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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatctatatctgtaatgtttgtattccattgttgcatttatatttttattaatcttattctttaatcattaatgtcgttcctggttacattttaaacagGTATGACAATCTTGTCATTCGGTTGATAGGGCTAACCGTTTTTGCCTTTGCAACTGCCTTTATACTACTAATGATGGAGAGTCTTAGTGCTTTTCTTCAT

Basic information

species Glycine max
transcript GLYMA15G04970.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G04970.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv06s0004g03450.t01 (Vitis vinifera), 3'ss of exon 17
-ttatctatatctgtaa---tgtttgtattccattgttgcatttatatttttattaatcttattctttaatcattaatgtcgttcctggttacattttaaacagGTATGACAATCTTGTCATTCGGTTGATAGGGCTAACCGTTTTTGCCTTTGCAACTGCCTTTATACTACTAATGATGGAGAGTCTTAGTGCTTTTCTTCAT
  | |  |||   | ||       || | ||  | ||   ||  |  |  ||   | | |  || ||| |  | |||  ||  |  | | |   | ||  |||||||| | ||  ||||||| ||| || | |||||| | |||||||||||||| ||||| || |||||||| ||||||||||  ||||||||||| || |||
cctgtaaataggggaaaaaacacatgcactctctggtgatat--acttgattgaaagtatgtttgtttgagtaataagatcactttttgatggttatt--acagGTATAATAACTTTGTCATCCGGATGGTGGGGCTAGCAGTTTTTGCCTTTGCTACTGCTTTCATACTACTCATGATGGAGACACTTAGTGCTTTCCTCCAT
















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|27425984|gb|CA937504.1|CA937504
EST:     TCAGAACTTTCTACTGTTTTCTATGAGAAAGTCCTGCTTCTTGCTTGGGG                         GTATGACAATCTTGTCATTCGGTTGATAGGGCTAACCGTTTTTGCCTTTGC
genomic: TCAGAACTTTCTACTGTTTTCTATGAGAAAGTCCTGCTTCTTGCTTGGGGgtaagcttga ... ttttaaacagGTATGACAATCTTGTCATTCGGTTGATAGGGCTAACCGTTTTTGCCTTTGC
EST: gi|27425844|gb|CA937364.1|CA937364
EST:     TCAGAACTTTCTACTGTTTTCTATGAGAAAGTCCTGCTTCTTGCTTGGGG                         GTATGACAATCTTGTCATTCGGTTGATAGGGCTAACCGTTTTTGCCTTTGC
genomic: TCAGAACTTTCTACTGTTTTCTATGAGAAAGTCCTGCTTCTTGCTTGGGGgtaagcttga ... ttttaaacagGTATGACAATCTTGTCATTCGGTTGATAGGGCTAACCGTTTTTGCCTTTGC
EST: gi|14999778|gb|BI320592.1|BI320592
EST:     TCAGAACTTTCTACTGTTTTCTATGAGAAAGTCCTGCTTCTTGCTTGGGG                         GTATGACAATCTTGTCATTCGGTTGATAGGGCTAACCGTTTTTGCCTTTGC
genomic: TCAGAACTTTCTACTGTTTTCTATGAGAAAGTCCTGCTTCTTGCTTGGGGgtaagcttga ... ttttaaacagGTATGACAATCTTGTCATTCGGTTGATAGGGCTAACCGTTTTTGCCTTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattaatcttattctttaatcattaatgtcgttcctggttacattttaaacagGTATGACAATCTTGTCATTCGGTTGATAGGGCTAACCGTTTTTGCCTTTGCAACTGCCTTTATACTACTAATGATGGAGAGTCTTAGTGCTTTTCTTCAT
     taatcttattctttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatctatatctgtaatgtttgtattccattgttgcatttatatttttattaatcttattctttaatcattaatgtcgttcctggttacattttaaacagGTATGACAATCTTGTCATTCGGTTGATAGGGCTAACCGTTTTTGCCTTTGCAACTGCCTTTATACTACTAATGATGGAGAGTCTTAGTGCTTTTCTTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttcctg