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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactatagcaagtagcaacatacttaattttcttttttatatctatatttggttcaaattttggcgttcctatgtgttgatctttcaattgcagTTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAAAGCCTGGGAGCATCAAGAGTTCTGCGTGGTGCAGCTGCTGCAGCAACTG

Basic information

species Glycine max
transcript GLYMA09G37720.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv15s0021g01810.t01 (Vitis vinifera), 3'ss of exon 12
gtaactatagcaagtagcaaca--tacttaattttcttttttatatctatatttggttcaaattttggcgttcctatgtgt-tgatctttcaattgcagTTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAAAGCCTGGGAGCATCAAGAGTTCTGCGTGGTGCAGCTGCTGCAGCAACTG
|||  | || | | |  || |   |   | |  ||  ||||   |||   | ||   ||   |||  |   |   ||| || | |  |||   ||| ||||  |||| |||||||| ||||||||  |||||||||| | |||  |||| ||| |||||||| || | ||||| |||||||||||||| ||||||||||
gtagatttatctattgccatccattttctgaagttggttttctcatcaccactt--ctc---tttctgaaatatgatgggtgtaacgttttggttgtagTTCTCCATCCCTGGTGGTCGACATGCTGTGCACCATGCGACCCTTTTGCAGAGCGTGGGAGCAGCACGGGTTCTACGTGGTGCAGCTGCAGCAGCAACTG
















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|7588079|gb|AW703882.1|AW703882
EST:     GAAATCCATCATCTATACTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAG                         TTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
genomic: GAAATCCATCATCTATACTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAGgtaactatag ... tcaattgcagTTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
EST: gi|214005584|gb|DB984592.1|DB984592
EST:     GAAATCCATCATCTATACTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAG                         TTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
genomic: GAAATCCATCATCTATACTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAGgtaactatag ... tcaattgcagTTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
EST: gi|26058746|gb|CA801660.1|CA801660
EST:     GAAATCCATCATCTATACTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAG                         TTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
genomic: GAAATCCATCATCTATACTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAGgtaactatag ... tcaattgcagTTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
EST: gi|22932923|gb|BU550062.1|BU550062
EST:     CTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAG                         TTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
genomic: CTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAGgtaactatag ... tcaattgcagTTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
EST: gi|7685215|gb|AW755863.1|AW755863
EST:     GAAATCCATCATCTATACTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAG                         TTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
genomic: GAAATCCATCATCTATACTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAGgtaactatag ... tcaattgcagTTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
EST: gi|18040948|gb|BM309242.1|BM309242
EST:     GAAATCCATCATCTATACTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAG                         TTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
genomic: GAAATCCATCATCTATACTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAGgtaactatag ... tcaattgcagTTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
EST: gi|13481420|gb|BG510763.1|BG510763
EST:     CTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAG                         TAGACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
genomic: CTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAGgtaactatag ... tcaattgcagTTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
EST: gi|24136575|gb|BU927085.1|BU927085
EST:     GAAATCCATCATCTATACTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAG                         TTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
genomic: GAAATCCATCATCTATACTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAGgtaactatag ... tcaattgcagTTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
EST: gi|17020708|gb|BM091742.1|BM091742
EST:     GAAATCCATCATCTATACTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAG                         TTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA
genomic: GAAATCCATCATCTATACTCAAGGCTTGTGCAGCATTTGCTCTTCTCCAGgtaactatag ... tcaattgcagTTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctatatttggttcaaattttggcgttcctatgtgttgatctttcaattgcagTTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAAAGCCTGGGAGCATCAAGAGTTCTGCGTGGTGCAGCTGCTGCAGCAACTG
                                   tgttgat  putative branch site (score: 4)
                                         tctttc  CT-rich tract
             ttcaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactatagcaagtagcaacatacttaattttcttttttatatctatatttggttcaaattttggcgttcctatgtgttgatctttcaattgcagTTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAAAGCCTGGGAGCATCAAGAGTTCTGCGTGGTGCAGCTGCTGCAGCAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG