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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgactgtactaagtactttccccctttcctctcgcttgtggtaattgtgaaccaatttgcaaaattgcaatattttataactgatgtaccctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGA

Basic information

species Glycine max
transcript GLYMA18G00590.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G00590.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G14040.1 (Arabidopsis thaliana), 3'ss of exon 3
tgactgtactaagtactttccccctttcctctcgcttgtggtaattgtgaaccaatttgcaaaattgcaatattttataactgatgtaccctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGA
       | ||   ||   |     |     |    |||| ||   || | | | | || ||  ||      ||||     || |||    |   ||||||| || || |||||||||||| ||||||||||||| | ||| || ||||| ||| | ||||| |||||| | ||||| |||| |   |||||  | ||||
--gtaacatta--caccaacataaatgttgatgatctgtgtta---gtaaccaagtatgtaagcttattgggtttt-----tgttgttatgtggttgcagATCAGATTCTTGCATGATCCTTCTAAAGATACAGGGTATGTTGGGAGTGCTTTGTCTAGTAATATGATAAGGTTTTTCAAGAACAGTGATGACACGTGGA

upper sequence: GLYMA18G00590.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G14030.1 (Arabidopsis thaliana), 3'ss of exon 4
------tgactgtactaag-tactttcccc-ctttcctctcgcttgtggtaattgtgaaccaatttgcaaaattgcaatattttataactgatgtaccctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGA
      |  || |   ||  ||   ||     ||| || ||   ||   ||| || |||  || |  |   |  |     | |||||||| || |    |   ||||||| || || |||||||||||  ||||||||||||| ||||| || ||||| ||| | ||||| |||||| ||||||| |||| |   |||||| ||||||
gtaacatatctctttcaaaatatgatctgtatttttctttcaggtgatataaatg-gaaggaagtatcgtgaccggttgttgttataacttatatg---tggttgcagATTAGATTCTTGCATGATCCATCTAAAGATACAGGGTTTGTTGGGAGTGCCTTGTCGAGTAATATGATAAGATTTTTCAAGAACAGTGATGAAACATGGA

upper sequence: GLYMA18G00590.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------tgactgtactaagtactttccccctttcctctcgcttgtg-gtaattgtgaaccaatttgcaaa-attgcaatattt-------tataactgatgtaccctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGA
                                                  ||  || | ||       ||||       |||   || ||| ||| |  || ||  ||   |  | ||| |       |||     || |  | |   |||||||||| ||  ||||||||||| ||||||||||||| ||||| ||  |||| || ||||| |||||| | |||||||| ||||||| |||||  |||||||
gtgagttttggaaatataatccaccattgctttgctttttggttaagaaatagcaaatgctacatttttttctctaattttgcatgttattatgaccatatgtgttaacggtttactatctacatgtgtatcttcaatctttcttgcttgcagATAAGATTCCTGCATGATCCTTCTAAAGATACAGGGTTTGTAGGTTGTGCCTTAACAAGCAACATGGTGCGATTTTTCAAGACCCCAGATGGGTCATGGA

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|193708578|gb|FK644536.1|FK644536
EST:     AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAG                         ATAAGGTTTTTGCATGATCCTG
genomic: AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAGgtaagttgtt ... ctaaatgcagATAAGGTTTTTGCATGATCCTG
EST: gi|192321462|gb|FK011748.1|FK011748
EST:     AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAG                         ATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
genomic: AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAGgtaagttgtt ... ctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
EST: gi|308098167|gb|HO761338.1|HO761338
EST:     AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAG                         ATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
genomic: AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAGgtaagttgtt ... ctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
EST: gi|6454871|gb|AW185620.1|AW185620
EST:     AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAG                         ATAAGGGTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
genomic: AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAGgtaagttgtt ... ctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
EST: gi|208059645|gb|GD860349.1|GD860349
EST:     AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAG                         ATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
genomic: AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAGgtaagttgtt ... ctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
EST: gi|10847443|gb|BF070130.1|BF070130
EST:     GGTGATTCAGGGCTTATACCCTTAGAG                         ATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
genomic: GGTGATTCAGGGCTTATACCCTTAGAGgtaagttgtt ... ctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
EST: gi|254328939|gb|GR833311.1|GR833311
EST:     AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAG                         ATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
genomic: AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAGgtaagttgtt ... ctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
EST: gi|209724301|gb|BW662914.1|BW662914
EST:     AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAG                         ATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGCCCA
genomic: AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAGgtaagttgtt ... ctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
EST: gi|254318556|gb|GR832724.1|GR832724
EST:     AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAG                         ATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
genomic: AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAGgtaagttgtt ... ctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
EST: gi|192321461|gb|FK011747.1|FK011747
EST:     AACTGAGACAAACAATGGA-CTTGGTGATTCAGGGCTTATA-CCTTAGAG                         ATAAGG-TTTTGCATGATCCTGCTAAAGATACAGG-TTTGTCGGCAGTGCA
genomic: AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAGgtaagttgtt ... ctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
EST: gi|308098505|gb|HO760246.1|HO760246
EST:     AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAG                         ATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
genomic: AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAGgtaagttgtt ... ctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
EST: gi|193687270|gb|FK629125.1|FK629125
EST:     AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAG                         ATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
genomic: AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAGgtaagttgtt ... ctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
EST: gi|207810533|gb|GD781642.1|GD781642
EST:     AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAG                         ATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
genomic: AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAGgtaagttgtt ... ctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
EST: gi|19269932|gb|BM886188.1|BM886188
EST:     GGTGATTCAGGGCTTATACCCTTAGAG                         ATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
genomic: GGTGATTCAGGGCTTATACCCTTAGAGgtaagttgtt ... ctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCA
EST: gi|151410035|gb|EV279843.1|EV279843
EST:     AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAG                         ATAAGGTTTTT
genomic: AACTGAGACAAACAATGGACCTTGGTGATTCAGGGCTTATACCCTTAGAGgtaagttgtt ... ctaaatgcagATAAGGTTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgaaccaatttgcaaaattgcaatattttataactgatgtaccctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGA
        aatttgcaaaattgca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgactgtactaagtactttccccctttcctctcgcttgtggtaattgtgaaccaatttgcaaaattgcaatattttataactgatgtaccctaaatgcagATAAGGTTTTTGCATGATCCTGCTAAAGATACAGGTTTTGTCGGCAGTGCATTGACAAGTAACATGATACGATTTTTTAAGACCCAAGATGAATCATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- actgtac
- - - - - - - - -ttccccc
- - - - - - - - - - - - - tcctctc
- - - - - - - - - - - - - - - - -gcttgtg
- - - - - - - - - - - - - - - - - - - - - - -tgtgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgatg