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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttttttagtatctgggaattttaaattgcactaaaagaatcattagtttgcttgtgcttattttaatatgggtcgtgatacaaatcttaaactcatcatatttgttgagctatttgcttgtgttgactgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACATCAGACGCCCTTGGAGGTTCACGTGCAAACCCAGCTAAGAGGCGGGAGAT

Basic information

species Glycine max
transcript GLYMA12G01290.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G01290.1 (Glycine max), 3'ss of exon 20
lower sequence: AT3G63460.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaattttttttagtatctgggaattttaaattgcactaaaagaatcattagtttgcttgtgcttattttaatatgggtcgtgatacaaatcttaaactcatcatatttgttgagctatttgcttgtgttgactgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACATCAGACGCCCTTGGAGGTTCACGTGCAAACCCAGCTAAGAGGCGGGAGAT
                                                         | || |    ||| ||  |   | |    |   | |    || |  | | |  |  |   ||   ||  |||  ||||  ||||  || || |  ||| |  |  |||| |||||||||||||||||||||||||| || || || |||||  ||||||| ||  |  |||||| ||| |||||
------------------------------------------------------gtatcgtacgacgtttcattagcaccttatctctgttttgtttctgagtaaagtcatataatgatcacctcttgtaaactgatccagCCCACCAGAAACCTGTGATAGCAACGTTGACAAGGCTTTTCAATGAGACATCGGAAGCACTGGGAGGCGCACGTGCGAATACTACTAAGAAGCGTGAGAT

upper sequence: GLYMA12G01290.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv13s0158g00140.t01 (Vitis vinifera), 3'ss of exon 20
gtaattttttttagtatctgggaattttaaattgcactaaaagaatcattagtttgcttgtgcttattttaatatgggtcgtgatacaaat-cttaaactcatcatatttgttgagctatttgcttgtgttgactgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACATCAGACGCCCTTGGAGGTTCACGTGCAAACCCAGCTAAGAGGCGGGAGAT
                                     | | |   | ||||  | |    |  || | ||| |    ||  | ||  |  | |||  | || | | |    |||| ||   | ||  | |  | |   ||||  || |||| |||  | ||  |||| |||||||| || |||||||| || ||||| ||||| ||||||||||||||||||||||| |||| |||||| ||
---------------------------------ttttttatacttttattaaatgggcaatatttgtattatt----gttatcatctagttacttgcattcttgaaa---attgaccttgctcctcttct--atttctccagCCCAGCAAAGGCCAGTAGTTGCAACATTGACAAGACTGTTCAATGAAACGTCAGAGGCCCTGGGAGGTTCACGTGCAAACCCAGCCAAGAAGCGGGAAAT
















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|8285921|gb|BE023480.1|BE023480
EST:     TGCAGCTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: TGCAGCTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaatttttt ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
EST: gi|5677132|gb|AI938262.1|AI938262
EST:     TGCAGCTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: TGCAGCTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaatttttt ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
EST: gi|151406859|gb|EV276674.1|EV276674
EST:     TGCAGCTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: TGCAGCTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaatttttt ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
EST: gi|10237897|gb|BE806785.1|BE806785
EST:     TGCAGCTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: TGCAGCTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaatttttt ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
EST: gi|17963212|gb|BM269964.1|BM269964
EST:     CTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: CTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaatttttt ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
EST: gi|11274739|gb|BF325074.1|BF325074
EST:     TGCAGCTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: TGCAGCTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaatttttt ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
EST: gi|17402051|gb|BM178833.1|BM178833
EST:     TGCAGCTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: TGCAGCTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaatttttt ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
EST: gi|17401849|gb|BM178631.1|BM178631
EST:     TGCAGCTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTG                         GGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT
genomic: TGCAGCTCCTCCTCCTACTTTGCAGACTGCTGATACTTCAAAAGTACCTGgtaatttttt ... actgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatcttaaactcatcatatttgttgagctatttgcttgtgttgactgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACATCAGACGCCCTTGGAGGTTCACGTGCAAACCCAGCTAAGAGGCGGGAGAT
                                        tgttgac  putative branch site (score: 3)
              atcatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttttttagtatctgggaattttaaattgcactaaaagaatcattagtttgcttgtgcttattttaatatgggtcgtgatacaaatcttaaactcatcatatttgttgagctatttgcttgtgttgactgtgccagGGCATCAAATGCCTATTGTCACAACTTTGACAAGGCTTTTCAATGAGACATCAGACGCCCTTGGAGGTTCACGTGCAAACCCAGCTAAGAGGCGGGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT