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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttctgagaaccaatttctggtttttatttcagaaacaattaaggtttattttttatttaattcacaattgactgatgtgtcattggcttcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAGAGAAATCCAGTGATGAGGAGATGAGTGAAGATGAATATGATTCTAGTGA

Basic information

species Glycine max
transcript GLYMA09G39370.4
intron # 5
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|298176485|gb|HO026720.1|HO026720
EST:     TGCCGCTTTAATGATGCGTGACCGACCAAGTTATGAACAAAGGGTTAAAG                         AGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
genomic: TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAGgtattgattt ... tcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
EST: gi|151393517|gb|EV263392.1|EV263392
EST:     TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAG                         AGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
genomic: TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAGgtattgattt ... tcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
EST: gi|254327210|gb|GR836819.1|GR836819
EST:     TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAG                         AGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
genomic: TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAGgtattgattt ... tcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
EST: gi|192294831|gb|FG987520.1|FG987520
EST:     TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAG                         AGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
genomic: TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAGgtattgattt ... tcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
EST: gi|254324140|gb|GR836265.1|GR836265
EST:     TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAG                         AGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
genomic: TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAGgtattgattt ... tcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
EST: gi|151395834|gb|EV265711.1|EV265711
EST:     TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAG                         AGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
genomic: TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAGgtattgattt ... tcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
EST: gi|298193444|gb|HO033878.1|HO033878
EST:     TGCCGCTTTAATGATGCGTGACCGACCAAGTTATGAACAAAGGGTTAAAG                         AGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
genomic: TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAGgtattgattt ... tcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
EST: gi|298195504|gb|HO043895.1|HO043895
EST:     TGCCGCTTTAATGATGCGTGACCGACCAAGTTATGAACAAAGGGTTAAAG                         AGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAA
genomic: TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAGgtattgattt ... tcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAA
EST: gi|254327211|gb|GR836820.1|GR836820
EST:     TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAG                         AGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
genomic: TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAGgtattgattt ... tcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
EST: gi|22929004|gb|BU546143.1|BU546143
EST:     TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAG                         AGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
genomic: TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAGgtattgattt ... tcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
EST: gi|17020964|gb|BM091998.1|BM091998
EST:     TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAG                         AGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
genomic: TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAGgtattgattt ... tcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
EST: gi|298191356|gb|HO038835.1|HO038835
EST:     TGCCGCTTTAATGATGCGTGACCGACCAAGTTATGAACAAAGGGTTAAAG                         AGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
genomic: TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAGgtattgattt ... tcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
EST: gi|21285429|gb|BQ473300.1|BQ473300
EST:     TGCCGCTTTAATGATGCGTGACCGACCAAGTTATGAACAAAGGGTTAAAG                         AGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
genomic: TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAGgtattgattt ... tcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
EST: gi|16343018|gb|BI968613.1|BI968613
EST:     TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAG                         AGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG
genomic: TGCCGCTTTAATGATGCGTGACCGACCAAGTTACGAACAAAGGGTTAAAGgtattgattt ... tcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttattttttatttaattcacaattgactgatgtgtcattggcttcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAGAGAAATCCAGTGATGAGGAGATGAGTGAAGATGAATATGATTCTAGTGA
                          gactgat  putative branch site (score: 3)
     ttttttatttaattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttctgagaaccaatttctggtttttatttcagaaacaattaaggtttattttttatttaattcacaattgactgatgtgtcattggcttcgatgtcagAGTACTGTGAGAAGTATGCTAAACCCGAAGACATAGGGGAAGCCACAGAAGAGAAATCCAGTGATGAGGAGATGAGTGAAGATGAATATGATTCTAGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG