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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggaatttgacaagttgctattcaaacatgtggtttcctaataacactattttttttttcttttatcaagaatggtgtattggataacatcatgtgccatattttttttatagttaaattgccaatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATCCCATATATTGCGGCCTCGTTTGGTGGCTGTGAGAGCATTGTGGATCAAC

Basic information

species Glycine max
transcript GLYMA09G37020.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G37020.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0108g01110.t01 (Vitis vinifera), 3'ss of exon 9
gtgggaatttgacaagttgctattcaaacatgtggtttcctaataacactattttttttttcttttatcaagaatggtgtattggataacatcatgtgccatattttttttatagttaaattgccaatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATCCCATATATTGCGGCCTCGTTTGGTGGCTGTGAGAGCATTGTGGATCAAC
                                  ||   |   |   || |||||  | | ||  | | | |  | ||  ||  |  |     || |    |  || ||   || |||||||        ||||| ||||||||||  ||   ||||| || || ||| ||||| ||||||||||||| ||||||||  | || || || ||||||||||||||||| ||||| |
----------------------------------gtaagcatttgtaaccattttcatgtgctggtgtgagg--ttgttcatctggaagttggattttaagtgcttattgc-tatttaaatt--------tgcagGTTGATGGAGACTTAACCACCACCATCAAGTTTGTTGATGCATTGAAAATCCCTTATATTGCCCCATCCTTCGGAGGCTGTGAGAGCATTGTTGATCAGC
















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|254313663|gb|GR831292.1|GR831292
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|9204521|gb|BE330745.1|BE330745
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|5666752|gb|AI930788.1|AI930788
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|214008139|gb|DB987044.1|DB987044
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACAAAAATAAAATTTATTGATTCATTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|208232694|gb|GE029927.1|GE029927
EST:     GAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
genomic: GAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|151406835|gb|EV276650.1|EV276650
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|17153398|gb|BM143331.1|BM143331
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAGTTTATTGATTCACTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|209724849|gb|BW672632.1|BW672632
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|208249269|gb|GE044542.1|GE044542
EST:     GAGGCAGATGACTGGTTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
genomic: GAGGCAGATGACTGG-TTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|12691080|gb|BG157416.1|BG157416
EST:     AGCTTGCCAAGA-GCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|13790160|gb|BG652751.1|BG652751
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCAC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCAC
EST: gi|18720947|gb|BM523284.1|BM523284
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAGTTTATTGATTCACTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|305377733|gb|HO651964.1|HO651964
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|254313664|gb|GR831293.1|GR831293
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|213606242|gb|DB974652.1|DB974652
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACGACAATAAAATTTATTGATTCATTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|254343669|gb|GR857425.1|GR857425
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAGTTTATTGATTCACTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|6914460|gb|AW395990.1|AW395990
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|17023490|gb|BM094524.1|BM094524
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|9899860|gb|BE608828.1|BE608828
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAGTTTATTGATTCACTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|209724723|gb|BW651466.1|BW651466
EST:     TGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
genomic: TGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|12688526|gb|BG154862.1|BG154862
EST:     CTTGCCAAGAGGCAGATGACTGGTTTNCGGTGGNTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
genomic: CTTGCCAAGAGGCAGATGACTGGTTT-CGGTGG-TGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
EST: gi|15812404|gb|BI784679.1|BI784679
EST:     AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAG                         ATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC
genomic: AGCTTGCCAAGAGGCAGATGACTGGTTTCGGTGGTGTTGTCAGTTTTGAGgtgggaattt ... aatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attggataacatcatgtgccatattttttttatagttaaattgccaatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATCCCATATATTGCGGCCTCGTTTGGTGGCTGTGAGAGCATTGTGGATCAAC
   ggataac  putative branch site (score: 3)
                    atattttttttatagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggaatttgacaagttgctattcaaacatgtggtttcctaataacactattttttttttcttttatcaagaatggtgtattggataacatcatgtgccatattttttttatagttaaattgccaatattgcagATTGATGGAGATCTACATACCACAATAAAATTTATTGATTCATTGAAAATCCCATATATTGCGGCCTCGTTTGGTGGCTGTGAGAGCATTGTGGATCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA