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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggaaggatgttgtaggtttaaatgttttagagaataatgtctatcttgtgaacttgtctttttgtgcctattgtgttcttatgtctttgattttctcagAGTTGCTGTGAAGGGATTGAACAAGCAAAGTCCAATAACAAGGGCTGGATTATAGCAGAGGAGGCAGTTGTAGCTCAATGTGAGGAACCCTTGGCCGTTC

Basic information

species Glycine max
transcript GLYMA04G39660.1
intron # 4
splice site 3'
intron type U2

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|21677415|gb|BQ629766.1|BQ629766
EST:     TGGTGGAAAAATGGGATTGGATGACCCTTATTGTATATACTTGCTCAGAG                         AGTTGCTGTGAAGGGATTGAACAAGCAAAGTCCAATAACAAGGGCTGGATT
genomic: TGGTGGAAAAATGGGATTGGATGACCCTTATTGTATATACTTGCTCAGAGgttggtattc ... attttctcagAGTTGCTGTGAAGGGATTGAACAAGCAAAGTCCAATAACAAGGGCTGGATT
EST: gi|13562779|gb|BG550999.1|BG550999
EST:     TGGTGGAAAAATGGGATTGGATGACCCTTATTGTATATACTTGCTCAGAG                         AGTTGCTGTGAAGGGATTGAACAAGCAAAGTCCAATAACAAGGGCTGGATT
genomic: TGGTGGAAAAATGGGATTGGATGACCCTTATTGTATATACTTGCTCAGAGgttggtattc ... attttctcagAGTTGCTGTGAAGGGATTGAACAAGCAAAGTCCAATAACAAGGGCTGGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtgaacttgtctttttgtgcctattgtgttcttatgtctttgattttctcagAGTTGCTGTGAAGGGATTGAACAAGCAAAGTCCAATAACAAGGGCTGGATTATAGCAGAGGAGGCAGTTGTAGCTCAATGTGAGGAACCCTTGGCCGTTC
                                        ctttgat  putative branch site (score: 5)
                                       tctttgattttctc  CT-rich tract
                                         tttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggaaggatgttgtaggtttaaatgttttagagaataatgtctatcttgtgaacttgtctttttgtgcctattgtgttcttatgtctttgattttctcagAGTTGCTGTGAAGGGATTGAACAAGCAAAGTCCAATAACAAGGGCTGGATTATAGCAGAGGAGGCAGTTGTAGCTCAATGTGAGGAACCCTTGGCCGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
tggaagg
- - - - tgttgta
- - - - - - - - - - - - - - - - - - - - - - tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgccta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtctttg