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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtctctcacttgtgaggttatttgtctctgttgttcaattgaatacaaatttgataattaaatgtgtccaaacttaactgagaatcacaattttgtgtagGAAATGGCAAATACAGAATACTTGGATGACCAAGATGCTGAAGAGCCGGATGACTTCATCATTTCGCTCACTGCACAG

Basic information

species Glycine max
transcript GLYMA20G32370.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32370.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv13s0019g04770.t01 (Vitis vinifera), 3'ss of exon 19
gtttgtctctcacttgtgaggttatttgtctctgttgttcaattgaatacaaatttgataattaaatgtgtccaaacttaactgagaatcacaattttgtgtagGAAATGGCAAATACAGAATACTTGGATGACCAAGATGCTGAAGAGCCGGATGACTTCATCATTTCGCTCACTGCACAG
||||||     |    | || ||| |  | | ||    ||||||| |    |   |               |  ||||||  | || |   ||||||     |||||||| | |  |  ||||||||||||||||||||||||||||| || ||||| || || ||||| ||||||||||||
gtttgtgaaatatacat-agtttactaatatttgcc--tcaattggaagtgagacta--------------cttaacttatat-agcacttcaatttaa-acagGAAATGACCAGCAGGGAATACTTGGATGACCAAGATGCTGAAGAACCAGATGATTTTATTATTTCACTCACTGCACAG
















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|254330664|gb|GR841929.1|GR841929
EST:     TCAAGGTTTTACGCATAGAGATGCAATTGGAGACAGTATTCCATATGCAG                         GAAATGGCAAATACAGAATACTTGGATGACCAAGATGCTGAAGAGCCGGAT
genomic: TCAAGGTTTTACGCATAGAGATGCAATTGGAGACAGTATTCCATATGCAGgtttgtctct ... ttttgtgtagGAAATGGCAAATACAGAATACTTGGATGACCAAGATGCTGAAGAGCCGGAT
EST: gi|192297269|gb|FG990617.1|FG990617
EST:     TCAAGGTTTTACGCATAGAGATGCAATTGGAGACAGTATTCCATACGCAG                         GAAATGGCAAATACAGAATACTTGGATGACCAAGATGCT
genomic: TCAAGGTTTTACGCATAGAGATGCAATTGGAGACAGTATTCCATATGCAGgtttgtctct ... ttttgtgtagGAAATGGCAAATACAGAATACTTGGATGACCAAGATGCT
EST: gi|51343541|gb|CO984274.1|CO984274
EST:     ACGCATAGAGATGCAATTGGAGACAGTATTCCATATGCAG                         GAAATGGCAAATACAGAATACTTGGATGACCAAGATGCTGAAGAGCCGGAT
genomic: ACGCATAGAGATGCAATTGGAGACAGTATTCCATATGCAGgtttgtctct ... ttttgtgtagGAAATGGCAAATACAGAATACTTGGATGACCAAGATGCTGAAGAGCCGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatttgataattaaatgtgtccaaacttaactgagaatcacaattttgtgtagGAAATGGCAAATACAGAATACTTGGATGACCAAGATGCTGAAGAGCCGGATGACTTCATCATTTCGCTCACTGCACAG
                          acttaac  putative branch site (score: 3)
     ttgataattaaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtctctcacttgtgaggttatttgtctctgttgttcaattgaatacaaatttgataattaaatgtgtccaaacttaactgagaatcacaattttgtgtagGAAATGGCAAATACAGAATACTTGGATGACCAAGATGCTGAAGAGCCGGATGACTTCATCATTTCGCTCACTGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA