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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatcttcgtttccctccatttgcacatatatttttctatttgttcattttcaattcaatcttcgtataggatttggtgatgtttattgtttaaaattattcatatccaatattgtggttctttctatgctaattataacttttttttctcttcatagGTGTGAAGTTGGTATTCAGGAGCTTCCAAAGAATTCTCCCTTGGGAAGACTAAGAGGAAGTGATAATGTG

Basic information

species Glycine max
transcript GLYMA20G11950.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G11950.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0009g01460.t01 (Vitis vinifera), 3'ss of exon 9
gcatcttcgtttccctccatttgcacatatatttttctatttgttcatt-ttcaattcaatcttcgtataggatttggtgatgtttattgtttaaaattattcatatccaatattgtggttctttctatgctaattataacttttttttctcttcatagGTGTGAAGTTGGTATTCAGGAGCTTCCAAAGAATTCTCCCTTGGGAAGACTAAGAGGAAGTGATAATGTG
                                         |||| ||  ||   ||   | || ||| |  | ||  | || ||   |      || | |   |           |  ||| ||  ||  |  | ||||||   ||||   |   ||||  |||||||||  | |  |||||||| ||  ||||||| ||||||||||||||||||||| ||||| | 
----------------------------------------atgttaataattttgttagcttttagtaaaaaaattaataattttggctc-----aactttctgt-----------taattcatttcatattgctgataactcactttt---tgggtagGACTGAAGTTGGCTTACGAGAGCTTCCTAAAGATTCTCCTTTGGGAAGACTAAGAGGAAGTAATAATATT
















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|192305169|gb|FG997491.1|FG997491
EST:     GCTTCAAATGGAAATGTGTTGCGCTATGTCTGTGTGATCATGGGTTCAAG                         GTGTGAAGTTGGTATTCAGGAGCTTCCAAAGAACTCTCCCTTGGGAAGACT
genomic: GCTTCAAATGGAAATGTGTTGCGCTATGTCTGTGTGATCATGGGTTCAAGgcatcttcgt ... ctcttcatagGTGTGAAGTTGGTATTCAGGAGCTTCCAAAGAATTCTCCCTTGGGAAGACT
EST: gi|18040511|gb|BM308805.1|BM308805
EST:     GCTTCAAATGGAAATGTGTTGCGCTATGTCTGTGTGATCATGGGTTCAAG                         GTGTGAAGTTGGTATTCAGGAGCTTCCAAAGAATTCTCCCTTGGGAAGACT
genomic: GCTTCAAATGGAAATGTGTTGCGCTATGTCTGTGTGATCATGGGTTCAAGgcatcttcgt ... ctcttcatagGTGTGAAGTTGGTATTCAGGAGCTTCCAAAGAATTCTCCCTTGGGAAGACT
EST: gi|209725589|gb|BW677891.1|BW677891
EST:     GCTTCAAATGGAAATGTGTTGCGCTATGTCTGTGTGATCATGGGTTCAAG                         GTGTGAAGTTGGTATTCAGGAGCTTCCAAAGAATTCTCCCTTGGGAAGACT
genomic: GCTTCAAATGGAAATGTGTTGCGCTATGTCTGTGTGATCATGGGTTCAAGgcatcttcgt ... ctcttcatagGTGTGAAGTTGGTATTCAGGAGCTTCCAAAGAATTCTCCCTTGGGAAGACT
EST: gi|209698411|gb|BW667206.1|BW667206
EST:     GCTTCAAATGGAAATGTGTTGCGCTATGTCTGTGTGATCATGGGTTCAAG                         GTGTGAAGTTGGTATTCAGGAGCTTCCAAAGAATTCTCCCTTGGGAAGACT
genomic: GCTTCAAATGGAAATGTGTTGCGCTATGTCTGTGTGATCATGGGTTCAAGgcatcttcgt ... ctcttcatagGTGTGAAGTTGGTATTCAGGAGCTTCCAAAGAATTCTCCCTTGGGAAGACT
EST: gi|22930193|gb|BU547332.1|BU547332
EST:     GCTTCAAATGGAAATGTGTTGCGCTATGTCTGTGTGATCATGGGTTCAAG                         GTGTGAAGTTGGTATTCAGGAGCTTCCAAAGAATTCTCCCTTGGGAAGACT
genomic: GCTTCAAATGGAAATGTGTTGCGCTATGTCTGTGTGATCATGGGTTCAAGgcatcttcgt ... ctcttcatagGTGTGAAGTTGGTATTCAGGAGCTTCCAAAGAATTCTCCCTTGGGAAGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatccaatattgtggttctttctatgctaattataacttttttttctcttcatagGTGTGAAGTTGGTATTCAGGAGCTTCCAAAGAATTCTCCCTTGGGAAGACTAAGAGGAAGTGATAATGTG
                              ttataac  putative branch site (score: 2)
                              ttataacttttttttc  CT-rich tract
                  tttctatgctaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatcttcgtttccctccatttgcacatatatttttctatttgttcattttcaattcaatcttcgtataggatttggtgatgtttattgtttaaaattattcatatccaatattgtggttctttctatgctaattataacttttttttctcttcatagGTGTGAAGTTGGTATTCAGGAGCTTCCAAAGAATTCTCCCTTGGGAAGACTAAGAGGAAGTGATAATGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA