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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttttgtatgtagtctgtttgcaattttctagttgatttgctaatataagcttacatgctgtttagtgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC

Basic information

species Glycine max
transcript GLYMA05G25780.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g50510.1 (Oryza sativa), 3'ss of exon 8
---gcttttgtatgtagtctgttt--gcaattttctagttgatttgctaatataagcttacatgctgtttagtgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
     || || ||||  ||||| |  ||| | ||||  || |       |||  |  |||||   | ||   | ||  | ||  ||          ||  ||      || | || ||| | ||| |  |  | || |   | ||||||||||||||| ||||||| |||||||| ||||| ||||| |||||||||||      
gtgagttatgcatgttttctgtcttagcattattctcattaacc-atggataggattttacaccattttcctttcatgtacagGAT----------ATAAGG------ATCCAGAGCCTTCCAAGGCAAACTTACCCCTGCTACATGAGTGGCATTTCCGATCTGGCCTTGATCGATACATATGGATTATTGGAATGAT------

upper sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g44040.1 (Oryza sativa), 3'ss of exon 8
gcttttgtatgtagtctgtttgcaattttctagttgatttgctaatataagcttacatgctgtttagtgcaaatgcataattgtaatttttatgtggcagGTTATA------CTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
          || |  | ||   |  |||| |  ||   |  |  | ||   || |  | |   |  ||  ||    |  ||   | |||| ||  ||||| || |      | || ||| ||||  |  |  | || |   ||||||||||||||||| ||||||| |||||||| || || ||||| |||||||||||      
----------gttggttattcttatatttcgatgtgtcattttcct-taccattcctagataaatcatgttaacatgtgttttgtacttttgtgatgcagGCTACAAGGACCCAGAGCCTTCAAAAGCAAACTTACCACTGTTGCATGAGTGGCATTTCCGATCTGGCCTTGATCGTTATATATGGATTATTGGAATGAT------

upper sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G147351_T01 (Zea mays), 3'ss of exon 2
gcttttgtatgtagtctgtttgcaattttctagttgatttgctaatataagcttacatgctgtttagtgcaaatgcataattgtaatttttatgtgg-cagGTTATACTGATCCTGCA------AAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
      ||| ||  |   |  | | |||| ||    |||  |   ||  ||    ||||||    ||| || |  ||  |   ||||| || | |   |||| ||||  |||||  ||      ||| |  |  | ||     | ||||||||||||||| ||||||| || ||||| ||||| ||||| |||||||||||      
------gtaagttattgat--gtagttttgtatgacattctccc-taccagt---catgctcaggagttcagaacca--accttaattattttctattcagGCTATAAAGATCCATCACCATCCAAGGCACACTTACCCGTGCTACATGAGTGGCATTTCTGATCTGGCCTCGATCGATACATATGGATTATTGGAATGAT------

upper sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G458538_T01 (Zea mays), 3'ss of exon 3
gcttttgtatgtagtctgtttgcaattttctagttgatttgctaatataagcttacat-gctgtttagtgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCA------AAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
      ||| ||  |   |  | | |||| ||    |||  |      |  | | | | |  ||| ||  | ||  | ||||| |  ||| |||    |||| ||||  |||||  |       ||| |  |  | || |   | ||||||||||||||| ||||||| || ||||| ||||| ||||| |||||||||||      
------gtaagttattgat--gtagttttgtatgacattctccctaccagtcatgcttaggagttcaggaccaac-cttaattat--tttctatt---cagGCTATAAAGATCCATCGCCATCCAAGGCACACTTACCCCTGCTACATGAGTGGCATTTCCGATCTGGCCTCGATCGATACATATGGATTATTGGAATGAT------

upper sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G370741_T01 (Zea mays), 3'ss of exon 3
gcttttgtatgtagtctgtttgcaattttctagttgatttgctaatataagcttacat-gctgtttagtgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCA------AAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
      ||| ||  |   |  | | |||| ||    |||  |      |  | | | | |  ||| ||  | ||  | ||||| |  ||| |||    |||  ||||  |||||  ||      ||| |  |  | || |   | ||||||||||||||| ||||||| || ||||| ||||| || || |||||||||||      
------gtaagttattgat--gtagttttgtatgacattctccctaccagtcatgcttaggagttcaggaccaac-cttaattat--tttctatt---cagACTATAAAGATCCATCACCATCCAAGGCACACTTACCCCTGCTACATGAGTGGCATTTCCGATCTGGCCTCGATCGATACATATGTATTATTGGAATGAT------

upper sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G463445_T01 (Zea mays), 3'ss of exon 3
gcttttgtatgtagtctgtttgcaattttctagttgatttgctaatataagcttacat-gctgtttagtgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCA------AAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
      ||| ||  |   |  | | |||| ||    |||  |      |  | | |   |  ||||||  | ||  | ||||| |  ||| |||    |||| ||||  |||||  ||      ||| |  |  | || |   | ||||||||||||||| ||||||| ||  |||| ||||| ||||| |||||||||||      
------gtaagttattgat--gtagttttgtatgacattctccctaccagtcatgctcaggagtttaggaccaac-cttaattat--tttctatt---cagGCTATAAAGATCCATCACCATCCAAGGCACACTTACCCCTGCTACATGAGTGGCATTTCCGATCTGGCCTCAATCGATACATATGGATTATTGGAATGAT------

upper sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 8
------------------------------------------------------------gcttttgtatgtagtctgtttgcaat-tttctagttgatttgctaatataagcttacatgctgtttagtg-caaatgcataattgtaatttttatgtgg---cagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
                                                             ||| ||     |   |  |  |||| ||| | ||   || |  | |  ||       |  ||| |  || | ||    || || |  |  |||        |||| || |||||||| || || || || || || |   | ||||| ||||| |||||||| || ||||| |||||||| ||||| ||||||||||| |||||
gtcagtatcagactcttctcatatcttttactgtgttcggcatggtcgactgcatatccgtcttgtgctaaaaaaatcctgccaatgtttgttgtcacttggtcactggaattagtgtttttgtatgttgactaacatttagtttttttccttacacaagtacagGATACACTGATCCAGCTAAACCAGAACTACCACTTTTACATGAATGGCACTTCAGATCAGGACTTGACCGCTACATATGGATCATTGGAATGATATATGC

upper sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G29890.2 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------------gcttttgt-atgtagtctgtttgcaattttctagttgatttgctaatataagcttacatgct--------gtttagtg-caaatgcata-attgtaatttttatgtgg---cagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
                                  |||||| |||| |    | || | || | |  |  |       || |  | |  ||||||          || ||  | || |   | ||| |   ||| |        |||| || || ||||| || || || || || || ||  | || || ||||||||||||||||| |||||||||||||| ||||| || || ||||| |||||
gtcagtaacaaatttctctcatttttcataccatttttgtcatgtggctgatctgtagttctgtcttctacacaaatattttggatggcatgcttgaataaaaattggtaactaacgttgatattctgtctttaacacaaatacagGGTACACAGATCCAGCTAAACCAGACCTTCCACGTCTACACGAATGGCATTTCAGATCTGGACTTGATCGCTACATATGGATCATCGGCATGATATATGC

upper sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 9
-------gctttt--gtatgtagtctgtttgcaattttctagttgatttgctaata-taagcttacatgctgtttagtgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
       |||| |  | |  |  |    || | | | |  | |    ||  | ||| |    ||| | |  ||||     |  || ||| |  |  |   ||     ||||||| | ||| ||||| ||||| ||||| | |||  ||||||| ||||| || ||||| || |||||||||||||| ||||| || ||||||||||||||
gtggttagcttatccgaaattgattgaattcccaatgtggaatgagattattcataatggaattagaagaagtttctaatatttgtatattacttgtgaata-actccagGTTACAATGACCCTGCCAAGCCCGATCTTCATCGGCTGCATGAATGGCACTTTAGATCAGGCCTTGATCGCTACATATGGATCATCGGAATGATTTATGC

upper sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 3
gcttttgtatgtagtctgtttgcaatt--ttctagttgatttgctaatataagcttacatgctgtttagtgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTG------CAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
  |  | |||  |    |||||    |  ||| |  |  |    ||| |  |  |||  |  |||||  | ||| |    ||       ||||   |||||||||| | |||||| |      | || |  | |||||||||| ||||||| |||||||| |||||||||||||||||||| || ||||| || ||||||||      
attactatattgaactggtttgttgctagttcaatctagtggcttaacaccaagttaagttgtgttt--tccaagttttcaaactagtattttcaatggcagGTTACAGTGATCCAGATCCTTCTAAACAAGGTCTCCCTCGACTGCATGAATGGCATTTTAGATCTGGGCTTGATCGCTATATTTGGATCATCGGAATGAT------

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|208134024|gb|GD926973.1|GD926973
EST:     TTTTGGACGCCCTATTTGC-TTATTTTTGG                         GTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATT
genomic: TTTTGGA-GCCC-ATTTGCTTTATTTTTGGgtgagtgata ... tatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATT
EST: gi|24136282|gb|BU926792.1|BU926792
EST:     AATCCCTGGATTCTTTGACATATTTTGGAGCCCATTTGCTTTATTTTTGG                         GTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATT
genomic: AATCCCTGGATTCTTTGACATATTTTGGAGCCCATTTGCTTTATTTTTGGgtgagtgata ... tatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATT
EST: gi|193338485|gb|FK303412.1|FK303412
EST:     AATCCCTGGATTCTTTGACATATTTTGGAGCCCATTTGCTTTATTTTTGG                         GTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATT
genomic: AATCCCTGGATTCTTTGACATATTTTGGAGCCCATTTGCTTTATTTTTGGgtgagtgata ... tatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATT
EST: gi|208161302|gb|GD963476.1|GD963476
EST:     TTTGCTTTATTTTTGG                         GTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATT
genomic: TTTGCTTTATTTTTGGgtgagtgata ... tatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATT
EST: gi|208321022|gb|GE123849.1|GE123849
EST:     AATCCCTGGATTCTTTGACATATTTTGGAGCCCATTTGCTTTATTTTTGG                         GTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAA
genomic: AATCCCTGGATTCTTTGACATATTTTGGAGCCCATTTGCTTTATTTTTGGgtgagtgata ... tatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAA
EST: gi|208215598|gb|GE015525.1|GE015525
EST:     AATCCCTGGATTCTTTGACATATTTTGGAGCCCATTTGCTTTATTTTTGG                         GTTATACTGANCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATT
genomic: AATCCCTGGATTCTTTGACATATTTTGGAGCCCATTTGCTTTATTTTTGGgtgagtgata ... tatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataagcttacatgctgtttagtgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
    agcttac  putative branch site (score: 3)
                                         tttttat  putative PPT
                         aaatgcataattgtaa  TA-rich tract