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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttattgcttctccaattttatattgatggtttgtattttcccaagatcagaattgttcttcacaattgagaatttatgttcaaattttgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCAAGACTCCTTTCTTCAACCAACCAGCCTAGCTTTTTGAGCCCTAAAGATT

Basic information

species Glycine max
transcript GLYMA06G09320.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G09320.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 13
tttttattgcttctccaattttatattgatggtttgtattttcccaagatcagaattgttcttcacaattga---------gaatttatgttcaa--attttgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCAAGACTCCTTTCTTCAACCAACCAGCCTAGCTTTTTGAGCCCTAAAGATT
    ||   | |   | ||     | | |   ||| | ||    ||| |  | ||    ||| | | | ||            |||  |||   |  | |   ||   ||||| ||||  |||| ||||||||| |||   |||||||| || |||||||||||||| || || |||||||||||||| || ||  | |||   |||||| 
---gtaagtcattcgctatagggcagttaaactttctgttaatacaaaaaaaaaaaaactctgctccactgctctccatactgattactgtcttatcactaaaattttcagAGGATCACAGAGAAGCAGAACAAAGTTTCAATTACTGATAGGATGTGGGCAAGACTTCTCTCCTCAACCAACCAGCCAAGTTTCCTCAGCAAGAAAGATG

upper sequence: GLYMA06G09320.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 10
---------------tttttattgcttctccaatttta-tattga---tggtttgtattttccca--agatcagaattgt-tcttcacaat-tgagaatttatgttcaaattttgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCAAGACTCCTTTCTTCAACCAACCAGCCTAGCTTTTTGAGCCCTAAAGATT
               | ||| |   |  || |  |||| | || |     |||    | ||| ||  |||    ||   | || | | ||| ||   | | |   ||      |  |   ||||||||||  |||| |||||||||||| ||||| || ||||| |||||||| ||  | || |  || || ||||||||  ||||  ||||||   | ||  
gtaagtccagaacactctttttcaatgatcaatctttagtgttcagttcagttcagttcttcacaccagacatcaaccatatcctgataatctggacactgaaactccggcgatt-tctacagAGAATCACGGAGAAGCAGAACAAGGTGGTGATCACGGACAGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCATGCTTCCTGAGCCACGAGGACG

upper sequence: GLYMA06G09320.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 12
---tttttattgcttctccaattttatattgatggtttgtatttt---cccaagatcagaattgttcttcacaattgagaatttatgttcaaattttgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCAAGACTCCTTTCTTCAACCAACCAGCCTAGCTTTTTGAGCCCTAAAGATT
     || || |  ||  |  | ||  ||  ||| |||   | ||           |||||  |||       |   |   ||| | ||  |    ||||   ||| | ||||||||||| | ||||||||||||||| || ||||| ||||||||||| |||||||| ||||| |||||||| |||||   || ||| |||||| 
aagaattcatggtgtcctc--tcttgaatgaatgattttgctcttaggttttgacacagaacagttgag-gttacaaaacttttgtatttga---ctgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCAAGGCTCCTTTCGTCAACAAACCAGCCAAGCTTCCAGAACCCCAAAGATG

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|254330797|gb|GR842062.1|GR842062
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATTgttagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|57576052|gb|CX549023.1|CX549023
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATTgttagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|207775996|gb|GD748225.1|GD748225
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATTgttagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|15814347|gb|BI786622.1|BI786622
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATTgttagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|193599972|gb|FK549737.1|FK549737
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATTgttagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|254334741|gb|GR844526.1|GR844526
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATTgttagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|193666112|gb|FK610533.1|FK610533
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATTgttagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|298176657|gb|HO026778.1|HO026778
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATTgttagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|254334742|gb|GR844527.1|GR844527
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATTgttagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|208136778|gb|GD935062.1|GD935062
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGCTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATTgttagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|254320047|gb|GR830963.1|GR830963
EST:     GATTTACAGTTGGACT-GTCAAT-GCAGACAGAC-TATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATTgttagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|254320046|gb|GR830962.1|GR830962
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATTgttagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|254339207|gb|GR847924.1|GR847924
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATTgttagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|58024605|gb|CX711346.1|CX711346
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATTgttagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|17024115|gb|BM095149.1|BM095149
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATTgttagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatcagaattgttcttcacaattgagaatttatgttcaaattttgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCAAGACTCCTTTCTTCAACCAACCAGCCTAGCTTTTTGAGCCCTAAAGATT
                                          ttttgat  putative branch site (score: 4)
                            aatttatgttcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttattgcttctccaattttatattgatggtttgtattttcccaagatcagaattgttcttcacaattgagaatttatgttcaaattttgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCAAGACTCCTTTCTTCAACCAACCAGCCTAGCTTTTTGAGCCCTAAAGATT

- - - - -cttctcc
- - - - - - - - - - - - - -gatggtt
- - - - - - - - - - - - - - - - - - - - ttcccaa