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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttttgtatgtagtctgtttgcaattttctagttgatttgctaatataagcttacatgctgtttagtgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC

Basic information

species Glycine max
transcript GLYMA05G25780.1
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
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttttgtatgtagtctgtttgcaattttctagttgatttgctaatataagcttacatgctgtttagtgcaaatgcataattgtaatttttatgtggcagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC

- - -tgtatgt
- - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcataa