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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccgctgcaccagggcttgccctcaaattgtttattgcaaataatcttttaaaaacttttcatatgcttaatttttgtttttttgggttatttattcagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATGGTTTAGCATTATGTCCTTGGCTATGTGCATTGCAGTTTCTGGTTTGCAA

Basic information

species Glycine max
transcript GLYMA05G30330.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30330.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0034g01440.t01 (Vitis vinifera), 3'ss of exon 3
--------taccgctgcaccagggcttgccctcaaattgttt--attgcaaataatcttttaaaaacttttcatatgcttaatttttgtttttttgggttatttatt-cagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATGGTTTAGCATTATGTCCTTGGCTATGTGCATTGCAGTTTCTGGTTTGCAA
        ||  | |  |   ||    ||    ||  | |||  ||||| ||| |  |     | ||   | |     ||   |    |||||||||  | ||  |  ||| ||||| || |||||||  ||||| |||||||||||||  |||||||||||||  ||||| ||||| ||||   | |||||||||||||| | |||||| 
gtaatttttatggttttagttggaacagcatctaatgtttttgcattgctaatcaattagatcataccagttac-catttttctcccatttttttggacttttactcacagAGAAGCAGAAATGAGGATGGTGAGCGAAAAAACAAATGCAAGAGTGGCATGGTACAGCATCATGTCATTGGGCGTCTGCATTGCAGTTTCAGCTTTGCAG
















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|298169454|gb|HO020814.1|HO020814
EST:     GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGTGAG
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGTGAG
EST: gi|9987066|gb|BE661174.1|BE661174
EST:     GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|192325154|gb|FK019085.1|FK019085
EST:     GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|298165642|gb|HO011691.1|HO011691
EST:     GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGTGAG
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGTGAG
EST: gi|193698781|gb|FK637192.1|FK637192
EST:     AAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGT
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGT
EST: gi|192314293|gb|FK007031.1|FK007031
EST:     GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|151407142|gb|EV276957.1|EV276957
EST:     GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|207785148|gb|GD755665.1|GD755665
EST:     GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCCCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|298177574|gb|HO027241.1|HO027241
EST:     GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGTG
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGTG
EST: gi|208106478|gb|GD906463.1|GD906463
EST:     GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGTGAGTGAAAAAACAA-TGGCAGAGTGGCATG
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|208263549|gb|GE063809.1|GE063809
EST:     GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|151394892|gb|EV264763.1|EV264763
EST:     GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|192314294|gb|FK007032.1|FK007032
EST:     GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGTGAGTGAAAAA-CAAATGGCAGAGTGGCATG
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|192322896|gb|FK014827.1|FK014827
EST:     GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|151411095|gb|EV280906.1|EV280906
EST:     GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
EST: gi|151405471|gb|EV275285.1|EV275285
EST:     GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAG                         GGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG
genomic: GAAGGAGCAGTAGAGGCCATCCATGAGAACTTGCTCTATCTTAAGGGAAGgtaattccaa ... atttattcagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttaaaaacttttcatatgcttaatttttgtttttttgggttatttattcagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATGGTTTAGCATTATGTCCTTGGCTATGTGCATTGCAGTTTCTGGTTTGCAA
                     gcttaat  putative branch site (score: 4)
                                              tttattc  putative PPT
     taaaaacttttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taccgctgcaccagggcttgccctcaaattgtttattgcaaataatcttttaaaaacttttcatatgcttaatttttgtttttttgggttatttattcagGGAAGCTGATATGAGGACTGTGAGTGAAAAAACAAATGGCAGAGTGGCATGGTTTAGCATTATGTCCTTGGCTATGTGCATTGCAGTTTCTGGTTTGCAA

- - - tgcacca
- - - - - - - - cttgccc
- - - - - - - - - - - - - - - - -tattgca
- - - - - - - - - - - - - - - - - - - - - - - - - taaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catatgc