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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtatgtttaaaataacctgttttgcaacatgtgctattattttgtgcatatcaggctttgagtgaatgcagtcttcagcataatattttatgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGACCACTTCTTTTGTGAAAATTGCTCTGCTGAAGGTCAAAAAAAGTTGCAA

Basic information

species Glycine max
transcript GLYMA04G01140.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G01140.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g00160.t01 (Vitis vinifera), 3'ss of exon 3
----tgtatgtttaaaataacctgttttgcaacatgtgctattattttgtgcatatcaggctttgagtgaatgcagtcttcagcataatattttatgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGACCACTTCTTTTGTGAAAATTGCTCTGCTGAAGGTCAAAAAAAGTTGCAA
       | || |   ||||       | | |  | ||   | | || ||| ||      ||| ||   || ||| ||||||||||  || ||| || ||||||||| |||||||| |||||||||||||||   || ||||| |||||||| || ||||| || ||  ||||||| ||| |||||| |||||| |||||||  
agccaacaagtatcctataaaaaaaacttccatttctggggtaaatt-gtgaattatgcacttagaccaaa-gcaatcttcagcatgctacttt-tg-attcagGTTTCATCCTGCTTGTATAGACATGACTCCAGAGGAAGCTAAAAGACTCGAGCACTTTTTCTGCCAAAATTGTTCTTCTGAAGATCAAAAGAAGTTGCTG
















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|298196200|gb|HO044591.1|HO044591
EST:     CCTTACAACCCTGATGACCTAATGGTCCAATGTGTGGGCTGCACTGACTG                         GTTCCATCCTGCATGTATAGACA
genomic: CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagttgaa ... atgtattcagGTTCCATCCTGCATGTATAGACA
EST: gi|151404297|gb|EV274107.1|EV274107
EST:     CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG                         GTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagttgaa ... atgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|298184224|gb|HO029437.1|HO029437
EST:     CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG                         GTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagttgaa ... atgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|20811514|gb|BQ295992.1|BQ295992
EST:     CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG                         GTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagttgaa ... atgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|298169727|gb|HO021087.1|HO021087
EST:     CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG                         GTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagttgaa ... atgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|193618792|gb|FK572118.1|FK572118
EST:     CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTG                         GTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagttgaa ... atgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|27427183|gb|CA938703.1|CA938703
EST:     CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG                         GTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagttgaa ... atgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|254330184|gb|GR839737.1|GR839737
EST:     CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG                         GTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagttgaa ... atgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|254316702|gb|GR828239.1|GR828239
EST:     CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG                         GTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagttgaa ... atgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|208110150|gb|GD904900.1|GD904900
EST:     CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG                         GTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagttgaa ... atgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|254330185|gb|GR839738.1|GR839738
EST:     CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG                         GTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagttgaa ... atgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|15285488|gb|BI469379.1|BI469379
EST:     CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG                         GTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTC-A
genomic: CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagttgaa ... atgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|298163162|gb|HO011895.1|HO011895
EST:     CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG                         GTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGC-AAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagttgaa ... atgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|254316701|gb|GR828238.1|GR828238
EST:     CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG                         GTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagttgaa ... atgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatatcaggctttgagtgaatgcagtcttcagcataatattttatgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGACCACTTCTTTTGTGAAAATTGCTCTGCTGAAGGTCAAAAAAAGTTGCAA
                                   ataatattttatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtatgtttaaaataacctgttttgcaacatgtgctattattttgtgcatatcaggctttgagtgaatgcagtcttcagcataatattttatgtattcagGTTCCATCCTGCATGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGACCACTTCTTTTGTGAAAATTGCTCTGCTGAAGGTCAAAAAAAGTTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
tgtatgt
- - - - -aaaataa
- - - - - - - - cctgttt
- - - - - - - - - - - - - - catgtgc
- - - - - - - - - - - - - - - - - - - - - - -tgcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - ggctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgca