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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctctatgcaattgatacacttgcaatcttatgctcctgtttcattatcttggactcttttttttccaacttgtcatgcttgcgattttcatctctccccgaggggtgcaatacctaatcagtttatgttgtttttaacttaaatctctcttatgatcagAATGCTATTCCCTTAGAAAAAAGTCCCGACTGTAGCTGGGCTCCTATTTTTATTAGGCCATCAAATTTCAAGCTACCAGTTGATCATTCAATTCCTATTA

Basic information

species Glycine max
transcript GLYMA06G10180.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G10180.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv18s0001g07630.t01 (Vitis vinifera), 3'ss of exon 13
gtagctctatgcaattgatacacttgcaatcttatgctcctgtttcattatcttggactcttttttttccaacttgtcatgcttgcgattttcatctctccccgaggggtgcaatacctaatcagtttatgttgtttttaacttaaatctctct----tatgatcagAATGCTATTCCCTTAGAAAAAAGTCCCGACTGTAGCTGGGCTCCTATTTTTATTAGGCCATCAAATTTCAAGCTACCAGTTGATCATTCAATTCCTATTA
                  ||    || | | |||      |||| | ||   |   |   ||||| |  |   ||||  | |||    | || ||      ||    ||   |  || |||    ||  |   |  | ||||||  || | | |    ||  ||||||||||  || | ||||| ||||| |   ||| |||||||||||||||||||||||||||||||||||||||  |||| ||||||| ||  | ||| ||||
-----------------gtagtactgaagtattaaata--tgttgcttttggtcaaa---tttttctgtctgtttgtt-tactt-tagtatttatt-----ccagatggcatacgacttaac---ttcttacagaatctaacttccatttttatcaattaaaatcagAATGCAGTTTCTTTAGAGAAAAGCCATAACTCTAGCTGGGCTCCTATTTTTATTAGGCCATCAAATTTCAAATTACCTGTTGATCCTTTGACTCCAATTA
















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|15200214|gb|BI424233.1|BI424233
EST:     CAACTCCCACTGGTAGAATTCACAAAGGAGTATGTTCAACCTGGATGAAG                         AATGCTATTCCCTT
genomic: CAACTCCCACTGGTAGAATTCACAAAGGAGTATGTTCAACCTGGATGAAGgtagctctat ... ttatgatcagAATGCTATTCCCTT
EST: gi|23729064|gb|BU762615.1|BU762615
EST:     CAACTCCCACTGGTAGAATTCACAAAGGAGTATGTTCAACCTGGATGAAG                         AATGCTATTCCCTTAGAAAAAAGTCCCGACTGTAGCTGGGCTCCTATTTTT
genomic: CAACTCCCACTGGTAGAATTCACAAAGGAGTATGTTCAACCTGGATGAAGgtagctctat ... ttatgatcagAATGCTATTCCCTTAGAAAAAAGTCCCGACTGTAGCTGGGCTCCTATTTTT
EST: gi|17400562|gb|BM177344.1|BM177344
EST:     CAACTCCCACTGGTAGAATTCACAAAGGAGTATGTTCAACCTGGATGAAG                         AATGCTATTCCCTTAGAAAAAAGTCCCGACTGTAGC
genomic: CAACTCCCACTGGTAGAATTCACAAAGGAGTATGTTCAACCTGGATGAAGgtagctctat ... ttatgatcagAATGCTATTCCCTTAGAAAAAAGTCCCGACTGTAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcaatacctaatcagtttatgttgtttttaacttaaatctctcttatgatcagAATGCTATTCCCTTAGAAAAAAGTCCCGACTGTAGCTGGGCTCCTATTTTTATTAGGCCATCAAATTTCAAGCTACCAGTTGATCATTCAATTCCTATTA
                           ttttaac  putative branch site (score: 2)
                                       tctctcttat  putative PPT
                 tttatgttgtttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctctatgcaattgatacacttgcaatcttatgctcctgtttcattatcttggactcttttttttccaacttgtcatgcttgcgattttcatctctccccgaggggtgcaatacctaatcagtttatgttgtttttaacttaaatctctcttatgatcagAATGCTATTCCCTTAGAAAAAAGTCCCGACTGTAGCTGGGCTCCTATTTTTATTAGGCCATCAAATTTCAAGCTACCAGTTGATCATTCAATTCCTATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT