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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatatggtttgaactttaccatatcagcatatgttgatttgctctttgttgtctaaaggaaaacaatatatttcagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGTCAACA

Basic information

species Glycine max
transcript GLYMA16G04580.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 5
gtgagatatggtttgaactttaccatatcagcatatgttgatttgctctttgttgtctaaaggaaaacaatatatttcagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGTCAACA
|| ||   | || | | | ||  |  ||      |  ||  |||  |      ||   |||       ||  | |||||||| |||||||| || || || |||||||||||||| |||||||||||||| ||   
gtcag---tcgtataagcattttctaattgtttgagattcttttcttaacaactgctaaaatttg--taacct-tttcagGTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGAC

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 5
gtgag---atatggtttgaactttaccatatcagcatatgttgatttgctctttgttgtctaaaggaaaacaatatatttcagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGTCAACA
|||||   |      || |     |   |||      |||  | |   |   |  |    |||    ||  || || || ||||||||||| |||||||| ||||| ||||||||||| ||||||||  | || ||   
gtgagtttactgaagttaataaccattctatgctgccatggagctcaacgtatcttgacttaatcttaattaaaattttccagGTCATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCATTAGGGCAGAC

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 5
gtgagatatggtttgaactttaccatatcagcatatgttgattt-gctctttgttgtctaaaggaaaacaatatatttcagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGTCAACA
             |||  |  |   ||| |   ||| |   |   ||||     ||| ||       | | | | |||||||| ||||| |||||||| ||||| ||||||||||| ||||||||  | || ||   
------------gtgagttcgat--tattactctatttcattgcagctcaacaatgtttattcactta-actttttttcagGTAATGGATATGCTTGGTCCCAGCCTTTGGGATGTGTGGAATTCGATGGGGCAGGC

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 2
gtgagatatggtttgaactttaccatatcagcatatgttgattt-gctctttgttgtctaaaggaaaacaatatatttcagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTC--TGTTGGTCAACA------------------------------------------
             |||  |  |   ||| |   ||| |   |   ||||     ||| ||       | | | | |||||||| ||||| ||||||||  |||| ||||||||||| ||||||||  ||  ||    ||                                          
------------gtgagttcgat--tattactctatttcattgcagctcaacaatgtttattcactta-actttttttcagGTAATGGATATGCTTGGTACCAGCCTTTGGGATGTGTGGAATTCGATGGGGGCAGGCATAAGTATCTTTCATTCTTTTTTATGGTATCTTTTGTCACTCA

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagatatg-gtttgaactttaccatatcagcatatgttgatttgctctttgttgtctaaaggaaaacaatatatttcagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGTCAACA
|| || | |  || ||| | |   || |     | |||         |||||  ||   |||     | ||| |||||||||||||||||||||||||||| || ||||||||||| ||||||||| | | ||||  
gtaagcttttcgtatgagcctagtcacacattgagatgaatcaggtatctttaatgaagaaacatttataat-tatttcagGTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCTCAATC

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 5
--gtgagatatggtttgaactttaccatatcagcat---atgttgatt-tgctctt-tgt-tgtctaaaggaaaacaatatatttcagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGTCAACA
   ||  || |    ||| ||||   | ||   | |   || |||||| || | |  |||     ||| |  | |  ||||| |||||||||||||||||||||| || ||||| |||||||| |||||||||   || |||  
gtatgtaatttacaatgagctttgttaaatatactttcgatattgattgtgttatcatgtacaagtaatgctataatatatacttcagGTCATGGACATGCTTGGTCCGAGTCTCTGGGATGTTTGGAATTCTTCGGGGCAATC

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 5
gtgagatatggtttgaactttaccat-atcagcatatgttgatttgctctttgt---tgtctaaaggaaaacaatatatttcagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGTCAACA
||||| | ||||||||| ||   ||| ||||| |  |    |||| | | ||||   ||  | ||  |||| || | || |||||||||||||||| | ||||| |||||||||||| | ||||||||||| || ||   
gtgagttttggtttgaaattgttcatcatcaggacttccaaatttacacattgtgcctgaattaaataaaataa-acatgtcagGTCATGGACATGTTGGGGCCAAGTCTTTGGGATCTTTGGAATTCTGTAGGCCAGAC

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------gtgagatatggtttgaactttaccatatcagcatatgttgatttgctctttgtt---gtctaaaggaaaacaatatatttcagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGTCAACA
                                       | || | |  | ||  | |     | |||   | |  | ||    | |||  |    | |  |        ||||  | ||||||||||| ||||||||||| ||||| |||||||| ||||| |||   ||||||  
gtgagtcacctattgaattgttgtagtccaagcagaccttcagttttcatgtggtcgtcttgttttcaaacttttctcatgatttttttaattcgatttcgacttcgttcatatgctgcagGTCATGGATATGCTTGGGCCAAGTCTCTGGGATGTCTGGAACTCTTCAGGTCAAGC

upper sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------gtgagatatggtttgaactttaccatatcagcatatgttgatttgctctttgttgtctaaaggaaaacaatatattt------------------cagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGTCAACA
                                      ||| | ||   |||   || |  ||  | | || ||    |||  |    ||| |||   | || ||| | ||||                   ||||||||||| ||||||||||| |||||||||||||| ||||| |||   || ||   
gtgggctattcacagaaaatagatgaatttacacatgctgatagatttcttgtctttgattattcccg-atttgaaatttttgtacgagttctcttccgaaatacattttattcacccgttgatatcttgtccagGTCATGGATATGCTTGGGCCAAGTCTTTGGGATGTTTGGAACTCTTCAGGCCAGGC

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|193666102|gb|FK612189.1|FK612189
EST:     GCATTCCCTGGGTTCATTACAAGGGTCGGCAAGGAGATTTCTACATTTTG                         GTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGT
genomic: GCATTCCCTGGGTTCATTACAAGGGTCGGCAAGGAGATTTCTACATTTTGgtgagatatg ... tatatttcagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGT
EST: gi|18692787|gb|BM521635.1|BM521635
EST:     GCATTCCCTGGGTTCATTACAAGGGTCGGCAAGGAGATTTCTACATTTTG                         GTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGT
genomic: GCATTCCCTGGGTTCATTACAAGGGTCGGCAAGGAGATTTCTACATTTTGgtgagatatg ... tatatttcagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcagcatatgttgatttgctctttgttgtctaaaggaaaacaatatatttcagGTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGTCAACA
                             gtctaaa  putative branch site (score: 3)
                                      aaaacaatatatttca  TA-rich tract