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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcgtacctggatgaataaaaatgaaactgagtatggaagtacccttttctatctttagcattgattgatcaatcattgacatccattttatttttacagAGTTCATCTAGATCATCATGTTCCTATTTCAAGAGAGTTCCCAAATCAAGTGCTATAAAGGTTATTGATTTTGGCAGCACCACTTATGAGCGAGAAGATC

Basic information

species Glycine max
transcript GLYMA05G02740.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
------gtcgtacctggatgaataaaaatgaaactgagtatggaagtacccttttctatc--tttagc--att--gattgatcaatcat-tgacatccattttat--ttttaca----------gAGTTCATCTAGATCATCAT------GTTCCTATTTCAAGAGAGTTCCCAAATCAAGTGCTATAAAGGTTATTGATTTTGGCAGCACCACTTATGAGCGAGAAGATC
       | || | |  |   ||   |           | |  | ||   |||||    |  ||||||  |||  |||| | ||||  | ||  |||  | | ||  || ||||          |  ||||||  | ||  ||       ||||||||||||||    | ||||| || |||||||| ||||| ||||||||||||||||| || ||||| |         
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC------

upper sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 7
gtcgtacctggatgaataaaaatgaaactgagtatggaagtacccttttctatctttagcattgattgatcaatcattgacatccattttatttttacagAGTTCATCTAGATCATCATGTTCCTATTTCAAGAGAGTTCCCAAATCAAGTGCTATAAAGGTTATTGATTTTGGCAGCACCACTTATGAGCGAGAAGATC
         | ||   |  || || ||||| || ||     ||| |  | |  |       || | || | ||  | |    |    |||  |  | ||| | ||      |  |     |   |  |  || ||||| || ||||||||||| |||||||| ||||||||||| ||||| |||||||||||  | || |
---------gtatatctcgaa-tgcaactgtgtgtg-----accttaatgtggccaactatttaagtgctgaaggaatttggttgtgtttcctgatgcagGGGTCCCGATTACAAAGGGATGTATGCTATAAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC

upper sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 7
----gtcgtacctgga-tgaataaaaatgaaactgagtatggaagtacccttttctatctttagcatt---gattgatcaatcattg--acatccattt--tatttttacagAGTTCATCTAGATCATC-----ATG-TTCCTATTTCAAGAGAGTTCCCAAATCAAGTGCTATAAAGGTTATTGATTTTGGCAGCACCACTTATGAGCGAGAAGATC
      |  |  |  | |  ||    || ||   |  |||||   | |  | || |   ||  ||||     ||       | ||||  ||||  ||||  |   ||| |||  ||||||  | ||| |     ||| ||| || || |||||||| || |||||||||||||| || || ||||||||||| ||||| || |||||||||       
gtactccagatgttaacttgatgtgtattaagtggcatatggttttgctttattattctttctgcatctacaatgcccttgttattgtaacatatatttgttgcattttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAATCAAGTGCTATTAAAGTGATTGATTTTGGAAGCACAACATATGAGCGAC------

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|21994008|gb|BQ785536.1|BQ785536
EST:     AAAACATACTACTAGTTTCACCCGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCATCATGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: AAAACATACTACTAGTTTCACCCGAGTATGTCAAAGTTCCTGACTACAAGgtgcttttct ... atttttacagAGTTCATCTAGATCATCATGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|208116354|gb|GD920377.1|GD920377
EST:     AAAACATACCACTAGTTTCACCCGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCATCATGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: AAAACATACTACTAGTTTCACCCGAGTATGTCAAAGTTCCTGACTACAAGgtgcttttct ... atttttacagAGTTCATCTAGATCATCATGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
EST: gi|58016463|gb|CX703205.1|CX703205
EST:     AAAACATACTACTAGTTTCACCCGAGTATGTCAAAGTTCCTGACTACAAG                         AGTTCATCTAGATCATCATGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT
genomic: AAAACATACTACTAGTTTCACCCGAGTATGTCAAAGTTCCTGACTACAAGgtgcttttct ... atttttacagAGTTCATCTAGATCATCATGTTCCTATTTCAAGAGAGTTCCCAAATCAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctatctttagcattgattgatcaatcattgacatccattttatttttacagAGTTCATCTAGATCATCATGTTCCTATTTCAAGAGAGTTCCCAAATCAAGTGCTATAAAGGTTATTGATTTTGGCAGCACCACTTATGAGCGAGAAGATC
                             cattgac  putative branch site (score: 3)
                                     tccattttattttt  CT-rich tract
                                    atccattttattttta  TA-rich tract