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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttttagttctttggttccttttcctgaagttgtcagcttgtcaaattaccaagtctgaataactcaattttgataacaaaataatttcttcttacagATTGAAGGATCTTTTATCCAAGGGTTGGGTTTTTTCATGCTTGAAGAATATGAAACAAATCTTGACGGTTTGATCTTGGTAGATGGTACATGGAACTACA

Basic information

species Glycine max
transcript GLYMA02G44000.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G44000.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G43600.1 (Arabidopsis thaliana), 3'ss of exon 7
ttgttttagttctttggttccttttcctgaagttgtcagcttgtcaaattaccaagtctgaataactcaattttgataacaaa----ataatttcttcttacagATTGAAGGATCTTTTATCCAAGGGTTGGGTTTTTTCATGCTTGAAGAATATGAAACAAATCTTGACGGTTTGATCTTGGTAGATGGTACATGGAACTACA
                            | | |    |    |  | |   |  |     ||| | ||  ||||| |||         |   ||  |  | |||||||||||||||||| | |||||  | || ||||||||||||||||| ||   |  | |||  || ||  |  |  ||   ||| | |||||||  ||||
----------------------------gtaatatatatgaagagagacctcagaaagcaaatgaatcttttttg-taatgtgttttgtgtgtttctgcttcagATTGAAGGATCTTTTGTTCAAGGACTTGGGTTTTTCATGCTTGAAGAGTACATAGAAGATCCAGAAGGACTCCTTCTGACGGATAGCACATGGACATACA
















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|105634745|gb|DW247655.1|DW247655
EST:     TTATCTATGATTGTGGACAGAGTCTCAACCCAGCTGTGGATTTAGGACAG                         ATTGAAGGATCTTTTATCCAAGGGTTGGGTTTTTTCATGCTTGAAGAATAT
genomic: TTATCTATGATTGTGGACAGAGTCTCAACCCAGCTGTGGATTTAGGACAGgtaagctaat ... cttcttacagATTGAAGGATCTTTTATCCAAGGGTTGGGTTTTTTCATGCTTGAAGAATAT
EST: gi|6724807|gb|AW309206.1|AW309206
EST:     TTATCTATGATTGTGGACAGAGTCTCAACCCAGCTGTGGATTTAGGACAG                         ATTGAACGATCTTTTATCCAAAGGTAGGGTTTTTTCATGCTTGAAGAATAT
genomic: TTATCTATGATTGTGGACAGAGTCTCAACCCAGCTGTGGATTTAGGACAGgtaagctaat ... cttcttacagATTGAAGGATCTTTTATCCAAGGGTTGGGTTTTTTCATGCTTGAAGAATAT
EST: gi|10232634|gb|BE801522.1|BE801522
EST:     TTATCTATGATTGTGGACAGAGTCTCAACCCAGCTGTGGATTTAGGACAG                         ATTGAAGGATCTTTTATCCAAGGGTTGGGTTTTTTCATGCTTGAAGA
genomic: TTATCTATGATTGTGGACAGAGTCTCAACCCAGCTGTGGATTTAGGACAGgtaagctaat ... cttcttacagATTGAAGGATCTTTTATCCAAGGGTTGGGTTTTTTCATGCTTGAAGA
EST: gi|105632325|gb|DW246413.1|DW246413
EST:     TTATCTATGATTGTGGACAGAGTCTCAACCCAGCTGTGGATTTAGGACAG                         ATTGAAGGATCTTTTATCCAAGGGTTGGGTTTTTTCATGCTTGAAGAATAT
genomic: TTATCTATGATTGTGGACAGAGTCTCAACCCAGCTGTGGATTTAGGACAGgtaagctaat ... cttcttacagATTGAAGGATCTTTTATCCAAGGGTTGGGTTTTTTCATGCTTGAAGAATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattaccaagtctgaataactcaattttgataacaaaataatttcttcttacagATTGAAGGATCTTTTATCCAAGGGTTGGGTTTTTTCATGCTTGAAGAATATGAAACAAATCTTGACGGTTTGATCTTGGTAGATGGTACATGGAACTACA
                            tgataac  putative branch site (score: 2)
                                          tttcttcttac  putative PPT
               aataactcaattttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttttagttctttggttccttttcctgaagttgtcagcttgtcaaattaccaagtctgaataactcaattttgataacaaaataatttcttcttacagATTGAAGGATCTTTTATCCAAGGGTTGGGTTTTTTCATGCTTGAAGAATATGAAACAAATCTTGACGGTTTGATCTTGGTAGATGGTACATGGAACTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - tggttcc
- - - - - - - - - - - - tcctgaa
- - - - - - - - - - - - - - - - - - - gcttgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaataac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa