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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtgttgtatttctgcttcaatgctttgaaattgaattatgtaattctttgcttgagatagctgtggttttagttgactgaaccttttttcataatagGAGAAAGGAAGGGGTGGACGCCATGGAAAAACGATTAATATCTTTTCAATTGCTTCTGGACACTT

Basic information

species Glycine max
transcript GLYMA08G20020.1
intron # 29
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 29
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 30
tttgtgttgtatttctgcttcaatgctttgaaattgaattatgtaa-ttctttgcttgagatagctgtgg-------ttttagttgactgaaccttttttcataatagGAGAAAGGAAGGGGTGGACGCCATGGAAAAACGATTAATATCTTTTCAATTGCTTCTGGACACTT
          || ||   |  |||   | || |||   ||   |||  | || | | | ||| | || |        |||||    |   ||  || |||  |   |||   | ||||  |||||| | | ||| |||||||||||||| ||||| |||||||||||||||||
--------caatatcaattctaatttgtggatattttttttactaagcttttcgatggtgattggtgggacatttttttttaaaaaaaaaaaaattctttattttcagGGACATGGAAAAGGTGGAAGACGTGGGAAAACGATTAATATTTTTTCCATTGCTTCTGGACACTT
















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|7283494|gb|AW596101.1|AW596101
EST:     GTTTCATTAGTAGTAATGAACAACCTAAAAATGCTGAAACCAATTCACCA                         GAGAAAGGAAGGGGTGGACGCCATGGAAAAACGATTAATATCTTTTCAATT
genomic: GTTTCATTAGTAGTAATGAACAACCTAAAAATGCTGAAACCAATTCACCAgtgagttttt ... ttcataatagGAGAAAGGAAGGGGTGGACGCCATGGAAAAACGATTAATATCTTTTCAATT
EST: gi|33389227|gb|CA852434.1|CA852434
EST:     GCTGAAACCAATTCACCA                         GNAGAAAGGAAGGGGTGGACGCCATGGAAAAACGATTAATATCTTTTCAAT
genomic: GCTGAAACCAATTCACCAgtgagttttt ... ttcataatagG-AGAAAGGAAGGGGTGGACGCCATGGAAAAACGATTAATATCTTTTCAAT
EST: gi|208045567|gb|GD838897.1|GD838897
EST:     GTTTCATTAGTAGTAATGAACAACCTAAAAATGCTGAAACCAATTCACCA                         GAGAAAGGAAGGGGTGGACGCCATGGAAAAACGATTAATATCTTTTCAATT
genomic: GTTTCATTAGTAGTAATGAACAACCTAAAAATGCTGAAACCAATTCACCAgtgagttttt ... ttcataatagGAGAAAGGAAGGGGTGGACGCCATGGAAAAACGATTAATATCTTTTCAATT
EST: gi|193705135|gb|FK641923.1|FK641923
EST:     GTTTCATTAGTAGTAATGAACAACCTAAAAATGCTGAAACCAATTCACCA                         GAGAAAGGAAGGGGTGGACGCCATGGAAAAACGATTAATATCTTTTCAATT
genomic: GTTTCATTAGTAGTAATGAACAACCTAAAAATGCTGAAACCAATTCACCAgtgagttttt ... ttcataatagGAGAAAGGAAGGGGTGGACGCCATGGAAAAACGATTAATATCTTTTCAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctttgcttgagatagctgtggttttagttgactgaaccttttttcataatagGAGAAAGGAAGGGGTGGACGCCATGGAAAAACGATTAATATCTTTTCAATTGCTTCTGGACACTT
                            agttgac  putative branch site (score: 4)
                                       ccttttttcat  putative PPT
                                         ttttttcataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtgttgtatttctgcttcaatgctttgaaattgaattatgtaattctttgcttgagatagctgtggttttagttgactgaaccttttttcataatagGAGAAAGGAAGGGGTGGACGCCATGGAAAAACGATTAATATCTTTTCAATTGCTTCTGGACACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - tgttgta
- - - - - - - ctgcttc
- - - - - - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaacc