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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtaacattttcactaaggattccttgtacttgtgattgaatttgaacttataaatatctaaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACAATGGAAGACATTTTGATGCAATTGAAGAAAGAAATGATATCTCCACAAA

Basic information

species Glycine max
transcript GLYMA05G35000.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G35000.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 3
gtaggtaacattttcactaaggattccttgtact----tgtgattgaatttgaacttataaatatctaaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACAATGGAAGACATTTTGATGCAATTGAAGAAAGAAATGATATCTCCACAAA
|| |||||  ||| |  | | || |  || | ||    | || ||||   | | ||||| | |    |||||||||||| || ||   | | || || |||||||||| |||||| || |||  ||||||||| ||||| ||||  |||||||||||||||||||| ||||| || |
gtgggtaat-tttactttcaagaatttttatgctgtggtatgtttgataataagcttatga-tggtcaaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACAATGGAGGACATATTGACTCAATTGAAGAAAGAAATGATGTCTCCCCAGA
















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|254348770|gb|GR852449.1|GR852449
EST:     GATTTCAGACTAGGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTG                         GTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA
genomic: GATTTCAGACTAGGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTGgtaggtaaca ... aaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA
EST: gi|6069685|gb|AW099309.1|AW099309
EST:     GATTTCAGACTAAGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTG                         GTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA
genomic: GATTTCAGACTAGGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTGgtaggtaaca ... aaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA
EST: gi|15201955|gb|BI425146.1|BI425146
EST:     ATTAACATGACTTGTGTCAACCAAGAAACTGGAGTG                         GTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA
genomic: ATTAACATGACTTGTGTCAACCAAGAAACTGGAGTGgtaggtaaca ... aaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA
EST: gi|254342628|gb|GR858790.1|GR858790
EST:     GATTTCAGACTAGGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTG                         GTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA
genomic: GATTTCAGACTAGGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTGgtaggtaaca ... aaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA
EST: gi|192319728|gb|FK011866.1|FK011866
EST:     GATTTCAGACTAGGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTG                         GTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA
genomic: GATTTCAGACTAGGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTGgtaggtaaca ... aaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA
EST: gi|19934908|gb|BQ079938.1|BQ079938
EST:     GATTTCAGACTAGGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTG                         GTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA
genomic: GATTTCAGACTAGGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTGgtaggtaaca ... aaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA
EST: gi|21889833|gb|BQ743046.1|BQ743046
EST:     GATTTCAGACTAGGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTG                         GTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA
genomic: GATTTCAGACTAGGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTGgtaggtaaca ... aaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA
EST: gi|24135406|gb|BU925916.1|BU925916
EST:     GATTTCAGACTAGGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTG                         GTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA
genomic: GATTTCAGACTAGGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTGgtaggtaaca ... aaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggattccttgtacttgtgattgaatttgaacttataaatatctaaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACAATGGAAGACATTTTGATGCAATTGAAGAAAGAAATGATATCTCCACAAA
                                         atctaaa  putative branch site (score: 3)
                    attgaatttgaactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtaacattttcactaaggattccttgtacttgtgattgaatttgaacttataaatatctaaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACAATGGAAGACATTTTGATGCAATTGAAGAAAGAAATGATATCTCCACAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA