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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgatatgctgctaattaattagttaattttgagagaaatgaagttggctagctagtaatgagacaaatatattaatgagaattgtactggtaacaccagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA

Basic information

species Glycine max
transcript GLYMA11G11310.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 3
gtgatatgctgctaattaattagttaattttgagagaaatgaagttggctagc--tagtaatgagacaaatatattaatgagaattgtactggtaacaccagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
    |||    ||    | |   || ||||| |   || | ||  |  ||     ||||| | |   ||  |  | | | ||   || | ||  ||  | ||||||||||||||||||||||||  ||| || |||||||||||  | ||| | ||||| ||  |||| |||||||| |||||||| || |||||  | || 
tatctataaaacttgggagtagattgattttaaccaaagtcaaaataacttatagtagtagtaat-taagaaagtaattaagggatgaaatgcaaatgc-agGGAGATAATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGCTGGCGACGGTGTACGTGCTGACGCTGACGCTGCCGTCGGCGTCGGCG

upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 5
--gtgatat--gctgctaattaattagttaattttgagagaaatga---agttggctagctagtaatgagacaaatatattaatgagaattgtactggtaacaccagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGC-AGCA
  || | ||     | | |       || |||  ||  | || |||   |  || | |   |||  || |||||   ||    |||      |  ||||     ||||||||| |||||||||||||||| ||| || |||||||||||  | ||| |  |||| || ||||| |||||||| |||||||| || ||||| || ||| 
cagttacatcgatcgtttacagcagcgtcaatactgtaataattgaccaaactgtcaaagcagtt-tgtgacaacattacgtgtga------ttttggtgcgcgcagGGAGATCATGCACGCGATGTGGAGGCCGCAGAAGTTCAAGGCGATCTACCTGATGGCGACGCTGTACGTGCTGACGCTGACGCTGCCGTCGGCGGCGAGC-

upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G129413_T01 (Zea mays), 3'ss of exon 1
gtgatatgctgctaattaattagtta-attttgagagaaatgaagttggctagcta-----gtaatgagacaaatatattaatgagaattgtactggtaacaccagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
      |||  |  |   ||  ||   |   ||  |  |   |   || || | |      ||  |          | ||  |||   |  |||    |     |||||||| |||||||||||||||   ||||| |||||||||||| | ||| | ||||| || ||||| |||||||| ||||| || || || || || || 
------tgccaccgacacatgggtcccagcctgccacgaggcaccatgactcgttgcttccgttgttgtgtgcgcttctttttgacgttgatacatacatatgtagGGAGATCATGCACGCGATGTGGCGTCCTCAGAAGTTCAAGGCCATCTACCTGCTGGCGACGCTGTACGTGCTGACGCTGACCCTCCCTTCCGCCGCCGCC

upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G149481_T04 (Zea mays), 3'ss of exon 4
----gtgatatgctgctaattaattagttaattttgagagaaatgaagttggctagctagtaatgagacaaatatattaatgagaattgtactggtaacaccagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGC-AGCA
      |   | ||   ||||||||      |     ||   |   |   |  |    |||||| ||  ||   | |  | |     | ||    ||    ||||||||| |||||||||||||||  ||| || |||||||||||  | ||| |  |||| || ||||| |||||||| |||||||| || ||||| || ||| 
atcaaagcagtactagcaattaattgaaaggtgactggactgaacgaacagcatcaacagtaattag-taatggtttgcacgca---tatatatatacacgcagGGAGATCATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGATGGCGACGCTGTACGTGCTGACGCTGACGCTGCCGTCGGCGGCCAGC-

upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 5
---------------------------gtgatatgctgctaattaattagttaattttgagagaaatga-agtt---ggctagctagtaatgagacaaatatattaatgag-----aattgtactggtaacaccagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
                              |||  |    |    |  ||| || |||  |  |  | | ||||    ||||  ||   | | ||  | | |   | || |     || ||  | |||     ||||||||| ||||||||||||||||| || || |||||||||  | | ||| |  |||| || ||||| |||||||| |||||||| || || ||  | || 
gtaagcctcagctgccagcagtctatatctatacccacacacagcagaagtgaagtttaggtcacttcagagttcagagctacgtacgtacgtgatgagtgtcacagtgtgtgtacaaatgggccggttggtgcagGGAGATCATGCACGCGATGTGGAAACCGCACAAGTTCAAGCTCATCTACCTGGTGGCGACGCTGTACGTGCTGACGCTGACGCTGCCGTCCGCCTCCGCC

upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 5
gtgatatgctgctaattaattagttaattttgagagaaatgaa--gttggctagctagtaatgagacaaatatattaa----tgagaattgtactggtaacaccagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
      |  ||  ||  | ||      | ||   | |  | ||   |||  |||  | |  | |  ||| | ||| ||    | ||  ||  | |  |     ||| ||||||||||| || |||||||| || || || ||||||||| ||||| | ||||| ||| ||||||||||||||||||| ||||| || || ||||||
------ttttgaaaaacagtttccacttattccaaaattttaattattgtttagaaaattctaaatcaagtgtataaaaacataaggttttgatttttttttgcagAGAGATAATGCATGCAATGTGGAAACCACAGAAATTCAAGGCCATATACCTGCTGGCTACCGTGTATGTGCTGACACTGACACTTCCGTCCGCGGCAGCA

upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 5
gtgatatgctgctaattaattagttaattttgagagaaatgaagttggctagctagtaatgagacaaatatattaatgagaattgtactggtaacaccagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
                        |||  ||  |     |    |   || ||  | |  || |   || |  | || |   |||  ||       |||||||||| |||||||||||||||||||| ||||||||||||    | ||  |  | || ||| | || ||  | ||  |||| || || || ||  | |||
-----------------------gtaagctttcgcttctttcgctgttcttgcatggatcgataggcatcttctcataaactttgatct-----tcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA

upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
gtgatatgctgctaattaattagttaattttgagagaaatgaagttggctagctagtaatgagacaaatatattaatgagaattgtactggtaacaccagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
    || |||     ||  || | |  | |||   | |  ||  | |||||  | || ||        | |  | || |   |||  ||       |||||||||| |||||||||||||||||||| ||||||||||||    | ||  |  | || ||| | || ||  | ||  |||| || || || ||  | |||
---gtaagctttcgcttctttcgctgttcttgcatggatcga--taggctatgttgtcatc-------ttttctcataaactttgatct-----tcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA

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|24206334|gb|BU965587.1|BU965587
EST:     ACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT                         GGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTT
genomic: ACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGTgtaagacaat ... gtaacaccagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTT
EST: gi|298180126|gb|HO025341.1|HO025341
EST:     ACGGGGGCCACAAACATTCTCTACACATCCGGGGGACATGCTGTTACTGT                         GGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTT
genomic: ACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGTgtaagacaat ... gtaacaccagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggctagctagtaatgagacaaatatattaatgagaattgtactggtaacaccagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
                                           tggtaac  putative branch site (score: 2)
                    aaatatattaatgaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatatgctgctaattaattagttaattttgagagaaatgaagttggctagctagtaatgagacaaatatattaatgagaattgtactggtaacaccagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA

- - -atgctgc
- - - - - - - - - - - - - - - - - - -aatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagacaaa