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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacttgcgtgaaaacagcaggtctacacaatgtgttacatagtttattaagtagcttgattttggttagttaagcacgtttctacttgtcactgtcatagGATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGGGAATACCCATTTGCAGTAGCTGGAATCAATATTTCTTTTATGTTAGCAC

Basic information

species Glycine max
transcript GLYMA19G29990.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G29990.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G03610.1 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------------------cacttgcgtgaaaacagcaggtctacacaatgtgttacatagtttattaagtagcttgattttggttagttaagcacgtttctacttgtcactgtcatagGATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGGGAATACCCATTTGCAGTAGCTGGAATCAATATTTCTTTTATGTTAGCAC
                                      ||      ||  |  |  | |  |||||       ||||   |||   |  ||   |     | |    | || | ||     | ||| | | | |||| ||||||||| |||| || ||||||||||||||||| ||||| || |||||||| || || || || ||||| |||||||| || || ||| | ||||
gtctgtgatgcatctctaattctcatctacatttttgatttaagagaactaataactttttacaattctaagtataggg-attttatctctgagtcgctatgatcctaacaagatttgtgatatcattatgacagGAATCATTCCAGAGATTGTTACATAAACAAGATGGAACTAGAGCGGAATGGGAATATCCTTTCGCGGTGGCTGGCATCAATATCTCATTCATGCTGGCAC

upper sequence: GLYMA19G29990.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv08s0056g00790.t01 (Vitis vinifera), 3'ss of exon 7
cacttgcgtgaaaacagcaggtctacacaa---tgtgttac-atagtttat-taagtagcttgattttggttagttaagcacgtttctacttgtcactgtcatagGATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGGGAATACCCATTTGCAGTAGCTGGAATCAATATTTCTTTTATGTTAGCAC
      || | ||  || | | | || |||   | | |||| | |  | |  |   |   |  |||     | |  |   || ||    | | |  ||   | ||||| |||||||| | || || || ||||  || |||| ||| || || ||||| || || ||||| |||||||| ||||||||||||||||||||   ||
-----ccgagcaacaaggaagaccacgcaagtatatattactacaaatgacattttttattccattgaacgtggagacatactttctctcctttttcttcaacagGATACATTCCAGAGGTTGTTACACAAACTTGACGGAAACAGGGCCGATTGGGAGTATCCCTTTGCTGTAGCTGGCATCAATATTTCTTTTATGTTGATAC
















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|13789800|gb|BG652391.1|BG652391
EST:     GAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTATCCT                         GATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGG
genomic: GAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTATCCTgtaagtttct ... actgtcatagGATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGG
EST: gi|6134331|gb|AW132724.1|AW132724
EST:     GAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTATCCT                         GATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGG
genomic: GAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTATCCTgtaagtttct ... actgtcatagGATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGG
EST: gi|22523888|gb|BU082699.1|BU082699
EST:     GAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTATCCT                         GATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGG
genomic: GAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTATCCTgtaagtttct ... actgtcatagGATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGG
EST: gi|27423797|gb|CA935317.1|CA935317
EST:     GAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTATCCT                         GATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGG
genomic: GAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTATCCTgtaagtttct ... actgtcatagGATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGG
EST: gi|193651462|gb|FK594633.1|FK594633
EST:     GAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTATCCT                         GATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGG
genomic: GAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTATCCTgtaagtttct ... actgtcatagGATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGG
EST: gi|15813140|gb|BI785415.1|BI785415
EST:     GAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTATCCT                         GATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGG
genomic: GAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTATCCTgtaagtttct ... actgtcatagGATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGG
EST: gi|12774852|gb|BG239718.1|BG239718
EST:     GAGGATTTATTTCATTA-AGAATCTCATCTTCTTTGCGATGAAGTATCCT                         GATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGG
genomic: GAGGATTTATTTCATTAGAGAATCTCATCTTCTTTGCGATGAAGTATCCTgtaagtttct ... actgtcatagGATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaagtagcttgattttggttagttaagcacgtttctacttgtcactgtcatagGATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGGGAATACCCATTTGCAGTAGCTGGAATCAATATTTCTTTTATGTTAGCAC
        gcttgat  putative branch site (score: 5)
          ttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacttgcgtgaaaacagcaggtctacacaatgtgttacatagtttattaagtagcttgattttggttagttaagcacgtttctacttgtcactgtcatagGATTCATTCCAGCGATTATTGCATAAACAAGATGGAACCAGAGCTGAGTGGGAATACCCATTTGCAGTAGCTGGAATCAATATTTCTTTTATGTTAGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
cacttgc
- - - - - - - - - - - ctacaca