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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctggttttgtaagtgctgctattttttatttttatttgttttatgaaatatggtgggatagttttttgtttgtgaccactcatgtgcttattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCAGAAGACTATGGATGGGAAGGTGAGTAACAGTAAT

Basic information

species Glycine max
transcript GLYMA04G41600.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G53120.1 (Arabidopsis thaliana), 3'ss of exon 1
---------gtctggttttgtaagtgctgctattttttatttttatttgttttatgaaatatggtgggatagttttttgtttgtgaccactcatgtgcttattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCAGAAGACTATGGATGGGAAGGTGAGTAACAGTAAT
          |       ||| |||  |  ||  | || ||  | |||||    | || |   ||| |     |  | |||||       |  | ||  || | ||||||| |||||||  | ||||||||| ||  | ||||||||  | ||  |||| |||||||| ||||||||| |||||||||||||||| ||||||       
ctgaaatctattcaacggtgttagt-tttttaagtctttttgatttttgtgccttcaagttgtgtgtggattctcatggtttgctgtt-tttgtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAA-------

upper sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G53120.5 (Arabidopsis thaliana), 3'ss of exon 1
gt-ctggttttgtaagtgctgctattttttatttttatttgttttatgaaatatggtgggatagttttttgtttgtgaccactcatgtgcttattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCAGAAGACTATGGATGGGAAGGTGAGTAACAGTAAT
||  | ||||| |||||  |  |  ||||| |   |    ||| | ||   |    |   || ||||  ||||| ||        | ||  || | ||||||| |||||||  | ||||||||| ||  | ||||||||  | ||  |||| |||||||| ||||||||| |||||||||||||||| ||||||       
gtgttagttttttaagtctttttgatttttgtgccttcaagttgtgtg---tggattctcatggtttgctgtttttg--------tttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAA-------

upper sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G53120.2 (Arabidopsis thaliana), 3'ss of exon 1
--gtctggttttgtaagtgctgctattttttatttttatttgttttatgaaatatggtgggatagttttttgtttgtgaccactcatgtgcttattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCAGAAGACTATGGATGGGAAGGTGAGTAACAGTAAT
   |       ||| |||  |  ||  | || ||  | |||||    | || |   ||| |     |  | |||||       |  | ||  || | ||||||| |||||||  | ||||||||| ||  | ||||||||  | ||  |||| |||||||| ||||||||| |||||||||||||||| ||||||  | |||
ctattcaacggtgttagt-tttttaagtctttttgatttttgtgccttcaagttgtgtgtggattctcatggtttgctgtt-tttgtttgtgtagtatacagAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAATGGAAAT

upper sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 2
gtctggttttgtaagtgctgctattttttatttttatttgttttatgaaatatggtgggatagttttttgtttgtgaccactcatgtgcttattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCAGAAGACTATGGATGGGAAGGTGAGTAACAGTAAT
   | ||||| |||||  |  |  ||||| |   |    ||| | ||   |    |   || ||||  ||||| ||        | ||  || | ||||||| |||||||  | ||||||||| ||  | ||||||||  | ||  |||| |||||||| ||||||||| |||||||||||||||| ||||||       
-gttagttttttaagtctttttgatttttgtgccttcaagttgtgtg---tggattctcatggtttgctgtttttg--------tttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAA-------

upper sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 1
--------gtctggttttgtaagtgctgctattttttatttttatt--tgttttatgaaatatggtgggatagttttttgtttgtgaccactcatgtgcttattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCAGAAGACTATGGATGGGAAGGTGAGTAACAGTAAT
        |   || |||  |||||   | |||   |||  |   |  ||  || |  | ||||  |  |     || |  || | || |      || ||  |||  ||||||||||||| | ||||||||  ||||| |||||||| ||||||||||| |||||||||||||| ||||| |||||||||||||| ||||||| | |  
catattttgatgggattttgaagtgaaac-attcaatatgatggctactgccttttctactatga-gaaactccattcttcttataacta------tgtttgatttctAGAGACTGGAGCCGGAGAAGAAAAAGATAATCTATGGAGGGCGGCGCAGGAAAAGGTTTGGAATGCCCGAAGATTATGGATGGGAAGGCGAGTAACGGGA--

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|16997075|gb|BM086447.1|BM086447
EST:     GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAG                         AGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
genomic: GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAGgcaagcaacg ... tattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
EST: gi|207806267|gb|GD778744.1|GD778744
EST:     GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAG                         AGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
genomic: GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAGgcaagcaacg ... tattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
EST: gi|207737556|gb|GD716020.1|GD716020
EST:     GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAG                         AGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
genomic: GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAGgcaagcaacg ... tattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
EST: gi|22525271|gb|BU084082.1|BU084082
EST:     GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAG                         AGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
genomic: GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAGgcaagcaacg ... tattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
EST: gi|254325922|gb|GR838803.1|GR838803
EST:     GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAG                         AGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
genomic: GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAGgcaagcaacg ... tattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
EST: gi|254327481|gb|GR837104.1|GR837104
EST:     GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAG                         AGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
genomic: GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAGgcaagcaacg ... tattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
EST: gi|192295186|gb|FG986905.1|FG986905
EST:     GTCGCTCGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAG                         AGACTGGAGCCTGTGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
genomic: GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAGgcaagcaacg ... tattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
EST: gi|208189977|gb|GD993565.1|GD993565
EST:     GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAG                         AGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
genomic: GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAGgcaagcaacg ... tattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
EST: gi|298177837|gb|HO027390.1|HO027390
EST:     GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCGTCAG                         AGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG
genomic: GTCGCTTGGCTTGTTCGCCTTCACTCTCCGACATTCACATCATTCATCAGgcaagcaacg ... tattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatatggtgggatagttttttgtttgtgaccactcatgtgcttattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCAGAAGACTATGGATGGGAAGGTGAGTAACAGTAAT
                                           cttatttt  CT-rich tract
              atagttttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctggttttgtaagtgctgctattttttatttttatttgttttatgaaatatggtgggatagttttttgtttgtgaccactcatgtgcttattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCAGAAGACTATGGATGGGAAGGTGAGTAACAGTAAT

-tctggtt
- - - - - - - gtgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - tggtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgc