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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagagcttatacacaagcacaactggacaagccagttggaactagttgttttatgatcctttgtcagtttgtccttactcattttctgccattatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC

Basic information

species Glycine max
transcript GLYMA10G35950.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35950.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g32300.1 (Oryza sativa), 3'ss of exon 4
tagagcttatacacaagcacaactggacaagcc---agttggaactagttgttttatgatcctttgtcagtt---tgtccttactcattttctgccattatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC
      |||    || |  | |   |   | |    | ||| || |  ||| | | ||| |  |  || ||    ||  || |  | |    |     | |   |||| ||||| ||||||||||||||  |||| ||||||  |||||| ||||| ||||| ||||| || || ||||||||||||||||||| ||| |   | |
-----attactgccatgtcctatgtggtgacctcttaattgaaaatt-ttgatctctgacctgtgatctgtcagatggactgaaacctaccataaatctttgctagGAACAAGTGAGAAGTGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGAGCAGTCATGCTACGGAGAAAATTTTACCCTGCTGCTATCAAATATCTAC

upper sequence: GLYMA10G35950.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g25890.1 (Oryza sativa), 3'ss of exon 1
tagagcttatacacaagcacaactggacaagccagttggaactagttgttttatg---atcctttgtcagtttgtccttactcattttctgccattatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC
   |  |||    || |  |     |     |   ||  ||   |||| | |       | || |||  ||| | |   | |  |    |   | | |   |||| ||||| ||||||||||||||  |||| ||||||  |||||| || || ||||| ||||| || || |||||||||||||| |||| ||| |   | |
--aacgttactgccatgtcctgtatggtggcctcatttaaaaatgttgatcttcatctgtgctctgtgggttggactggaatt-taccataaaactttactagGAACAAGTGAGAAGTGGTGATGCAAGTGCTACTGAGTATTTTGAGCTGGGAGCAGTCATGCTACGGAGAAAATTTTACCCTGCCGCTATCAAATATCTAC

upper sequence: GLYMA10G35950.3 (Glycine max), 3'ss of exon 4
lower sequence: AT1G22700.3 (Arabidopsis thaliana), 3'ss of exon 3
tagagcttatacacaagcacaactggacaagccagttggaactagttgttt-tatgatcctttgtcagtttgtccttactcattttctgccattatctc----agGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC
  || | | || ||      || | |  | ||  | |  |  |  |||||  | |||||     || |  ||   |   ||  ||  || | ||||  |    ||||||||||||| || || |||||  ||||||| ||||| ||||| ||||||||||||||| || | ||||| ||||| ||||| || | |||||| ||||
--gaacat-tagacttatttaagtagctatgcttgctcaacgtttttgttaatttgatcaa--atctggatgctatggttctattgttgtctttatgacctgaagGAGCAAGTAAGGAGCGGAGATGCAAGTGCAACAGAGCTCTTTGAGCTTGGTGCAGTGATGTTGAGAAGGAAGTTTTATCCTGCAGCCAACAAGTTTTTGC

upper sequence: GLYMA10G35950.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0072g00860.t01 (Vitis vinifera), 3'ss of exon 4
tagagcttatacacaagcacaactggacaagccagttggaactagttgttttatgatcctttgtcagtttgtcct--tactcattttctgccattatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC
      || |  |  |     | |   ||    | |    ||||     |   ||  |     || |||| |  |  ||  | | |  |      || |||||||||||||||||||||||||||  |||||||||| || ||||||||||| ||||||||| |||| ||||||||||| || |||||||| || |||||||
-gttttttctgaaggaaatttatttttcattataatgtatactaaagagtggctgg-caggaatctgtttcttatattatgcctctctttttggaatttcagGAGCAAGTAAGAAGTGGTGATGCCAGTGCAACTGAACTGTTTGAACTTGGAGCAGTGATGTTGCGGAGGAAATTTTATCCAGCTGCTACTAAATTCTTGC

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|21994168|gb|BQ785696.1|BQ785696
EST:     GCCAAGTTCTTGTCCGCAGAGAACTCGACCTATCTGCCAAAGAGTTGCAG                         GAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGT
genomic: GCCAAGTTCTTGTCCGCAGAGAACTCGACCTATCTGCCAAAGAGTTGCAGgtaagagcct ... attatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGT
EST: gi|16106191|gb|BI893931.1|BI893931
EST:     GCCAAGTTCTTGTCCGCAGAGAACTCGACCTATCTGCCAAAGAGTTGCAG                         GAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGT
genomic: GCCAAGTTCTTGTCCGCAGAGAACTCGACCTATCTGCCAAAGAGTTGCAGgtaagagcct ... attatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGT
EST: gi|192310568|gb|FG999563.1|FG999563
EST:     GCAGAGAACTCGACCTATCTGCCAAAGAGTTGCAG                         GAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGT
genomic: GCAGAGAACTCGACCTATCTGCCAAAGAGTTGCAGgtaagagcct ... attatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttttatgatcctttgtcagtttgtccttactcattttctgccattatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC
                          tccttac  putative branch site (score: 2)
                                              ttatctc  putative PPT
     ttatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagagcttatacacaagcacaactggacaagccagttggaactagttgttttatgatcctttgtcagtttgtccttactcattttctgccattatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT