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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgagcatgcttgtggacaaagttggtatccactttctattttattttataagttgacatctggtatgtcttgtaatagGTTAAACTTACCGAAATTGAGTCAGAGTTAACTGAGATGAATGCAAATGGTGAAAAGTTGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTC

Basic information

species Glycine max
transcript GLYMA11G12120.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G12120.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g00290.t01 (Vitis vinifera), 3'ss of exon 3
gtatgtgagcatgcttgtggacaaagttggtatccactttc---tattttattttataagttgacatctggtatgtcttgtaatagGTTAAACTTACCGAAATTGAGTCAGAGTTAACTGAGATGAATGCAAATGGTGAAAAGTTGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTC
            |  | |  | ||| ||         ||     |||| | |  | || ||| || |   | ||| | | |  ||||| ||||||   ||  ||||  ||||| |   ||| || ||||||||||| ||||||||||||||  | || |  |||||||  ||||||||||||||||
------------gtatatcaagaaatttatcccttgattaaaaatattatttgctgtatgttaaccttgtgcatg-catatgctagGTAAAACTTGGAGAGCTTGAAGCAGAGCTGGTTGAAATAAATGCAAATGGCGAAAAGTTGCAACGTGCTTATAGTGAGCTTGCAGAGTATAAGCTTGTTC
















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|213590384|gb|DB971532.1|DB971532
EST:     CACCAAAATATTCCACAACACCAGTTGATGTGAACATTGATGACCTTGAG                         GTTAAACTTACCGAAATTGAGTCAGAGTTAACTGAGATGAATGC
genomic: CACCAAAATATTCCACAACACCAGTTGATGTGAACATTGATGACCTTGAGgtatgtgagc ... cttgtaatagGTTAAACTTACCGAAATTGAGTCAGAGTTAACTGAGATGAATGC
EST: gi|209729738|gb|BW669838.1|BW669838
EST:     CACCAAAATATTCCACAACACCAGTTGATGTGAACATTGATGACCTTGAG                         GTTAAACTTACCGAAATTGAGTCAGAGTTAACTGAGATGAATGCAAATGGT
genomic: CACCAAAATATTCCACAACACCAGTTGATGTGAACATTGATGACCTTGAGgtatgtgagc ... cttgtaatagGTTAAACTTACCGAAATTGAGTCAGAGTTAACTGAGATGAATGCAAATGGT
EST: gi|209710094|gb|BW653549.1|BW653549
EST:     CACCAAAATATTCCACAACACCAGTTGATGTGAACATTGATGACCTTGAG                         GTTAAACTTACCGAAATTGAGTCAGAGTTAACTGAGATGAATGCAAATGGT
genomic: CACCAAAATATTCCACAACACCAGTTGATGTGAACATTGATGACCTTGAGgtatgtgagc ... cttgtaatagGTTAAACTTACCGAAATTGAGTCAGAGTTAACTGAGATGAATGCAAATGGT
EST: gi|208227861|gb|GE025941.1|GE025941
EST:     CACCAAAATATTCCACAACACCAGTTGATGTGAACATTGATGACCTTGAG                         GTTAAACTTACCGAAATTGAGTCAGAGTTAACTGAGATGAATGCAAATGGT
genomic: CACCAAAATATTCCACAACACCAGTTGATGTGAACATTGATGACCTTGAGgtatgtgagc ... cttgtaatagGTTAAACTTACCGAAATTGAGTCAGAGTTAACTGAGATGAATGCAAATGGT
EST: gi|209712503|gb|BW653686.1|BW653686
EST:     CACCAAAATATTCCACAACACCAGTTGATGTGAACATTGATGACCTTGAG                         GTTAAACTTACCGAAATTGAGTCAGAGTTAACTGAGATGAATGCAAATGGT
genomic: CACCAAAATATTCCACAACACCAGTTGATGTGAACATTGATGACCTTGAGgtatgtgagc ... cttgtaatagGTTAAACTTACCGAAATTGAGTCAGAGTTAACTGAGATGAATGCAAATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtatccactttctattttattttataagttgacatctggtatgtcttgtaatagGTTAAACTTACCGAAATTGAGTCAGAGTTAACTGAGATGAATGCAAATGGTGAAAAGTTGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTC
                           agttgac  putative branch site (score: 4)
         tttctattttatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgagcatgcttgtggacaaagttggtatccactttctattttattttataagttgacatctggtatgtcttgtaatagGTTAAACTTACCGAAATTGAGTCAGAGTTAACTGAGATGAATGCAAATGGTGAAAAGTTGCAACGGTCATACAACGAGCTTGTGGAGTATAAGCTTGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG