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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccataaaagctagtaagaggatttgtaggaggattaagaattattcctaagaggacttcgaagagtactcttgcttactgttctacatctgtctgtgcagGTGGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAACCTGCAGAACATTGTACGAAAACTTAAAACTGGGAAATGTGATTATCATT

Basic information

species Glycine max
transcript GLYMA17G01120.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01120.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G456690_T01 (Zea mays), 3'ss of exon 8
----ccataaaagctagtaagaggatttgtaggaggattaagaattattcctaagaggacttcgaagagtactcttgcttactgttctacatctgtctgtgcagGTGGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAACCTGCAGAACATTGTACGAAAACTTAAAACTGGGAAATGTGATTATCATT
    ||  |    || |   || |      |  |   ||||  ||| | ||||   ||| |    |      |     |||            |||   ||||||||||||| ||| | || ||||| ||||| || |||||||| ||| ||||||||||||| |||||  | ||  |||| |  || |||||||| ||||| |
gtaacctcattcccttgatggatggc--agaaaatcgttaattattttacctagctggagtgaatatgtgtataacaattagcaaatgctgcgtgtgcttgcagGTGGAGGGCAAACCTGTTTTGAAGTTTGCACTTTGTTATGGATTCAGGAACCTGCAGAATATTGTTAGGAAGATTAAGATGGGAAAATGTGAATATCACT

upper sequence: GLYMA17G01120.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G171998_T01 (Zea mays), 3'ss of exon 8
ccataaaagctagtaagaggatt-tgtaggaggattaagaattattc--ctaagaggacttcgaagagtactcttgcttactgttctacatctgtctgtgcagGTGGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAACCTGCAGAACATTGTACGAAAACTTAAAACTGGGAAATGTGATTATCATT
  | |     |     || |||  || |  |  | |||   | |     ||     || |      |  ||  ||    | ||  || | | ||   |  ||||||||||| ||| | || ||||| ||||| || |||||||| ||| |||||||||||||  ||||  | ||  |||| |  || |||||||| || || |
gtaaactcattcccttgatgatcatggaaaaccagtaattttcacctagcttgagtgattgtatgtataacaattagcaaatg--ctgcgtgtgctag--cagGTGGAGGGCAAACCTGTTTTGAAGTTTGCACTTTGTTATGGATTCAGGAACCTGCAGAATGTTGTTAGGAAGATTAAGATGGGAAAATGTGAATACCACT

upper sequence: GLYMA17G01120.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G16440.1 (Arabidopsis thaliana), 3'ss of exon 7
ccataaaagctagtaagaggatttgtaggaggattaagaattattcctaagaggacttcgaagagtactcttgcttactgttctacatctgtctgt-gcagGTGGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAACCTGCAGAACATTGTACGAAAACTTAAAACTGGGAAATGTGATTATCATT
      ||| |  ||    || |   |  ||  || | | ||  ||  |  |   |  |   ||      |||  |  |||||  ||||| | | | | || |||| || ||||||||||| |||||||| || ||||| ||||||| |||||| ||||| ||||| || | | | |||||  | ||||| |||||||| |
----gtaagttcttagccagactatgaacagttttgaaattttctctcattaatccccctcgga-----tttgtctcatgttcgtcatctttttcttgaagTTGGAAGGTAAAACAGTGTTAAAATTTGCGCTGTGTTACGGTTTCCAGAACCTCCAGAATATTGTTCGGAGAGTGAAAACGCGCAAATGCGATTATCAGT

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|6482176|gb|AW201447.1|AW201447
EST:     TGACCTTCAAAAACATCAGGAATTCAGATTTTCAGGAAGTTACTCTGGAG                         GTGGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAAC
genomic: TGACCTTCAAAAACATCAGGAATTCAGATTTTCAGGAAGTTACTCTGGAGgcaagtcctt ... gtctgtgcagGTGGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAAC
EST: gi|14992014|gb|BI317687.1|BI317687
EST:     TGACCTTCAAAAACATCAGGAATTCAGATTTTCAGGAAGTTACTCTGGAG                         GTGGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAAC
genomic: TGACCTTCAAAAACATCAGGAATTCAGATTTTCAGGAAGTTACTCTGGAGgcaagtcctt ... gtctgtgcagGTGGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAAC
EST: gi|10709530|gb|BF009254.1|BF009254
EST:     TGACCTTCAAAAACATCAGGAATTCAGATTTTCAGGAAGTTACTCTGGAG                         GTAGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAAC
genomic: TGACCTTCAAAAACATCAGGAATTCAGATTTTCAGGAAGTTACTCTGGAGgcaagtcctt ... gtctgtgcagGTGGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAAC
EST: gi|19269650|gb|BM885906.1|BM885906
EST:     CAGATTTTCAGGAAGTTACTCTGGAG                         GTGGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAAC
genomic: CAGATTTTCAGGAAGTTACTCTGGAGgcaagtcctt ... gtctgtgcagGTGGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctaagaggacttcgaagagtactcttgcttactgttctacatctgtctgtgcagGTGGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAACCTGCAGAACATTGTACGAAAACTTAAAACTGGGAAATGTGATTATCATT
                          tgcttac  putative branch site (score: 2)
                                          tctgtct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccataaaagctagtaagaggatttgtaggaggattaagaattattcctaagaggacttcgaagagtactcttgcttactgttctacatctgtctgtgcagGTGGAGGGAAAAACAGTGTTGAAATTTGCTCTCTGTTATGGTTTCCGGAACCTGCAGAACATTGTACGAAAACTTAAAACTGGGAAATGTGATTATCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
ccataaaa
- - - - - - - - - ggatttg