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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgagttcatctattctttatagaaatcaactagagtgatgtctgtattttggtttcttaactctttatttttttttttcatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTCATCATGACATTGCAAAGGAAATACCAGTACATCTTCAAAGGATCCAGTA

Basic information

species Glycine max
transcript GLYMA06G45160.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 4
--gtatttgagttcatctattctttataga-aatcaactagagtgatgtctgtattttggtt-----tcttaactctttatttttttttttcatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTCATCATGACATTGCAAAGGAAATACCAGTACATCTTCAAAGGATCCAGTA
   ||||   | | || |  |  ||||      ||   |  | |    | |  ||||| |||     |  |  || |  | | ||| ||||  ||| ||||||| || || || || |||||||| |||||||| || ||||| || ||||||||||||||| |||| || |||||| | || || |||||||| || ||
ggctattcttgctaattttgtgcttatgtttgttctgttgcaatctattttccattttagttgttgcttctgcctttcaactctttcttttatttttcagCTGGGATTGTCATTGAAGAGAAAAACTGGCCACCCTTCTTCCCTATTATTCATCATGACATTTCAAATGAGATACCAATCCACCTACAAAGGATGCAATA

upper sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G100809_T01 (Zea mays), 3'ss of exon 4
----------gtatttgagttcatcta-ttctttatagaaatcaactagagtgatgtctgtattttggtttcttaactctttatttttttttttcat-ttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTCATCATGACATTGCAAAGGAAATACCAGTACATCTTCAAAGGATCCAGTA
          | ||| | | |  |  |   |  |  |||||||   | |  || | | | | ||   | || |  |||     || || | ||  || || ||||||| || || ||||| |||||||||||||| || ||||||||| |||| || ||||||||| | || || |||||  | ||||| |||||||| || ||
agaatcagttggattggtggtggtaaaacaccctgaagaaatc---tcggttgctatatat-ttcgagcttgtgcactaacctttattatcttctatctttcagCTGGCATTGTGATAGAAGAGAAAAATTGGCCTCCCTTTTTCCCCCTCATCCACCATGACATTTCTAATGAGATACCTATCCATCTACAAAGGATGCAATA

upper sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 4
-gtatttgagttcatctattctttataga--aatcaactagagtgatgtctgt--attttggtttct--taactctttatttttttttttcatttg-cagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTCATCATGACATTGCAAAGGAAATACCAGTACATCTTCAAAGGATCCAGTA
  || || || | || | ||  |||| |   |  |  |     |  |  ||||    | ||  || |  |||   |    |||||  |||| |||| ||||||| || || || || || || ||||||||||| ||| | ||||| ||||||||||||||| | || || |||||| | || || |||||||| |||||
actaattaagctaatttgttgcttattgcccatgctgcagtccttttacctgttaggtctgtcttttaataataataccctttttcctttcgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTA

upper sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatttgagttcat-ctattctttatagaaatcaactagagtgatgtctgtattttggtttcttaactctttatttttttttttcatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTCATCATGACATTGCAAAGGAAATACCAGTACATCTTCAAAGGATCCAGTA
|||| |  ||  ||  |||  ||| |||||| |   |    |   ||    || |    | || |     | || ||| ||||      | ||| ||||| || ||||| |||||||| |||||||| ||||| ||  |||| |||||||||||| |||| || |||||  | ||||| || || ||||| ||
gtatctttgtcaatattatcttttgtagaaacc---tgacatttcgttc-catgtgaaatgctcatgctgtcatctttattttg-----gtagCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA

upper sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 4
gtatttgagt-tcatctattctttatagaaatcaactagagtgatgtctgtattt-tggtttcttaactctttatttttttttttcatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTCATCATGACATTGCAAAGGAAATACCAGTACATCTTCAAAGGATCCAGTA
   ||||  | |  | |||    |     |||||| |||  |||    ||| ||  ||   |||  | |||  || |  || |||| || ||||||||||| || ||||||||||||||||||||||| ||||||||| | |||||||||||||||||||| ||||||||| | ||||  || | | | |||||
--gtttgtctgttgtttatatcattagtgaatcaattaggttgagtagtgttttcatgcagtctacaatctaaatatcattctttctttggcagCTGGAATTGTCATAGAGGAGAAAAATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTA

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|193537659|gb|FK497592.1|FK497592
EST:     GAACTAAAACGAAGGGAAGATGCTATAGCACGAG                         CTGGAATAGTTATAGAGGAGAAAAATTGGCCTACCTTTTTTCCCCATCATT
genomic: GAACTAAAACGAAGGGAAGATGCTATAGCACGAGgtatttgagt ... tcatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCC-ACCTTTTTTCCCCATCATT
EST: gi|193726147|gb|FK656437.1|FK656437
EST:     GAACTAAAACGAAGGGAAGATGCTATAGCACGAG                         CTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTC
genomic: GAACTAAAACGAAGGGAAGATGCTATAGCACGAGgtatttgagt ... tcatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTC
EST: gi|13181293|gb|BG352633.1|BG352633
EST:     TAAAACGAAGGGAAGATGCTATAGCACGAG                         CTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTC
genomic: TAAAACGAAGGGAAGATGCTATAGCACGAGgtatttgagt ... tcatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTC
EST: gi|298178903|gb|HO024638.1|HO024638
EST:     GAACTAAAACGAAGGGAAGATGCTATAGCACGAG                         CTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTC
genomic: GAACTAAAACGAAGGGAAGATGCTATAGCACGAGgtatttgagt ... tcatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTC
EST: gi|193536034|gb|FK491332.1|FK491332
EST:     GAACTAAAACGAAGGGAAGATGCTATAGCACGAG                         CTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTC
genomic: GAACTAAAACGAAGGGAAGATGCTATAGCACGAGgtatttgagt ... tcatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTC
EST: gi|193668046|gb|FK610618.1|FK610618
EST:     GAACTAAAACGAAGGGAAGATGCTATAGCACGAG                         CTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTC
genomic: GAACTAAAACGAAGGGAAGATGCTATAGCACGAGgtatttgagt ... tcatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTC
EST: gi|21887940|gb|BQ741153.1|BQ741153
EST:     GAACTAAAACGAAGGGAAGATGCTATAGCACGAG                         CTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTC
genomic: GAACTAAAACGAAGGGAAGATGCTATAGCACGAGgtatttgagt ... tcatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtgatgtctgtattttggtttcttaactctttatttttttttttcatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTCATCATGACATTGCAAAGGAAATACCAGTACATCTTCAAAGGATCCAGTA
                      tcttaac  putative branch site (score: 2)
                    tttcttaactctttat  CT-rich tract
            tattttggtttcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgagttcatctattctttatagaaatcaactagagtgatgtctgtattttggtttcttaactctttatttttttttttcatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTCATCATGACATTGCAAAGGAAATACCAGTACATCTTCAAAGGATCCAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA