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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttatttggttgcaaggtgatcaactgaatttcttgcttgtgcagttctatcattcctctaattctgttgttctatcttcattctggtgtatatgcagGTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGTTTTATCAAAACATTGAAGAATGAT

Basic information

species Glycine max
transcript GLYMA03G14780.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G14780.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0007g01700.t01 (Vitis vinifera), 3'ss of exon 6
---ttcttatttggttgcaaggtgatcaactgaatttcttgcttgtgcagttctatcattcctctaattctgttgtt-ctatcttcattctggtgtatatgcagGTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGTTTTATCAAAACATTGAAGAATGAT
    || ||| ||| | ||| |      | || | ||   ||      |||  ||  ||   |  |  | |  |    ||   |   || ||||   | | ||||||||||| || |||||||||||||| |  ||||| || || || ||||||||| |||| || ||||||||||||
gaagtcatatgtggct-caatgcac---agtgtaattgaagccgtaaaagtcataatatcaattcagctgtaatacaacttgatgttttttggttccttttcagGTTAAGTCAAGGATGATGGGAGATTCCACATACAAAAATACACTGGATTGTTTTGTCAAGACTTTGAAGAATGAT
















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|254342278|gb|GR853415.1|GR853415
EST:     ATTGGCTCCCCAGTTGATGTG                         GTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
genomic: ATTGGCTCCCCAGTTGATGTGgtaatgtttt ... gtatatgcagGTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
EST: gi|10848284|gb|BF071710.1|BF071710
EST:     GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTG                         GTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
genomic: GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTGgtaatgtttt ... gtatatgcagGTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
EST: gi|19053009|gb|BM731676.1|BM731676
EST:     GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTG                         GTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
genomic: GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTGgtaatgtttt ... gtatatgcagGTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
EST: gi|22930316|gb|BU547463.1|BU547463
EST:     GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTG                         GTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
genomic: GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTGgtaatgtttt ... gtatatgcagGTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
EST: gi|10255376|gb|BE823142.1|BE823142
EST:     CCCCAGTTGATGTG                         GTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
genomic: CCCCAGTTGATGTGgtaatgtttt ... gtatatgcagGTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
EST: gi|209707510|gb|BW664969.1|BW664969
EST:     GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTG                         GTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
genomic: GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTGgtaatgtttt ... gtatatgcagGTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
EST: gi|7588265|gb|AW704064.1|AW704064
EST:     GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTG                         GTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
genomic: GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTGgtaatgtttt ... gtatatgcagGTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
EST: gi|15286162|gb|BI470053.1|BI470053
EST:     GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTG                         GTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
genomic: GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTGgtaatgtttt ... gtatatgcagGTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
EST: gi|213607924|gb|DB983879.1|DB983879
EST:     GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTG                         GTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
genomic: GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTGgtaatgtttt ... gtatatgcagGTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
EST: gi|151396786|gb|EV266659.1|EV266659
EST:     GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTG                         GTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT
genomic: GTCTTGGGGCAGGGTTTTTCGCCGTCTGTATTGGCTCCCCAGTTGATGTGgtaatgtttt ... gtatatgcagGTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttctatcattcctctaattctgttgttctatcttcattctggtgtatatgcagGTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGTTTTATCAAAACATTGAAGAATGAT
             ctctaat  putative branch site (score: 3)
     tatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttatttggttgcaaggtgatcaactgaatttcttgcttgtgcagttctatcattcctctaattctgttgttctatcttcattctggtgtatatgcagGTTAAGTCGAGAATGATGGGAGATTCTAGTTACAAGAACACCCTTGATTGTTTTATCAAAACATTGAAGAATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - tgcaagg
- - - - - - - - - - - -caactga
- - - - - - - - - - - - - - - - - - - cttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattctg