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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttctccaatctgtctctattctaattctaataagagtgacgttatggaattaacgtatgagatggtgtgttggtattttttatgaatgatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGTTTGTGGTGTTTCTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATG

Basic information

species Glycine max
transcript GLYMA07G39530.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G39530.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g39310.1 (Oryza sativa), 3'ss of exon 1
tttttctccaatctgtctctattct----aattctaataagagtgacgttatggaattaacgtatgagatggtgtgttggtattttttatgaatgatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGTTTGTGGTGTTTCTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATG
         ||| || |  |||  |    ||| |||  |    | ||     ||  |  |   ||   |   | | ||  |  ||  |     | |   |||||||     |||||||  || |||||||||||  | ||||| ||||||||||| ||||||||||||||||| || || ||  |||||||||| ||  | |||
--agagataaatgtgcccttatcttgctaaatgctagcatattttactgctcgg--tctattcattgaaccttttttttttccttggtcgtgtttacgaaccagTGCAAGTACTGGAGTAAAGAGAAGAGGTGGTCCAGGTGGGCTAAACAAAGTCTGTGGTGTTTCTCCTGAGCTGCAAGCTATTGTTGGTGAACCAACCATG

upper sequence: GLYMA07G39530.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0187g00190.t01 (Vitis vinifera), 3'ss of exon 1
-tttttctccaatctgtctctattctaattc-taataagagtgacgttatggaattaacgtatgagatggtgtgttggtattttttatgaatgatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGTTTGTGGTGTTTCTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATG
    ||   |  ||| ||| | |   |||    ||      |    || |  ||  || |  | | |   ||  |  || | | |||||  | | || | |||| || | ||| ||||||||||||||||||| | || |||||||||||||| ||||| |||||  ||||||||||||| |||||||| |||||  | |||
ggcattgctctttctttctatgtatgaatctgcaaccttcatttaatttttcaagaaaagggtaaaaatttg-atgtgtctgtattatggtttaattgc-agTGCTCCAGCTGCAGCCAAAAGAAGAGGTGGCTCGGGGGGTCTAAACAAAGTCTGTGGGGTTTCAACTGAACTTCAGGCTGTTGTTGGCGAGCCAACCATG

upper sequence: GLYMA07G39530.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0187g00240.t01 (Vitis vinifera), 3'ss of exon 1
-tttttctccaatctgtctctattctaattc-taataagagtgacgttatggaattaacgtatgagatggtgtgttggtattttttatgaatgatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGTTTGTGGTGTTTCTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATG
   || |||   ||| ||| | |   |||    ||      |    || |  ||  || |  | | |   ||  |  || | | |||||  | | || | |||| || | ||| | ||||||||||||| ||| | || |||||||||||||| ||||| |||||  ||||||||||||| |||||||| |||||  | |||
gcattgctcatttctttctatgtatgaatctgcaaccttcatttaatttttcaagaaaagggtaaaaatttg-atgtgtctgtattatggtttaattgc-agTGCTCCAGCTGCACCCAAAAGAAGAGGCGGCTCGGGGGGTCTAAACAAAGTCTGTGGGGTTTCAACTGAACTTCAGGCTGTTGTTGGCGAGCCAACCATG

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|26047410|gb|CA784213.1|CA784213
EST:     CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAG                         TGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
genomic: CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAGgtgcgatttt ... gatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
EST: gi|298170700|gb|HO019324.1|HO019324
EST:     CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAG                         TGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCT
genomic: CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAGgtgcgatttt ... gatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCT
EST: gi|209716952|gb|BW679626.1|BW679626
EST:     CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAG                         TGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
genomic: CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAGgtgcgatttt ... gatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
EST: gi|308098694|gb|HO760435.1|HO760435
EST:     CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAG                         TGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
genomic: CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAGgtgcgatttt ... gatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
EST: gi|298171705|gb|HO021297.1|HO021297
EST:     CCTCCTCGAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAG                         TGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
genomic: CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAGgtgcgatttt ... gatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
EST: gi|192306778|gb|FG998145.1|FG998145
EST:     CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAG                         TGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
genomic: CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAGgtgcgatttt ... gatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
EST: gi|209698471|gb|BW667268.1|BW667268
EST:     CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAG                         TGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
genomic: CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAGgtgcgatttt ... gatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
EST: gi|298173846|gb|HO017182.1|HO017182
EST:     CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAG                         TGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
genomic: CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAGgtgcgatttt ... gatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
EST: gi|209710490|gb|BW662026.1|BW662026
EST:     CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAG                         TGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
genomic: CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAGgtgcgatttt ... gatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
EST: gi|192305692|gb|FG998364.1|FG998364
EST:     CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAG                         TGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
genomic: CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAGgtgcgatttt ... gatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
EST: gi|213608595|gb|DB967098.1|DB967098
EST:     CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAG                         TGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
genomic: CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAGgtgcgatttt ... gatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
EST: gi|298186747|gb|HO037380.1|HO037380
EST:     CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAG                         TGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
genomic: CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAGgtgcgatttt ... gatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
EST: gi|16349396|gb|BI974991.1|BI974991
EST:     CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAG                         TGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT
genomic: CCTCCTCAAAATGCTCACACTGTTGCCCCTCCTCAAGTGCCCAAAGAAAGgtgcgatttt ... gatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggaattaacgtatgagatggtgtgttggtattttttatgaatgatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGTTTGTGGTGTTTCTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATG
     aattaac  putative branch site (score: 2)
                               tattttttatgaatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttctccaatctgtctctattctaattctaataagagtgacgttatggaattaacgtatgagatggtgtgttggtattttttatgaatgatttaccagTGTTCAAACTGGAGCCAAAAGAAGAGGTGGCGCTGGTGGTCTAAACAAAGTTTGTGGTGTTTCTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATG

- -ttctcca
- - - - - - ctgtctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtg