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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcactaatgcatcttgttatatgtaagcgcatttgtgttgttttaatttggtgcttgtattatttgtgaatttagtgtttcccatcttggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATTGTTATGGGAAAGTGGTTGGAGCTAGCATCATTGATGATTACCTCTGCTG

Basic information

species Glycine max
transcript GLYMA20G22090.1
intron # 1
splice site 3'
intron type U2

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|151404862|gb|EV274676.1|EV274676
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|208203506|gb|GD998834.1|GD998834
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|208046548|gb|GD849104.1|GD849104
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|15000159|gb|BI320973.1|BI320973
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|208278659|gb|GE080370.1|GE080370
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|207804567|gb|GD777740.1|GD777740
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|15000274|gb|BI321088.1|BI321088
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|193531663|gb|FK491413.1|FK491413
EST:     CCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|19271164|gb|BM887420.1|BM887420
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|193464573|gb|FK431913.1|FK431913
EST:     CCTGGGCCGGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCTGGGCC-GATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|298176542|gb|HO023129.1|HO023129
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|9819641|gb|BE555154.1|BE555154
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|193656165|gb|FK603281.1|FK603281
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|8283494|gb|BE021053.1|BE021053
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|19452639|gb|BM954049.1|BM954049
EST:     CCGTCGTTCGATTCNNNNNNNAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|209729516|gb|BW651856.1|BW651856
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|208136180|gb|GD939265.1|GD939265
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|7684961|gb|AW755609.1|AW755609
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|192326394|gb|FK015911.1|FK015911
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCTGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|193497465|gb|FK462979.1|FK462979
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|298176621|gb|HO023208.1|HO023208
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|298175563|gb|HO018274.1|HO018274
EST:     CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CCGTCGTTCGATTCGCCTCTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
EST: gi|15202225|gb|BI425289.1|BI425289
EST:     CTGAACTTGCCTGGGCCGATGCCGGTCCCGAG                         GTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT
genomic: CTGAACTTGCCTGGGCCGATGCCGGTCCCGAGgttactttct ... ggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttggtgcttgtattatttgtgaatttagtgtttcccatcttggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATTGTTATGGGAAAGTGGTTGGAGCTAGCATCATTGATGATTACCTCTGCTG
 ttttaat  putative branch site (score: 3)
              tattatttgtgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcactaatgcatcttgttatatgtaagcgcatttgtgttgttttaatttggtgcttgtattatttgtgaatttagtgtttcccatcttggtttgtcagGTTGCTGAGCCCCAAGTTAGCAGACTCTGCGTGGAGGCTGAAGAATTCATTGTTATGGGAAAGTGGTTGGAGCTAGCATCATTGATGATTACCTCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
-tgcacta
- - - - -tgcatct
- - - - - - - - - - - -tgtaagc
- - - - - - - - - - - - - - - gcatttg
- - - - - - - - - - - - - - - - - - -tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - tggtgct