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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttacctgctttgatgatgcagtgtcctctctcaatattgctcaatttaatgtttgtaattcattggtattttatttggtaattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATCACC

Basic information

species Glycine max
transcript GLYMA05G36620.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 7
gtttgttacctgctttgatgatgcagtgtcctctctcaatattgctcaatttaatgtttgtaattcattggtattttatttggtaattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATCACC
||||| | | ||    ||  |    ||   ||  |||||           | ||||  |  |   |  || ||| |  || | |||     |||||| || || || ||||| ||||||||||| || || ||||||||||| || || |||||||| || ||||||||||| || || || || |||||||| 
gtttgct-catgtccagaaaaaaatgttagcttactcaaa------tggataaatgaatccagcgc-ctgatatct-gttggttaaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGGCTGAGGACAAGGGCACCGGCAAGTCGGAGAAGATCACG

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 7
gtttgttacctgctttgatgatgcagtgtcctctctcaatattgctcaatttaatgtttgta--attcattggtattttatttggt-aattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATCACC
    || | | |||       | | | |     |     |||| |||  ||| |||  || |  | | | |    | || | || | || ||  |||||| || || || || || ||||||||||| || || |||||||| || ||||| |||||||| || ||||||||||| || || || || |||||||| 
----gtgagcagctaccggagtccggagataaat-----tattactctttttgatgaatggacgaatgaatccagtgttgtctgatgaactgtgcagGGGCACACCCCAGATCGAGGTGACCTTCGAGGTGGACGCCAACGGTATCCTAAACGTGAAGGCGGAGGACAAGGGCACGGGCAAGTCGGAGAAGATCACG

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttgttacctgctttgatgatgcagtgtcctctctcaatattgctcaatttaatgtttgtaattcattggtattttatttggtaattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATCACC
||||| | |||  | |  |    |   ||      | |||    |||| ||| |  | |  || | |||      | || | ||  ||  |||| || || |||||||| || || || || ||||| || |||||||| ||||| |||||||| ||||| |||||||  | |||||||||||| ||||| || 
gtttgcttcctcttcttttaccccttagtaaatggtaaattagtctcattttga-atatcaaaataattatc--ctgatctcgt--tttgacagAGGAACCCCTCAAATCGAGGTCACATTTGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACA

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttgttacctgctttgatgatgcagtgtcctctctcaatattgctcaatttaatgtttgtaattcattggtattttatttggtaattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATCACC
||||| | ||   | |  |    |   ||  |     |  |  |    ||||      |  || | |||      | || | ||  ||  |||| || || |||||||| || || || |||||||| || |||||||| ||||| |||||||| ||||| |||||||  | |||||||||||| ||||| || 
gtttgcttccacttcttttaccccttagtaatggtaaatcagagtctcattttgaacattaaaataattatc--ctgatctcgt--tttgacagAGGAACCCCTCAAATCGAGGTCACATTCGAAGTGGACGCCAACGGTATTCTTAATGTGAAAGCAGAGGACAAGGCGAGTGGTAAATCAGAGAAGATTACT

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G42020.2 (Arabidopsis thaliana), 3'ss of exon 6
-----------------------------------------------------------gtttgttacctgctttgatgatgcagtgtcctct---ctcaatattgctcaatttaatgtttgtaattcattggtattttatttggtaattgaacagGGGTACGCCTCAAATTGAAGTGA------CCTTCGAAGTTGATGCCAACGGCATTCTAAAT---GTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAA-AGATCACC
                                                           |    ||||   |    | || | || ||| |||   |  |  |  | |  |    ||| |            | | |||     | ||   || | ||  | |    | || || |  |      || | ||     | |   ||  |||    ||    ||||  |   | ||||||    | |  ||||  |||  |||| |  
gtggacgccaacggtattcttaatgtgaaagcagaggacaaggcgagtggtaaatcagagaagattacaatcacaaacga-gaagggtcgtctgagccaagaagagattgaccggatggtgaaggaggcagaggagtttgcagaggaagacaagaaggtgaaggagAAGATCGACGCCAGGAATGCCCTGGAGACATACGTGTACAACATGAAGAACCAAGTGAGCGACAAGGACAAGCTTGCAGACAAATTGGAAGGAGATGAGA

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 7
---gtttgttacctgctttgatgatgcagtgtcctctctcaatattgct--caatttaatgtttg-taattcattggtattttatttggtaattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATCACC
    |   | |     || |    ||   | ||   ||    |  | ||  ||| ||  |||||| | | | |   | ||    ||   |  ||| |||| || || |||||||||||||| || || || ||||||||||| |||||||||||||| ||||| |||||||| |   | || ||||| || || ||||| 
gttatccctcatgcctttggtctctgttctatctaatcatgtttctcctatcaaatttgtgtttgcttactgaccaggatcaacttgtttgtttggacagAGGGACCCCTCAAATTGAAGTCACGTTTGAGGTTGATGCCAATGGCATTCTAAATGTAAAGGCTGAAGACAAAGCTTCAGGGAAATCTGAGAAAATCACA

upper sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 7
gtttgttacctgctttgatgatgcagtgtcctctctcaatattgctcaatttaatgtttgtaattcat-tggtattttatttggta-attgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATCACC
|||||  |       ||   |  |    || ||| | ||   | |||    |   |   | |||| || || || | |  ||  ||  ||||||||||| || || ||||||||||| || || |||||||| || || || || |||||||| ||||| || ||||||||||| ||||||||||| |||||||||
gtttgcga---aacctgtccactccaactcttctgtaaaa--tactcctactgtaggcagaaattgatgtgataatctgattcctatgttgaacagGGGAACCCCACAAATTGAAGTCACGTTTGAAGTTGACGCAAATGGTATCCTAAATGTCAAGGCTGAGGACAAGGGCACGGGTAAATCAGAGAAGATCACC

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|192314531|gb|FK006345.1|FK006345
EST:     TGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAG                         GGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
genomic: TGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAGgtttgttacc ... aattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
EST: gi|254344498|gb|GR851195.1|GR851195
EST:     GGAATTCCTCCAGCCCCAAG                         GGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
genomic: GGAATTCCTCCAGCCCCAAGgtttgttacc ... aattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
EST: gi|254333979|gb|GR848897.1|GR848897
EST:     TGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAG                         GGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
genomic: TGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAGgtttgttacc ... aattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
EST: gi|26058351|gb|CA801265.1|CA801265
EST:     TGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAG                         GGGTACGCCTCAAATTGAAGTGA
genomic: TGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAGgtttgttacc ... aattgaacagGGGTACGCCTCAAATTGAAGTGA
EST: gi|192314502|gb|FK006344.1|FK006344
EST:     TGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAG                         GGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
genomic: TGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAGgtttgttacc ... aattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
EST: gi|7145970|gb|AW507892.1|AW507892
EST:     TCCTCCAGCCCCAAG                         GGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
genomic: TCCTCCAGCCCCAAGgtttgttacc ... aattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
EST: gi|254333980|gb|GR848898.1|GR848898
EST:     CCTTC-TGGGAAATTTGATCTGTCTGGAATTCCTCCCACCCCCAAG                         GGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
genomic: CCTTCTTGGGAAATTTGATCTGTCTGGAATTCCT-CCAGCCCCAAGgtttgttacc ... aattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
EST: gi|298196006|gb|HO044397.1|HO044397
EST:     TGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAG                         GGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
genomic: TGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAGgtttgttacc ... aattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
EST: gi|254330970|gb|GR842235.1|GR842235
EST:     TGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAG                         GGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
genomic: TGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAGgtttgttacc ... aattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
EST: gi|298172742|gb|HO019782.1|HO019782
EST:     TGCCGCCTTCTTGGGAAATTTGATCTGTCTAGAATTCCTCCAGCCCCAAG                         GGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
genomic: TGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAGgtttgttacc ... aattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
EST: gi|298169283|gb|HO020643.1|HO020643
EST:     TGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAG                         GGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT
genomic: TGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAGgtttgttacc ... aattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgctcaatttaatgtttgtaattcattggtattttatttggtaattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATCACC
         atttaat  putative branch site (score: 4)
        aatttaatgtttgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttacctgctttgatgatgcagtgtcctctctcaatattgctcaatttaatgtttgtaattcattggtattttatttggtaattgaacagGGGTACGCCTCAAATTGAAGTGACCTTCGAAGTTGATGCCAACGGCATTCTAAATGTGAAGGCAGAAGACAAGGGCACTGGTAAATCAGAAAAGATCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA