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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttctcccttagactaaccttatattttcgtggaattttgatattggtttgagcaaaaagcactttattattattattattattatttttgatgtggcagCAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGATGCAGCTGCAGGAAATTCAAGACAACATAAAGAGCAGGCGCAATAAGATC

Basic information

species Glycine max
transcript GLYMA10G08680.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G08680.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G06130.2 (Arabidopsis thaliana), 3'ss of exon 1
------cttctccct---tagactaaccttatattttcgtggaattttgatattggtttgagcaaaaagcactttattattattattattattatttttgatgtggcagCAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGATGCAGCTGCAGGAAATTCAAGACAACATAAAGAGCAGGCGCAATAAGATC
      ||| |  ||   || |  | |  ||   | |      ||| | || ||| ||  | |    |  |  |||||  | |  |   |||| |||         ||| ||||| || || ||||||||  ||||||| ||| | || ||| ||||||||||||| |||||||| ||||| ||||||| ||| || ||||||||||| 
gggagccttgtagctatgtatatgatctatagcgtgtataacgattatcattttgattctaactggtaatagattatttgtttggtggatattgttt---------cagTAACTTCTGTATCATTGAGGGATCAGAGACAGTTCAAGACTTTGTGCAGATGCAGCTTCAGGAAATCCAAGATAACATAAGGAGTAGACGCAATAAGATA

upper sequence: GLYMA10G08680.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g03000.t01 (Vitis vinifera), 3'ss of exon 1
cttctcccttagactaaccttat--attttcgtggaattttgatattggtttgagcaaaaagcacttt-attattattattattattatttttgatgtggcagCAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGATGCAGCTGCAGGAAATTCAAGACAACATAAAGAGCAGGCGCAATAAGATC
 |  |   ||      ||  |||  |||||| |   | |||  |||||   ||| | |      | |  | | |  || ||||| |    ||| || | |||||||||| |||||||| || || || ||||| ||  |||| ||| | ||||||||| | |||||||||||||| |||||||  ||  |||| || ||||||
gtgttagtttgatagtactgtattcattttcctaacacttttttattg---tgatctatggtttcatggagtgtgttttttattttacgatttcattttgcagCAACTTCTGCATTATAGAAGGACCGGAGACTGTCCAGGACTTTGTTCAGATGCAGGTTCAGGAAATTCAAGATAACATAAGTAGTCGGCGGAACAAGATC
















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|151406795|gb|EV276610.1|EV276610
EST:     GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAG                         CAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGAT
genomic: GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAGgttgttgcaa ... gatgtggcagCAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGAT
EST: gi|12773616|gb|BG238543.1|BG238543
EST:     GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAG                         CAACTTTTGCATTATTGAGGGGCCAGAGACG
genomic: GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAGgttgttgcaa ... gatgtggcagCAACTTTTGCATTATTGAGGGGCCAGAGACG
EST: gi|209716979|gb|BW654382.1|BW654382
EST:     GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAG                         CAACTTTTGCATTATTGAGGGGCC
genomic: GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAGgttgttgcaa ... gatgtggcagCAACTTTTGCATTATTGAGGGGCC
EST: gi|298172041|gb|HO021633.1|HO021633
EST:     GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAG                         CGACTTTTGCATTATCGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGAT
genomic: GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAGgttgttgcaa ... gatgtggcagCAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGAT
EST: gi|151401727|gb|EV271540.1|EV271540
EST:     GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAG                         CAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGAT
genomic: GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAGgttgttgcaa ... gatgtggcagCAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGAT
EST: gi|209708303|gb|BW683893.1|BW683893
EST:     GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAG                         CAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGAT
genomic: GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAGgttgttgcaa ... gatgtggcagCAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGAT
EST: gi|213587093|gb|DB965881.1|DB965881
EST:     GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAG                         CAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGAT
genomic: GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAGgttgttgcaa ... gatgtggcagCAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGAT
EST: gi|16995619|gb|BM084991.1|BM084991
EST:     GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAG                         CAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGAT
genomic: GTCTGCTTTTCTTCTTCAAAGGATGCAGGCTCCAGTGACAACACACCGAGgttgttgcaa ... gatgtggcagCAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttgagcaaaaagcactttattattattattattattatttttgatgtggcagCAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGATGCAGCTGCAGGAAATTCAAGACAACATAAAGAGCAGGCGCAATAAGATC
                                         ttttgat  putative branch site (score: 4)
         aaaaagcactttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttctcccttagactaaccttatattttcgtggaattttgatattggtttgagcaaaaagcactttattattattattattattatttttgatgtggcagCAACTTTTGCATTATTGAGGGGCCAGAGACGGTTGAGGATTTTATGCAGATGCAGCTGCAGGAAATTCAAGACAACATAAAGAGCAGGCGCAATAAGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
-ttctccc
- - - - - - actaacc
- - - - - - - - - - - - - - - - - - - - - - tggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaagca