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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaacttgagacctccagattttgtagctctcatctgcatcgctgtttatattatgtttatcatttagaatatttaaacttttatctttgtcatccttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGAAATGAGAAGCTGCAGTGCTTTTTAGATGCAGTGAAGGAACATCCTAATG

Basic information

species Glycine max
transcript GLYMA19G36580.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36580.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ12224 (Selaginella moellendorffii), 3'ss of exon 2
taaacttgagacctccagattttgtagctctcatctgcatcgctgtttatattatgtttatcatttagaatatttaaacttttatctttgtcatccttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGAAATGAGAAGCTGCAGTGCTTTTTAGATGCAGTGAAGGAACATCCTAATG
                                         |    |  | ||    || |||| |||  |  |    ||     |  |||     | |||||||||||||||| || || || || || ||||| || ||||||||| | || |||||||| ||||| ||||| ||||   | ||  | ||||| ||||
-----------------------------------------gtgagtggtgtttcaatt-tcatctagcgtgctcgcgct-----caatgtttctttcagGTTCATCCTTATGTCGCGACAGGCAACAAAAACTCCAAGTTTGGCATTCGCAACGAGAAGCTCCAGTGGTTTTTGGATGAGATAAAACAGCATCCCAATG
















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|209726441|gb|BW658048.1|BW658048
EST:     GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTG
genomic: GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAGgtatgttgtt ... tcatccttagGTTCATCCTTATGTTGCCACTG
EST: gi|208292173|gb|GE093379.1|GE093379
EST:     GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
genomic: GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAGgtatgttgtt ... tcatccttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
EST: gi|208076524|gb|GD873941.1|GD873941
EST:     GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
genomic: GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAGgtatgttgtt ... tcatccttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
EST: gi|19268834|gb|BM885090.1|BM885090
EST:     GAAGAAAGG-CAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATT
genomic: GAAGAA-GGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAGgtatgttgtt ... tcatccttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATT
EST: gi|26057499|gb|CA800413.1|CA800413
EST:     GGAAGAAGGGCAATGTTTTACTTCGGAATAATCCTGATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTGGAAATAAAAACTCTAAATTT
genomic: GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAGgtatgttgtt ... tcatccttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTT
EST: gi|193361576|gb|FK325240.1|FK325240
EST:     GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
genomic: GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAGgtatgttgtt ... tcatccttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
EST: gi|193579850|gb|FK534967.1|FK534967
EST:     GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
genomic: GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAGgtatgttgtt ... tcatccttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
EST: gi|17022163|gb|BM093197.1|BM093197
EST:     GTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
genomic: GTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAGgtatgttgtt ... tcatccttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
EST: gi|192296879|gb|FG990240.1|FG990240
EST:     GATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
genomic: GATGTGGATCCACAGgtatgttgtt ... tcatccttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
EST: gi|151406826|gb|EV276641.1|EV276641
EST:     GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
genomic: GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAGgtatgttgtt ... tcatccttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
EST: gi|193723463|gb|FK657143.1|FK657143
EST:     GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAG                         GTTCATCCTTA
genomic: GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAGgtatgttgtt ... tcatccttagGTTCATCCTTA
EST: gi|6454757|gb|AW185440.1|AW185440
EST:     GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTG-ATCCAC-G                         GTTCATCCT-ATGTTGC-ACTGGGAATA
genomic: GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAGgtatgttgtt ... tcatccttagGTTCATCCTTATGTTGCCACTGGGAATA
EST: gi|192317324|gb|FK010555.1|FK010555
EST:     GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAG                         GTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA
genomic: GGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAGgtatgttgtt ... tcatccttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatattatgtttatcatttagaatatttaaacttttatctttgtcatccttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGAAATGAGAAGCTGCAGTGCTTTTTAGATGCAGTGAAGGAACATCCTAATG
                                 cttttatctttgtc  CT-rich tract
     attatgtttatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaacttgagacctccagattttgtagctctcatctgcatcgctgtttatattatgtttatcatttagaatatttaaacttttatctttgtcatccttagGTTCATCCTTATGTTGCCACTGGGAATAAGAACTCTAAATTTGGCATTAGAAATGAGAAGCTGCAGTGCTTTTTAGATGCAGTGAAGGAACATCCTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - acctcca
- - - - - - - - - - - - - - - -catctgc
- - - - - - - - - - - - - - - - - - - - -gctgttt