: gi|58017910|gb|CX704652.1|CX704652
EST:     AGATTTTCGAGAGTACTCAATAC-TGNATAATCCCTCTCTGCCGTCAGAG                         GTAAAAAAGTCATGGCTTGATGTTCAGCTCTGTAAAGAAGGAACCCAAGAT
genomic: AGATTTTCGAGAGTACTCAATACTTG-ATAATCCCTCTCTGCCGTCAGAGgtactaaatg ... ttgagtgcagGTAAAAAAGTCATGGCTTGATGTTCAGCTCTGTAAAGAAGGAACCCAAGAT
EST: gi|17023093|gb|BM094127.1|BM094127
EST:     TAGATTTTCGAGAGTACTCAATACTTGATAATCCCTCTCTGCCGTCAGAG                         GTAAAAAAGTCATGGCTTGATGTTCAGCTCTGTAAAGAAGGAACCCAAGAT
genomic: TAGATTTTCGAGAGTACTCAATACTTGATAATCCCTCTCTGCCGTCAGAGgtactaaatg ... ttgagtgcagGTAAAAAAGTCATGGCTTGATGTTCAGCTCTGTAAAGAAGGAACCCAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtttcttgatttatgtgaatttaaacttatatgccttggttcttgagtgcagGTAAAAAAGTCATGGCTTGATGTTCAGCTCTGTAAAGAAGGAACCCAAGATTGTGATGCATCAGCATCAAATGATACCAATGTTGGAGGAGGAGTACTTA
      tcttgat  putative branch site (score: 4)
                                          ttctt  putative PPT
        ttgatttatgtgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactaaatgtctattacatcaaatttaaatcatgattcttgtttcttgatttatgtgaatttaaacttatatgccttggttcttgagtgcagGTAAAAAAGTCATGGCTTGATGTTCAGCTCTGTAAAGAAGGAACCCAAGATTGTGATGCATCAGCATCAAATGATACCAATGTTGGAGGAGGAGTACTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG