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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggattttgacggaagcttctttctttattttttattttttattctaattagagtatgacggaagtttctttaatattattaaaaaaagatttatctgtcggtgaatatgttctctttgtacatcattgaccttgcaactttttctcacctctttttcttttcttgcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT

Basic information

species Glycine max
transcript GLYMA11G01940.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g15420.1 (Oryza sativa), 3'ss of exon 2
gtaaggattttgacggaagcttctttctttattttttattttttattctaattagagtatgacggaagtttctttaatattattaaaaaaagatttatctgtcggtgaatatgttctctttgtacatcattgaccttgcaactttttctcacctctttttcttttcttgcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT
           |    |  |    |    || | ||   |||||||||   ||                |||||| ||| | || ||||       || |||     || ||     || |||| |  |      |   ||   || || |  | | | | || |     ||||||||||||||| | || |||||||| |||||||| || || ||||||||||| || || || || || ||| || | ||  |  |||||||||| | |
-----------gtaaaacacgctataaaatagtattatctttttattccttttta-------------cttcttttatacttttcaaaagcagca-atttgt-----aacat-----ctctgtaaagtaaaagtatctaaa---ttcctaaaatatgtcttttct-----agATTTGATGCTGTCGTTCATTTTGCTGGTCTGAAAGCTGTGGGTGAAAGTGTGCAGAAGCCATTGCTTTATTATGACCATAATGTTGCTGGGACAATAATT

upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G138410_T01 (Zea mays), 3'ss of exon 2
gtaaggattttgacggaagcttctttctttattttttattttttattctaattagagtatgacggaagtttctttaat-attattaaaaaaagatttatctgtcggtgaatatgttctctttgtacatcattgaccttgcaactttttctcacctctttttcttt-tcttgcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT
                                          | |  ||   | ||  ||     |  | | | |  | || |||||  ||  ||| |    |  |    | | |||| | |  |      ||  | ||  |||| ||   |    |  | |  | |  | ||||||||||||||| || || ||||||||||||||||| || ||||||||||| ||||| ||||| || || ||| || | ||  |   ||| ||||| | |
-----------------------------------------gtaaagcttgctggaagattggcaatatatatctgttcataattaattaactattcaatgtttagcct-tgtcttctatgtaaatgcatctgcacctggtacttatttatatgcatgctacgctgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT

upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 2
lower sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaggattttgacggaagcttctttctttattttttattttttattctaattagagtatgacggaagtttctttaatattattaaaaaaagatttatctgtcggtgaatatgttctctttgtacatcattgaccttgcaactttttctcacctctttttcttttcttgcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT
                                                                                   ||||||||| |||   | |   ||| || | | |      | || |||||     | |  |||  |     | |    || |     || |||||||| || ||||||||||||||||| ||||||||||| || |||||| | || ||||| || || ||||| || ||| |   ||| ||  | |||
----------------------------------------------------------------------------------gtaaaaaaagcttttcttttttatgattaggctgttg----atataattgaggggtcgaagtttaatggaaacgtggaattat--gatagGTTTGATGCAGTGATACACTTTGCTGGACTTAAAGCAGTAGGTGAGAGTGTGGAGAAGCCTTTGCTCTATTATAATAATAACATTGTTGGCACTGTTACT

upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 2
gtaaggattttgacggaagcttctttctttattttttattttttattctaattagagtatgacggaagtttctttaatattattaaaaaaagatttatctgtcggtg----aatatgttctctttgtacatcattg-accttgcaactttttctcacctctttttcttttcttgcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT
                                                                            | |   | || || ||||||     |    |    ||| ||| |   |||  || | ||     ||  |||||  | |  || | || | ||    ||||| |||||||||||||| |||||||||||  |||| ||||| || ||||||||||||||||| || || |||| | | |||||| | | ||| ||||| |||
----------------------------------------------------------------------------acagactgaagaatagatttgatgttacacgtagaaatttgtgcatcttgctcaactttatgttttataacttactttgtccaccttgt-ttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCCTTGCTTTACTTTGATAACAACCTTATTGGCACAATTACT

upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 2
gtaaggattttgacggaagcttctttctttattttttattttttattctaattagagtatgacggaagtttctttaatattattaaaaaaagatttatctgtcggtg----aatatgttctctttgtacatcattg-accttgcaactttttctcacctctttttcttttctt-----gcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT
                                                                                  | || || ||||||     |   ||    ||| | | ||  |||  || | ||     ||  |||| ||||| || |  |   | ||  ||     |||| |||||||||||||| |||||||||||  |||| ||||| || ||||||||||||||||| || || |||||| | |||||| | | ||| ||||| |||
----------------------------------------------------------------------------------tgaagaatagatttgatgttacatgtagaaatttatgcttcttgctcaactttatgttttataactctttcttactttgtccaccttgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCATTGCTTTACTATGATAACAACCTTATTGGCACAATTACT

upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 2
lower sequence: PP1S101_67V6.2 (Physcomitrella patens), 3'ss of exon 2
gtaaggattttgacggaagcttctttctttattttttattttttattctaattagagtatgacggaagtttctttaatattattaaaaaaagatttatctgtcggtgaatatgttctctttgtacatcattgaccttgcaactttttctcacctctttttcttttcttgcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT
                                                                  | | |   || | ||  | |  | |  |   | ||| | | || ||  |   || ||   | ||    | ||  |  | |||| ||      |||       |||| || ||||||||||| |||||||| || ||||| || |||||||||||||||   || ||||| |  ||||| | ||||||  | |   | || || | |
------------------------------------------------------------------aatgttgctagtgtttgtcattacacctaattttgt-gcttaagataatag-ttcgtggtttatcacacctgtgaaatattcttaca----attcaaaatcggcagGTTCGATGCTGTCATTCACTTTGCAGGCCTGAAGGCTGTAGGAGAAAGTGTGTCGAAGCCTTTGCGTTACTACAGCAACAATCTAATAAGCACCATTAAT

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|19346734|gb|BM891614.1|BM891614
EST:     GTGGACCTACGGGACAGGGATGCACTAGAGCAAATTTTTGTTTCCACACA                         ATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
genomic: GTGGACCTACGGGACAGGGATGCACTAGAGCAAATTTTTGTTTCCACACAgtaaggattt ... tttcttgcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
EST: gi|11275167|gb|BF325490.1|BF325490
EST:     GTGGACCTACGGGACAGGGATGCACTAGAGCAAATTTTTGTTTCCACACA                         ATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
genomic: GTGGACCTACGGGACAGGGATGCACTAGAGCAAATTTTTGTTTCCACACAgtaaggattt ... tttcttgcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
EST: gi|213598812|gb|DB968283.1|DB968283
EST:     GTGGACCTACGGGACAGGGATGCACTAGAGCAAATTTTTGTTTCCACACA                         ATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
genomic: GTGGACCTACGGGACAGGGATGCACTAGAGCAAATTTTTGTTTCCACACAgtaaggattt ... tttcttgcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
EST: gi|17022573|gb|BM093607.1|BM093607
EST:     GTGGACCTACGGGACAGGGATGCACTAGAGCAAATTTTTGTTTCCACACA                         ATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
genomic: GTGGACCTACGGGACAGGGATGCACTAGAGCAAATTTTTGTTTCCACACAgtaaggattt ... tttcttgcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
EST: gi|8283435|gb|BE020996.1|BE020996
EST:     GTGGACCTACGGGACAGGGATGCACTAGAGCAAATTTTTGTTTCCACACA                         ATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT
genomic: GTGGACCTACGGGACAGGGATGCACTAGAGCAAATTTTTGTTTCCACACAgtaaggattt ... tttcttgcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgtacatcattgaccttgcaactttttctcacctctttttcttttcttgcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT
                            ttctcac  putative branch site (score: 2)
                ccttgcaactttttct  CT-rich tract
                                      tttttctttt  TA-rich tract