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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgaatagaaactcatacataaggaatcctattcatcatcttgtactccttataaaaacatttttggattgatgtagacaatcctttatgccaagtgaatggttcatgaacttgatttttctaatgataactatacagGTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGCAATGACCGCTTATGGTTTAG

Basic information

species Glycine max
transcript GLYMA09G39500.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G39500.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 11
gttgaatagaaactcatacataaggaatcctattcatcatcttgtactccttataaaaacatttttggattgatgtagacaatcctttatgccaagtgaatggttcatgaacttgatttttctaatgataactatacagGTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGCAATGACCGCTTATGGTTTAG
                              |    |    ||| ||    | || |||| |||| |      ||  | |  |   |  | |  |||  | |   | || ||||   ||      || ||     | ||||||||||||||||||||||||||  || ||||  || |||||  ||||||| ||||| ||||||||| |||
------------------------------ttgggacgtgcttttagctttaatgaaaagatttat------attaaaaagaaattggaagggaagaaagtt-ctaatcaactcatttggatggatcattg--gttcagGTATGATTGGTTGGCAAAGAAGAGTCTCCGAGCAGGATACTTTGTGTGGGCCATGACTGCTTATGGTCTAG
















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|254320216|gb|GR829404.1|GR829404
EST:     GGTTTTGGGGACATCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAG                         GTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGC
genomic: GGTTTTGGGGACATCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAGgttgaataga ... aactatacagGTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGC
EST: gi|9900391|gb|BE609359.1|BE609359
EST:     GGTTTTGGGGACATCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAG                         GTATGATTGGTTGGCAAAGAAGAACCTTCGAAATGGGTACTTCTTGTGGGC
genomic: GGTTTTGGGGACATCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAGgttgaataga ... aactatacagGTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGC
EST: gi|9258837|gb|BE346984.1|BE346984
EST:     GGTTTTGGGGACATCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAG                         GTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGC
genomic: GGTTTTGGGGACATCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAGgttgaataga ... aactatacagGTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGC
EST: gi|208299697|gb|GE097180.1|GE097180
EST:     GGTTTTGGGGACATCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAG                         GTATGATTGGTTGGCAAAGAAGAA
genomic: GGTTTTGGGGACATCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAGgttgaataga ... aactatacagGTATGATTGGTTGGCAAAGAAGAA
EST: gi|22524144|gb|BU082955.1|BU082955
EST:     GGTTTTGTTTACTTCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAG                         GTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGC
genomic: GGTTTTGGGGACATCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAGgttgaataga ... aactatacagGTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGC
EST: gi|208088299|gb|GD889467.1|GD889467
EST:     ATCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAG                         GTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGC
genomic: ATCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAGgttgaataga ... aactatacagGTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGC
EST: gi|22523945|gb|BU082756.1|BU082756
EST:     GGTTTTGGTGACATCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAG                         GTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGC
genomic: GGTTTTGGGGACATCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAGgttgaataga ... aactatacagGTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGC
EST: gi|254320215|gb|GR829403.1|GR829403
EST:     GGTTTTGGGGACATCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAG                         GTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGC
genomic: GGTTTTGGGGACATCATCTTACCAGGGCTTCTAGTAGCATTTTCACTAAGgttgaataga ... aactatacagGTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttatgccaagtgaatggttcatgaacttgatttttctaatgataactatacagGTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGCAATGACCGCTTATGGTTTAG
                                         tgataac  putative branch site (score: 2)
                               atttttctaatgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgaatagaaactcatacataaggaatcctattcatcatcttgtactccttataaaaacatttttggattgatgtagacaatcctttatgccaagtgaatggttcatgaacttgatttttctaatgataactatacagGTATGATTGGTTGGCAAAGAAGAACCTTCGAGATGGGTACTTCTTGTGGGCAATGACCGCTTATGGTTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG