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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatcaagcacatttgcatatctgccaaatttgtgtgaaatgagatctatactactagatgctatacataatatattaatatttttacctattcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG

Basic information

species Glycine max
transcript GLYMA16G23870.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 4
gtatga-tcaagcacatttgcatatctgccaaatttgtgtgaaatgagatctatactactagatgctatacataatatattaatatttttacctattcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG
|||  | |  | | | ||   || |||    |||| ||||  | |  | |  ||| | |   |      |  | || ||  ||| |   ||  |    |  ||||| || ||||| ||||||||||| || || |||||||||||||| || ||||||||| ||||||| ||||||||||| |
gtagaaattgaacgctttca-atgtcttggcaattagtgtacattttggtg-atatttcattacttctcaggtcatgtaagaatgtacctattttccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG

upper sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 4
gtatga-tcaagcacatttgcatatctgccaaatttgtgtgaaatgagatctatactactagatgctatacataatatattaatatttttacctattcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG
|||  | ||||  || |     | | |||  |    ||  | | |  |   |||   ||||  | ||  |  | || ||  | | |   ||  |    |  ||||| || ||||| ||||| | ||| || ||||||||  ||||||| || ||||||||||||||||||||||| || || |
gtagaaatcaaatacttcaatctctttgcaca--cagtaagcatttggtgatatttcactacttcct-caggtcatgtaagactgtacctattttccttcccagAACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAG

upper sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 4
----gtatgatcaagcacatttgcatatctgccaaatttgtgtgaaatgagatctatactactagatgctatacataatatattaatatttttacctattcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG
    ||| |||  ||     ||  ||   ||   || |||    ||||   || | |   |  |  | |   || | |   |    |||  |  | ||  ||  ||||||||||| || ||||||||| |||||| |||| || ||||||| || ||||||||| |||| || |||||||| || |
gtaggtacgattcagtttgattcaatgcttg--gaaattgc---aaatcc-atatgtgaaagcatcttcatcactttaagaagagttatgatcccttaccctctcagAATTTTCTGTTCAAATCAACCGAAGAAGGTTCATCTCTAAAGGCTACAGATTTTGGTCTGTCGGACTTCATAAAGCCAG

upper sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgatcaagcacatttgcatatctgccaaatttgtgtgaaatgagatctatactactagatgctatacataatatattaatattt-----ttacctattcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG
                | || ||  | |   ||     ||       || | || || | | |  ||| || ||  ||||  | |||     | | ||  ||   ||||||||||| || ||||||||| |||||||||| ||| |||| || |||||||| ||||| || || |||||||| || |
---------------gtagcttaattactccatcatcatgtttctgaatgtgta-tagttggttttattcacaa-gtattgttttttactaatcatcttctcaaacagAATTTTCTGTTCAAATCAACCGAAGAAGATTCGCCTCTAAAAGCTACTGATTTCGGTTTATCTGACTTCATAAAGCCAG

upper sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 4
gtatgatcaagcacatttgcatatctgccaaatttgtgtgaaatgag-atctatactactagatgctatacataatatattaatatttttacctattcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG
|||| || |||     | ||| |  |   || ||||  |  |||  | | | ||  | |   ||| |        || |||    |||||| |    | || ||||||||||||| || ||||||||||| || || ||||| |||||||| ||||||||| | ||||| |||||||| ||||
gtataatgaagtttgctggcacacatcaaaattttggctttaatttgtagccattatgcctaatggtgcttcccttacatt----tttttatcg---catgtagAATTTTCTTTTCAAGTCAACCAAAGAGGACTCGCCTTTGAAGGCCACGGATTTTGGTCTATCAGACTTCATAAAGCCTG

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|193524793|gb|FK482328.1|FK482328
EST:     CCGGGATATGAAACCAGAG                         AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
genomic: CCGGGACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
EST: gi|193473081|gb|FK436670.1|FK436670
EST:     CAGCTGAGTGTCATTTACATGGTTTGGTACACCGGGACATGAAACCAGAG                         AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
genomic: CAGCTGAGTGTCATTTACATGGTTTGGTACACCGGGACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
EST: gi|193496517|gb|FK460703.1|FK460703
EST:     ATGGTTTGGTACACCGGGACATGAAACCAGAG                         AATTTTCTTTTTTAAATTCAACCAAAGAAGATTCACCTTTAAAGGCCACTG
genomic: ATGGTTTGGTACACCGGGACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTC-TTTTTAAA-TCAACCAAAGAAGATTCACCTTTAAAGGCCACTG
EST: gi|193668943|gb|FK612271.1|FK612271
EST:     CCGGGACATGAAACCAGAG                         AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
genomic: CCGGGACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
EST: gi|208080484|gb|GD878996.1|GD878996
EST:     CCGGGACATGAAACCAGAG                         AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
genomic: CCGGGACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
EST: gi|193451498|gb|FK417946.1|FK417946
EST:     ACATGAAACCAGAG                         AATTTTCTTTTTAAATTCAACCAAAGAAGATTCACCTTTAAAGGCCACTGA
genomic: ACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAA-TCAACCAAAGAAGATTCACCTTTAAAGGCCACTGA
EST: gi|193661924|gb|FK606938.1|FK606938
EST:     CCGGGACATGAAACCAGAG                         AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
genomic: CCGGGACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
EST: gi|193477388|gb|FK443525.1|FK443525
EST:     ACATGAAACCAGAG                         AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
genomic: ACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
EST: gi|193674208|gb|FK617300.1|FK617300
EST:     ACATGAAACCAGAG                         AATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT
genomic: ACATGAAACCAGAGgtatgatcaa ... attcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatactactagatgctatacataatatattaatatttttacctattcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG
                            tattaat  putative branch site (score: 2)
                                    tttttacctattctt  CT-rich tract
                 tatacataatatatta  TA-rich tract