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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatcagaatattccttgtttctcttaatgtcttcttgcatgtgaacttcttcccaaggtgatgaaaaaagctagaattctggttatggtgtttatgagggggtgaacaacttgttttgattacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAATGTCCAGTGTGCGCACAGTATTTTGTTGTAAGTTCATAATGACTTTT

Basic information

species Glycine max
transcript GLYMA07G03680.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03680.4 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g05080.1 (Oryza sativa), 3'ss of exon 4
---------gtgagtatcagaatattccttgtttct----cttaatg--tcttcttgcatgtgaacttcttcccaaggtg----atgaaaaaagctagaatt-ctggttatggtgttta-tgagggggtgaacaacttgttttgat---tacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAATGTCCAGTGTGCGCACAGTATTTTGTTGTAAGTTCATAATGACTTTT
          || | ||   ||| |||||||||| |      ||| |   ||||| | |||  | ||||| |   |  |     || || |    | || |  |     ||||  || | | |    |  ||   |     |||||   | ||||||| ||||||||||| || ||||||||| ||||||||| |||||| |||||||| || || ||| | ||||||||  | |                   
gtatagtacctgtgcatgctaat-ttccttgtttttgacctataaagaagcttctaggatgaaatcttctcctgcatcttctctataaatattcatcgactaaccaccaatggaattaacttaaactgcaaattgcaatgattgatattttcagAGGACGAGCATGATGTCGTGTGGTTTTGGTTGGAGAAAGGCAAGCCACATGAATGCCCTGTCTGCACTCAGTATTTC-TCG-------------------

upper sequence: GLYMA07G03680.4 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
gtgagtatcagaatattccttgtttctcttaatgtcttcttgcatgtgaacttcttcccaaggtgatgaaaaaagctagaattctggttatggtgtttatgagggggtgaacaacttgttttgattacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAATGTCCAGTGTGCGCACAGTATTTTGTTGTAAGTTCATAATGACTTTT
                        ||  | | |||   ||||  |   | |     | | |       ||| |   |  ||| |||||       ||| |             |||| |||   ||||||||||||||||||||||||| ||||| ||| || | |||||  | || ||||| || ||||| ||  |||| ||||||||                     
-----------------------gtcagtcagtgttgacttggctc--agcgaaaactctaaactgccaaatattatgcaatactggtatcaacattttt-----------tcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG--------------------

upper sequence: GLYMA07G03680.4 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g06000.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtatcagaatattccttgtttctcttaatgtcttcttgcatgtgaacttcttccca--aggtgat--gaaaaaagctagaattctggttatggtgttta-tgagggggtgaacaacttgtttt--gattacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAATGTCCAGTGTGCGCACAGTATTTTGTTGTAAGTTCATAATGACTTTT
|| ||  || |    || ||   ||   ||| | | |||     | |  | ||||| | |  |  | ||  | |      || | |  |  | ||  || ||  |  |    | |   | |||||||  |  | |||||||||||||||||||||||||||||||||||||||||| |||| | |||||||| || |||||| ||||||||||                        
gtaagcctctgtcacttactctctttaattattattttcc-atttatttatttcttacaattaattaatttgcatcccattaaattctttctaattttggttgctctgttatttatttatttgtttttcgtctgcagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCACATGAATGCCCTGTGTGCTCACAGTATTTCACG--------------------

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|14126582|gb|BG791020.1|BG791020
EST:     CAAATCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGTG                         AGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATG
genomic: CAAATCTTACTATGATAAAAGGATAGTCGGATGCCCAGGAGGTGAAGGTGgtgagtatca ... ttgattacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagaattctggttatggtgtttatgagggggtgaacaacttgttttgattacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAATGTCCAGTGTGCGCACAGTATTTTGTTGTAAGTTCATAATGACTTTT
                                           ttttgat  putative branch site (score: 4)
                                       cttgtttt  CT-rich tract
                                           ttttgatta  TA-rich tract