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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgaatattaaacaacagtactttttttattttatttttatcaattttgctattctaaatgtgcatgtatgctttatcattgggtgattgaactatatataattggttcattgtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAGAAACATGCATCAATCCCATTCAAGCTCCAGAAACCAACCTCAACTTCTG

Basic information

species Glycine max
transcript GLYMA13G40130.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G40130.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G60640.1 (Arabidopsis thaliana), 3'ss of exon 11
gtacgtgaatattaaacaacagtactttttttattttatttttatcaattttgctattctaaatgtgcatgtatgctttatcattgggtgattgaactatatataattggttcattgtgtctg---cagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAGAAACATGCATCAATCCCATTCAAGCTCCAGAAACCAACCTCAACTTCTG
                                  |   || |  |   | |||||    |   | |   | | |   ||   ||      |  |||  || | |  ||  ||  |||||| ||   ||||||||||| |||||||| || || ||||| || || ||||||||| | | |||||| ||| | ||||||||||| ||  |||||||  | |||||     
---------------------------------gtaagttctgcttcttcttgctgaaatggttttttctttgtagatttctataaa---accgaaaaatttgtc-ttcttttgttgtgtgtggagcagATTACTGTAGATACAGACCGCACTGTGGTTGCATTTTACAAGTTCTTAAGGAAACACGCAACGATCCCATTCAAACTGGAGAAACCTGCATCAACCGAAT

upper sequence: GLYMA13G40130.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv06s0004g02890.t01 (Vitis vinifera), 3'ss of exon 11
gtacgtgaatattaaacaacagtactttttttattttatttttatcaattttgctattctaaatgtgcatgtatgctttatcattgggtgattgaactatatataattggttcattgtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAGAAACATGCATCAATCCCATTCAAGCTCCAGAAACCAACCTCAACTTCTG
||| || | |  |  | || | | |  | |    |||    ||    ||| |||| | ||| || |  ||||  ||||| |               |||  ||     | | |   || |  |||||| || ||||| || ||||| ||||||||||| || ||||| ||||| |||| |||||||||||| || ||||| |||||||||||| | ||| ||||  
gtaagtca-tgcttcaaaata-tgcaatctggggttttcccttgaatattctgctttcctagatctatatgttggcttttttccc-----------ctagctaatggggatcctgggttttggcagATAACCGTTGACACTGATCGAACAGTGGTAGCATTGTACAAATTCCTGAAGACACATGCATCAATTCCTTTCAAACTCCAGAAACCAGCTTCAGCTTCAA
















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|209714609|gb|BW662245.1|BW662245
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|8403249|gb|BE058883.1|BE058883
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|193717911|gb|FK655983.1|FK655983
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|26059696|gb|CA802610.1|CA802610
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|6846143|gb|AW348433.1|AW348433
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|254316462|gb|GR827999.1|GR827999
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|4289796|gb|AI437977.1|AI437977
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|192331238|gb|FK020977.1|FK020977
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|192331239|gb|FK020978.1|FK020978
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|208225225|gb|GE022242.1|GE022242
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|13240110|gb|BG359419.1|BG359419
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|254316461|gb|GR827998.1|GR827998
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|6725175|gb|AW309574.1|AW309574
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|31462823|gb|CD404851.1|CD404851
EST:     CCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTGTACAAGTTCCTCAAG
genomic: CCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|192326874|gb|FK015131.1|FK015131
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|33387977|gb|CA851184.1|CA851184
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|6069456|gb|AW099142.1|AW099142
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|31464264|gb|CD406292.1|CD406292
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|23731199|gb|BU763711.1|BU763711
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|209714608|gb|BW662244.1|BW662244
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
EST: gi|7029455|gb|AW459238.1|AW459238
EST:     GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT                         ATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG
genomic: GATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCTgtacgtgaat ... gtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgctttatcattgggtgattgaactatatataattggttcattgtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAGAAACATGCATCAATCCCATTCAAGCTCCAGAAACCAACCTCAACTTCTG
                   attgaactatatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgaatattaaacaacagtactttttttattttatttttatcaattttgctattctaaatgtgcatgtatgctttatcattgggtgattgaactatatataattggttcattgtgtctgcagATTACTGTTGATACAGATCGTACAGTGGTAGCCTTCTACAAGTTCCTCAAGAAACATGCATCAATCCCATTCAAGCTCCAGAAACCAACCTCAACTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT