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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtttttttttaattacaccagtctttatttttttttaataaatttgcatttatctatcatcttgttagaactaagaggtttctattactacatcttcagGCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAACTTCTCTGCTCCTCTTGATGAAGCATTGATACATGTTTCACTG

Basic information

species Glycine max
transcript GLYMA20G28420.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28420.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G22425.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------ggtttttttttaattacaccagtctttatttt-------tttttaataaatttgcatttatctatc--------atcttgttagaactaagaggtt-tctatt-actacatcttcagGCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAACTTCTCTGCTCCTCTTGATGAAGCATTGATACATGTTTCACTG
                            | || ||||   |     ||||| |  | ||        | | |  ||   ||| ||    | ||        ||  ||||   |  ||     | | ||||   | | | |  ||||| |  |  | || ||||||||  | || || ||||||||||||||| ||||| | |||||||| ||||||||  | |||||||||||  ||
gtaagtcttactgtctttcgttttgccagcttcttttctctgttttcagtcatgctcttatgagacctatgagcaacagtgcgttgtcttttcctacggaaattgtgttgtgatgaaatccctgtgtatttgtttcttttctagGCTCTATTAAAGGCTCTTGGTGAGCGTAAAGGGATTAACCGGTTTGGTGACTTCACAGCTCCTCTAGATGAAGCGCTTATACATGTTTCCTTG
















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|254323948|gb|GR836180.1|GR836180
EST:     ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACA                         GCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
genomic: ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACAgtatgcaaac ... acatcttcagGCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
EST: gi|120496152|gb|EH224319.1|EH224319
EST:     ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACA                         GCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
genomic: ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACAgtatgcaaac ... acatcttcagGCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
EST: gi|192298863|gb|FG987608.1|FG987608
EST:     ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACA                         GCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
genomic: ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACAgtatgcaaac ... acatcttcagGCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
EST: gi|58021912|gb|CX708653.1|CX708653
EST:     CACACAAATGAAGACGTTGCCCTTGCTATTGGATCA                         GCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
genomic: CACACAAATGAAGACGTTGCCCTTGCTATTGGAACAgtatgcaaac ... acatcttcagGCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
EST: gi|120528942|gb|EH257076.1|EH257076
EST:     TATTGAGGATCATCACACAAATGAAGACGTTGCCATTGCTATTGGAACA                         GCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
genomic: TATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACAgtatgcaaac ... acatcttcagGCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
EST: gi|16278135|gb|BI942744.1|BI942744
EST:     ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACA                         GCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
genomic: ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACAgtatgcaaac ... acatcttcagGCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
EST: gi|151393539|gb|EV263414.1|EV263414
EST:     ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACA                         GCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
genomic: ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACAgtatgcaaac ... acatcttcagGCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
EST: gi|12691429|gb|BG157765.1|BG157765
EST:     ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACA                         GCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATNAACCGGGTTGGTAAC
genomic: ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACAgtatgcaaac ... acatcttcagGCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
EST: gi|192295567|gb|FG988141.1|FG988141
EST:     ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACA                         GCTTTGCTGCATGCCCTTGGCGATAGGAAGGGTATTAACCGGTTTGGTAAC
genomic: ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACAgtatgcaaac ... acatcttcagGCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
EST: gi|120528949|gb|EH257083.1|EH257083
EST:     ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACA                         GCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTAGGTAAC
genomic: ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACAgtatgcaaac ... acatcttcagGCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC
EST: gi|298186844|gb|HO033943.1|HO033943
EST:     ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACA                         GCTTTGCTGCATGCCCTTGGCGATAGGAAGGGTATTAACCGGTTTGGTAAC
genomic: ATATTGATGATCATCACACAAATGAAGACGTTGCCCTTGCTATTGGAACAgtatgcaaac ... acatcttcagGCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatttatctatcatcttgttagaactaagaggtttctattactacatcttcagGCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAACTTCTCTGCTCCTCTTGATGAAGCATTGATACATGTTTCACTG
                                              catcttc  CT-rich tract
                                  tttctatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtttttttttaattacaccagtctttatttttttttaataaatttgcatttatctatcatcttgttagaactaagaggtttctattactacatcttcagGCTTTGCTGCATGCCCTTGGTGATAGGAAGGGTATTAACCGGTTTGGTAACTTCTCTGCTCCTCTTGATGAAGCATTGATACATGTTTCACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC