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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgccatttatgcatgcaggctcttgttttacatggatttattgttcgacattaaagggtatctatcttgtcagtggctgatgttaacattccttttcagGGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGGAAACGGCTCTATGCTACCAACTCACTATTTAGTACATGGGACAAACAGT

Basic information

species Glycine max
transcript GLYMA11G36670.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G36670.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 6
ttgccatttatgcatgca-ggctcttgttttacatggatttattgttcgacattaaagggtatc----tatcttgtcagtggctgatgttaacattccttttcagGGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGGAAACGGCTCTATGCTACCAACTCACTATTTAGTACATGGGACAAACAGT
   |||||     || || |||   |||  || ||    |  ||| |    ||| |      |     |  | | | | |   |||  | | | |   ||||||||| || | |||| ||||||| ||||| ||||| || || |||||||||||||| ||||| |||| |||||||||||| || |||||||||||  | ||||
---ccattatctaattcatggcatgtgtcataaatttggtggttgctgagaattgagaacccttgaattgccatataaataaatgacttgatcctg--ttttcagGGAAAAAGGTTGCGAGGGGGACCTCAAATGATCCAGTTAAGTTTAGATGGGAAGCGGCTTTATGTTACCAACTCACTCTTCAGTACATGGGATCACCAGT
















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|58018645|gb|CX705387.1|CX705387
EST:     CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAG                         GGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG
genomic: CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAGgttattgcga ... tccttttcagGGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG
EST: gi|120493301|gb|EH221468.1|EH221468
EST:     CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAG                         GGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG
genomic: CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAGgttattgcga ... tccttttcagGGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG
EST: gi|120531913|gb|EH260046.1|EH260046
EST:     CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAG                         GGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG
genomic: CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAGgttattgcga ... tccttttcagGGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG
EST: gi|21887640|gb|BQ740853.1|BQ740853
EST:     CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAG                         GGCAACAAGTTGAGAGGGGGCCCTCAGATGATT
genomic: CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAGgttattgcga ... tccttttcagGGCAACAAGTTGAGAGGGGGCCCTCAGATGATT
EST: gi|209706000|gb|BW664875.1|BW664875
EST:     CCTGAGATTCAG                         GGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG
genomic: CCTGAGATTCAGgttattgcga ... tccttttcagGGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG
EST: gi|120493203|gb|EH221370.1|EH221370
EST:     CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAG                         GGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG
genomic: CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAGgttattgcga ... tccttttcagGGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG
EST: gi|209718082|gb|BW671919.1|BW671919
EST:     CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAG                         GGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG
genomic: CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAGgttattgcga ... tccttttcagGGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG
EST: gi|209703147|gb|BW664669.1|BW664669
EST:     CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAG                         GGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG
genomic: CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAGgttattgcga ... tccttttcagGGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG
EST: gi|9259532|gb|BE347687.1|BE347687
EST:     CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAG                         GGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG
genomic: CTATAACTGATGATGGTGAAACTTGGCAAGCTGAAGTGCCTGAGATTCAGgttattgcga ... tccttttcagGGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgacattaaagggtatctatcttgtcagtggctgatgttaacattccttttcagGGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGGAAACGGCTCTATGCTACCAACTCACTATTTAGTACATGGGACAAACAGT
                                    tgttaac  putative branch site (score: 2)
                                          cattccttttc  CT-rich tract
                                      ttaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgccatttatgcatgcaggctcttgttttacatggatttattgttcgacattaaagggtatctatcttgtcagtggctgatgttaacattccttttcagGGCAACAAGTTGAGAGGGGGCCCTCAGATGATTCAATTGAGTTTAGATGGGAAACGGCTCTATGCTACCAACTCACTATTTAGTACATGGGACAAACAGT

-tgccatt
- - - - - -gcatgca
- - - - - - - - - - - - - - - -catggat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctga