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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttttttattcctgtagaaggacaattgtgtttttggaaatttaggcttgttatatttggtgctgaacctgtatgatgctattttcagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGCTGCCTCCTGGTGGACTGGCAGTTC

Basic information

species Glycine max
transcript GLYMA12G03640.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G03640.1 (Glycine max), 3'ss of exon 14
lower sequence: AT4G38600.2 (Arabidopsis thaliana), 3'ss of exon 14
-------------------gtatgtttttttattcctgtagaaggacaattgtgtttttggaaatttaggcttgttatatttggtgctgaacctg--tatgatgctatttt-cagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGCTGCCTCCTGGTGGACTGGCAGTTC---------
                   ||  | | |  |||   | |  |     |  | |  |||||    ||  |    |||  |||   | ||||  |||  | | |  | |   |  ||||||| || || ||||||||| | ||| |||| |||||| | || ||||| |||||||| ||||| || |||||||| |||||||||||  | || ||||         
gtatgttatccatcaagttgttagatatcatatctttatttattcttacctttccttttgt---ttctgaaccgttg-attactttctgattctgattttcaccccaccctgtagttactggagATCATGGGAGAACTTACAGCAGATCAGCAGAGGGCTTTCTGCCAATTTGTAACTGGAGCTCCTAGGCTTCCTCCTGGTGGCTTAGCTGTTCTGAACCCAA

upper sequence: GLYMA12G03640.1 (Glycine max), 3'ss of exon 14
lower sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 14
-------------------gtatgtttttttattcctgtagaaggacaattgtgtttttggaaatttaggcttgttatatttggtgctgaacctg--tatgatgctatttt-cagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGCTGCCTCCTGGTGGACTGGCAGTTC
                   ||  | | |  |||   | |  |     |  | |  |||||    ||  |    |||  |||   | ||||  |||  | | |  | |   |  ||||||| || || ||||||||| | ||| |||| |||||| | || ||||| |||||||| ||||| || |||||||| |||||||||||  | || ||||
gtatgttatccatcaagttgttagatatcatatctttatttattcttacctttccttttgt---ttctgaaccgttg-attactttctgattctgattttcaccccaccctgtagTTACTGGAGATCATGGGAGAACTTACAGCAGATCAGCAGAGGGCTTTCTGCCAATTTGTAACTGGAGCTCCTAGGCTTCCTCCTGGTGGCTTAGCTGTTC

upper sequence: GLYMA12G03640.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 14
gtatgtttttttattcctgtagaaggacaattgtgtttttggaaatttaggcttgttatatttggtgctgaacctgtatgat----gctattttcagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGCTGCCTCCTGGTGGACTGGCAGTTC
||||| || ||     ||| |     | | |||  |    ||   |||    ||| | |||||  | |  |   ||| |  |    |   |||||||||||| || ||||||||||||||||  |||||||||||||| |||||||| || || || ||||| |||||||| ||||| |||||||| |||||||| |
gtatgcttcttc---tctggatttacaaagttg-atgcaagggggttttattttgctttatttcattcatatgatgtcttgtttctgaccttttcagTTACTTGAGATTATGGGAGAATTCAACCCAGAGCAGCAGCGGGCCTTCTGCCAGTTCGTCACTGGCGCACCTAGACTGCCGCCTGGTGGTCTGGCAGTGC

upper sequence: GLYMA12G03640.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 14
gtatgtttttttattcctgtagaaggacaattgtgttt--ttggaaatt-----------taggcttgttatatttggtgctgaacctgtatgatgctat---------tttcagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGCTGCCTCCTGGTGGACTGGCAGTTC
||| | || ||  |   | |    || || |||  |||  | |||||             ||    |  ||||||   |||   |  ||| |  ||  ||         ||  ||||||| ||||| |||||||||||||| || |||||||||| ||| ||||| |||||  ||||||||||||||||||| |||||||| || |||||| |  
gtaagattcttcctatatttg---gggcatttggatttagtgggaaacagggtgtaatgataactcttatatattgactgcatgatttgtttattgtaatgcctttgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGCCAATTCATTACTGGTGCACCTAGGCTTCCTCCTGGAGGTCTGGCAATGT

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|208074756|gb|GD869541.1|GD869541
EST:     ATAT-AAATTTGA-CATGGTTATACTGCCAAGAGCCCTGCCATAGTTAAT                         TTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
genomic: ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatgttttt ... ctattttcagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
EST: gi|193449879|gb|FK413498.1|FK413498
EST:     ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAAT                         TTACTCGAAATTATGGGAGAATTCACACTAGAGCAGCAGCGTGCCTTCTGT
genomic: ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatgttttt ... ctattttcagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
EST: gi|9259017|gb|BE347164.1|BE347164
EST:     ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAAT                         TTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
genomic: ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatgttttt ... ctattttcagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
EST: gi|15815265|gb|BI787540.1|BI787540
EST:     ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAAT                         TTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
genomic: ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatgttttt ... ctattttcagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
EST: gi|192314633|gb|FK008141.1|FK008141
EST:     ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAAT                         TTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
genomic: ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatgttttt ... ctattttcagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
EST: gi|192327460|gb|FK017817.1|FK017817
EST:     ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAAT                         TTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
genomic: ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatgttttt ... ctattttcagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
EST: gi|51335365|gb|CO979231.1|CO979231
EST:     ATATAAAATTTGACCATGGTTATACTGCCAAGAGCNNTGCCATAGTTAAT                         TTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
genomic: ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatgttttt ... ctattttcagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
EST: gi|254331304|gb|GR845883.1|GR845883
EST:     ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAAT                         TTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
genomic: ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatgttttt ... ctattttcagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
EST: gi|192314634|gb|FK008142.1|FK008142
EST:     ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAAT                         TTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT
genomic: ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatgttttt ... ctattttcagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaaatttaggcttgttatatttggtgctgaacctgtatgatgctattttcagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGCTGCCTCCTGGTGGACTGGCAGTTC
                                             ctattttc  CT-rich tract
              ttgttatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttttttattcctgtagaaggacaattgtgtttttggaaatttaggcttgttatatttggtgctgaacctgtatgatgctattttcagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGCTGCCTCCTGGTGGACTGGCAGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA