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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggatgctaggctgtaaacacggtgttttttaaaacttgtttagtacctgtgcttgcaattatgttatttaaattttcctattcgttatttttttgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAG

Basic information

species Glycine max
transcript GLYMA20G16170.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 14
-----------------------------------------------tgggatgctaggctgtaaa---cacggtgttttttaaaacttgtttagtacctgtgcttgcaattatgtt-atttaaattttccta-ttcgttat---ttttttgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAG
                                               ||  | | |   |  | ||   ||| |||| |     | |     ||    ||||   |    | | ||| || ||| | |    | |   ||||    | ||||||||| || || |||||||| ||  | || ||||| |||||||| ||||| || ||||||||||| || || |||||||| ||||| ||||
gtaagttcaagcatcatttttatctttcctttacatccagcaacaattgctaggttgcaccatgaagttcacagtgtatggatcaccaaacatacagtctgtttgtcatttaacgttgatctaagtataaaaaatgtattatatgctctttgcagGGTGTACCTGAACAGAAACTGAGGGCACACTTGGGTTCTTTCGGTGTTACAGGAAATCTTGCCCTCCAACCAATGTACACTTTATCAG

upper sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 14
---------------------------------------------------------------------------------------------tgggatgctaggctgtaaacacggtgttttttaaaacttgtttagtacc-tgtgcttgcaattatgttatttaaattttcctatt----cgttattt--ttttgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAG
                                                                                               |  |  |   ||    ||| | | | |    ||  |   | || |   ||| | | |  |    || |  | || |    | |     |||||||  | | ||||||||| |||||||| |||||  ||  |||||| |||||| |||| ||||| |||||||||||||||||||| ||||| ||||| ||||
gtaagttcccacacctgtaatatccctcttatttgcaggtttcagttaacatgagatcaaaattgagctaaatgtttcttgtattagagtttacagtcttgtctacttcttacaagttatatgcacaatttaagtaagcaaaatgtacataccctcggcttctcaatatgtcttaactggtatgttatttgatgtggcagGGAGTACCAGAACAAAAGCTGAGAAGTCACTTGGGTTCTCTTGGGGTAACTGGAAATCTTGCACTGCAGCCCATGTACACTTTATCAG

upper sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv02s0025g02160.t01 (Vitis vinifera), 3'ss of exon 14
tgggatgctaggctgtaaacacggtgttttttaaaacttgtttagtacctgtgcttgcaattatgttatttaaat---tttcctattcgttatt---tttttgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAG
       ||    | |      | | |  | |   | || |  | || || |      |||  | | |  | | |   |  |  ||  |  |||   || |||||||| || |||||||||||||| |||||||| |||||||| ||||||||||| ||||||||||| || ||||| ||||| ||||| || |
------tctccattttttgtgggttatcctcttctatttttggaatatcttttgcccgaatgttatcacatgagtgaatcactgatgtgaaattggcttcttgcagGGGGTGCCAGAACAGAAGCTCCGAGCTCATTTAGGTTCATTTGGTGTAACAGGAAATCTTGCTCTTCAGCCCATGTACACTTTATCTG

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|192323200|gb|FK015266.1|FK015266
EST:     GACTGGACTTATCCTCAAACCCTCTTCTGTATATGATGCGCTGCTATCCT                         GGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACC
genomic: GACTGGACTTATCCTCAAACCCTCTTCTGTATATGATGCGCTGCTATCCTgtgagttcct ... ttttttgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACC
EST: gi|10232016|gb|BE800904.1|BE800904
EST:     GACTGGACTTATCCTCAAACCCTCTTCTGTATATGATGCGCTGCTATCCT                         GGAGTTCCATAACAGAAGCTTCGAGCTCACTTATGTTCTTTTGGTGTAACC
genomic: GACTGGACTTATCCTCAAACCCTCTTCTGTATATGATGCGCTGCTATCCTgtgagttcct ... ttttttgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACC
EST: gi|10254011|gb|BE821777.1|BE821777
EST:     TATATGATGCGCTGCTATNNT                         NGAGNTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTNNNGTGTNNNC
genomic: TATATGATGCGCTGCTATCCTgtgagttcct ... ttttttgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACC
EST: gi|13789096|gb|BG651687.1|BG651687
EST:     GATTGGACTTATCCTCAAACCCTCTTCTGTATATGATGCGCTGCTATCCT                         GGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACC
genomic: GACTGGACTTATCCTCAAACCCTCTTCTGTATATGATGCGCTGCTATCCTgtgagttcct ... ttttttgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACC
EST: gi|22523787|gb|BU082598.1|BU082598
EST:     GACTGGACTTATCCTCAAACCCTCTTCTGTATATGATGCGCTGCTATCCT                         GGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACC
genomic: GACTGGACTTATCCTCAAACCCTCTTCTGTATATGATGCGCTGCTATCCTgtgagttcct ... ttttttgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACC
EST: gi|192322574|gb|FK014695.1|FK014695
EST:     GACTGGACTTATCCTCAAACCCTCTTCTGTATATGATGCGCTGCTATCCT                         GGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACC
genomic: GACTGGACTTATCCTCAAACCCTCTTCTGTATATGATGCGCTGCTATCCTgtgagttcct ... ttttttgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACC
EST: gi|15286165|gb|BI470056.1|BI470056
EST:     GACTGGACTTATCCTCAAACCCTCTTCTGTATATGATGCGCTGCTATCCT                         GGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACC
genomic: GACTGGACTTATCCTCAAACCCTCTTCTGTATATGATGCGCTGCTATCCTgtgagttcct ... ttttttgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacctgtgcttgcaattatgttatttaaattttcctattcgttatttttttgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAG
                             ttttcctattcgttat  CT-rich tract
             aattatgttatttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgggatgctaggctgtaaacacggtgttttttaaaacttgtttagtacctgtgcttgcaattatgttatttaaattttcctattcgttatttttttgcagGGAGTTCCAGAACAGAAGCTTCGAGCTCACTTAGGTTCTTTTGGTGTAACCGGAAATCTTGCACTGCAGCCAATGTATACTTTGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- ggatgct
- - - - -aggctgt
- - - - - - - - - - - ggtgttt
- - - - - - - - - - - - - - - - - - - - - - gtacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - gcttgca