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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttatagttaggagttaggaccatatatggaatcagaattgtttttaaaagatctctaatcgaattaattgggtctaaaccctaaacttcctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCTTTCCTCCAGACATTCTCGAAAATCATTGAAAACCCAGAAAGCCTGACAT

Basic information

species Glycine max
transcript GLYMA20G24830.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24830.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G121200_T01 (Zea mays), 3'ss of exon 5
tgttatagttaggagttaggaccatatatggaatcagaattgtttttaaaagatctctaatcgaattaattgggtc-taaaccctaaacttcctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCTTTCCTCCAGACATTCTCGAAAATCATTGAAAACCCAGAAAGCCTGACAT
  | | ||    | |  |  |  | |      |  |   | ||   ||| ||    | | |     |     | |  |  | |||    ||  |||||||||||||||| || ||||||||  | ||||| ||||| ||||| ||||| || ||||| || |||||  | || ||  ||||  | || ||| |||| ||||
-ctcacagaacaggggcaaaaaaaaaccccccacgatcctggtccataatagcaaccaattttccctgcagagatggttgatcctgccatttgtttttcagGTGAATGTTACTGCTGATCACAGGATTATCTATGGTGCTGATTTGGCAGCATTCCTGCAAACATTTGCAAAGATTGTTGAGGATCCTGAATGCCTCACAT

upper sequence: GLYMA20G24830.2 (Glycine max), 3'ss of exon 5
lower sequence: AT3G25860.1 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------tgttatagttag-gagttaggaccatatatggaatcagaattgtttttaa--aagatctctaatcgaattaattggg---tctaaaccctaaacttcctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCTTTCCTCCAGACATTCTCGAAAATCATTGAAAACCCAGAAAGCCTGACAT
                              || |    || | || | |   | |  ||   | |   || |    |||   |     | |        |||  |     |     |  |    ||   ||  ||||||||||| || || |||||||| ||| | ||||| ||||||||||| ||||| ||||| || ||  | || |||||||| || ||||| ||  |||| |
gtaagttttattttgacttaataaacttcctgatgggtttggtgaatcacttcgacttagaaagtttaaaatacgattagctatagcttttggctatgctaacagtaacattgtcgctttgttgttatgttggcagGTGAATGTGACTGCAGATCATCGCATTGTGTATGGAGCTGACTTGGCTGCTTTTCTCCAAACCTTTGCAAAGATCATTGAGAATCCAGATAGTTTGACCT

upper sequence: GLYMA20G24830.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0011g03380.t01 (Vitis vinifera), 3'ss of exon 5
tgttatagttaggagttaggaccatatatggaat-cagaattgtttttaaaagatctctaatcgaattaat---tgggtctaaaccctaaacttcctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCTTTCCTCCAGACATTCTCGAAAATCATTGAAAACCCAGAAAGCCTGACAT
   | ||  | |   |     |     | |  |  |  |||| ||  ||  |  | | |  | | |  ||      |  || ||   | ||  ||||||||||||| ||||| ||||||||||| |||||||| ||||| ||||||||||| || ||||| ||||| ||  | || ||| |||| |||||||||||| ||||||
--gtctaacttgtcttcttttctggggaggagacaccaaattcttcctaggaattttttttttgtagcaaaacactgaactgaattatgaa--tcctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCCTTCCTTCAGACCTTTGCAAAGATCGTTGAGAACCCAGAAAGCTTGACAT

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|207747462|gb|GD720223.1|GD720223
EST:     CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG                         GTGAGTGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
genomic: CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttact ... cctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
EST: gi|208183505|gb|GD987411.1|GD987411
EST:     GAAGAATAAAATGCTG                         GTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
genomic: GAAGAATAAAATGCTGgtgagttact ... cctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
EST: gi|9985549|gb|BE659657.1|BE659657
EST:     CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG                         GTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
genomic: CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttact ... cctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
EST: gi|21257189|gb|BQ454077.1|BQ454077
EST:     CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTG                         GTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT
genomic: CTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttact ... cctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaagatctctaatcgaattaattgggtctaaaccctaaacttcctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCTTTCCTCCAGACATTCTCGAAAATCATTGAAAACCCAGAAAGCCTGACAT
                                   ccctaaa  putative branch site (score: 3)
                                          cttcctttttc  CT-rich tract
            taatcgaattaatt  TA-rich tract