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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtataaattatttaatttatatccttgcgctgacatctttaaatttgtactaacagatgatttcctccccagGGATATTTCAAACAATAACTTAGTTGGTTCCATCCCTTCTTCCCTTGGTGACTTGGAACATCTTCTGAAGTT

Basic information

species Glycine max
transcript GLYMA17G34380.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G34380.2 (Glycine max), 3'ss of exon 16
lower sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 17
gtaagtataaattatttaatttatatccttgc-----gctgacatctttaaatttgtactaac-agatg-------atttcctccccagGGATATTTCAAACAATAACTTAGTTGGTTCCATCCCTTCTTCCCTTGGTGACTTGGAACATCTTCTGAAGTT
|||||||| | || | |  ||| | ||| |       |||||  | || || | | || |||  | ||        ||||  | | |||||| |||||||| || |   |   ||| ||||| |||||||||||||| |||||||| |||||||| ||  |
gtaagtattagttctattttttttttccctcttctctgctgaagttttaaattatttaataattatatatatatatattttttgctcagGGACATTTCAAATAACAGGATTACTGGCTCCATTCCTTCTTCCCTTGGAGACTTGGAGCATCTTCTAAAACT
















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|193692557|gb|FK627676.1|FK627676
EST:     CAGGGCGCAATTCCAATAGAACTGTCGCGGATTGGCAATTTGGATACATT                         GGATATTTCAAACAATAACTTAGTTGGTTCCATCCCTTCTTCCCTTGGTGA
genomic: CAGGGCGCAATTCCAATAGAACTGTCGCGGATTGGCAATTTGGATACATTgtaagtataa ... tcctccccagGGATATTTCAAACAATAACTTAGTTGGTTCCATCCCTTCTTCCCTTGGTGA
EST: gi|193312538|gb|FK275202.1|FK275202
EST:     CAGGGCGCAATTCCAATAGAACTGTCGCGGATTGGCAATTTGGATACATT                         GGATATTTCAAACAATAACTTAGTTGGTTCCATCCCTTCTTCCCTTGGTGA
genomic: CAGGGCGCAATTCCAATAGAACTGTCGCGGATTGGCAATTTGGATACATTgtaagtataa ... tcctccccagGGATATTTCAAACAATAACTTAGTTGGTTCCATCCCTTCTTCCCTTGGTGA
EST: gi|193363851|gb|FK329657.1|FK329657
EST:     CAGGGCGCAATTCCAATAGAACTGTCGCGGATTGGCAATTTGGATACATT                         GGATATTTCAAACAATAACTTAGTTGGTTCCATCCCTTCTTCCCTTGGTGA
genomic: CAGGGCGCAATTCCAATAGAACTGTCGCGGATTGGCAATTTGGATACATTgtaagtataa ... tcctccccagGGATATTTCAAACAATAACTTAGTTGGTTCCATCCCTTCTTCCCTTGGTGA
EST: gi|208193231|gb|GD992004.1|GD992004
EST:     CAGGGCGCAATTCCAATAGAACTGTCGCGGATTGGCAATTTGGATACATT                         GGATATTTCAAACAATAACTTAGTTGGTTCCATCCCTTCTTCCCTTGGTGA
genomic: CAGGGCGCAATTCCAATAGAACTGTCGCGGATTGGCAATTTGGATACATTgtaagtataa ... tcctccccagGGATATTTCAAACAATAACTTAGTTGGTTCCATCCCTTCTTCCCTTGGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatccttgcgctgacatctttaaatttgtactaacagatgatttcctccccagGGATATTTCAAACAATAACTTAGTTGGTTCCATCCCTTCTTCCCTTGGTGACTTGGAACATCTTCTGAAGTT
                              tactaac  putative branch site (score: 0)
                                           tttcctcccc  putative PPT
                    tttaaatttgtactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtataaattatttaatttatatccttgcgctgacatctttaaatttgtactaacagatgatttcctccccagGGATATTTCAAACAATAACTTAGTTGGTTCCATCCCTTCTTCCCTTGGTGACTTGGAACATCTTCTGAAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG