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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatttttgcccaattatattattgcttttaatattagttaaaatattagatttagaacaaggcattgaaattaaaagttttttgtttttaatcttactgcagGCTGAGACACTTGCTGATCATATAAAATTCGACCATGGGTACAATGCAAAGAGCCCTGCCATTGTTAAT

Basic information

species Glycine max
transcript GLYMA04G00530.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 13
gtgatttttgcccaattatattatt--gcttt--taatattagttaaaatattagatttaga--acaaggcattgaaattaaaagttttttgtttttaatcttactgcagGCTGAGACACTTGCTGATCATATAAAATTCGACCATGGGTACAATGCAAAGAGCCCTGCCATTGTTAAT
|| || |   |     |||||| |   |||||  | | |  ||  |   | | | || |  |     |   || | | ||||||    | || |||| ||||   |||||||||||||||||| |||||| ||||| ||||| ||||| ||||  || ||||||||||| ||  |||||
gtaatctgctcttttctatattgtgtagctttcctcacacaagccatgct-tgaaatctgtattgtgaattatagtagttaaaa----tatgattttcatct--atgcagGCTGAGACACTTGTTGATCACATAAAGTTCGATCATGGATACACCGCCAAGAGCCCTGCAATCATTAAT
















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|208248831|gb|GE049522.1|GE049522
EST:     CTCCTCAAGAACTAGATAATTTGCTTTGCGGCCGCAGGGAGTTGTGGGAG                         GCTGAGACACTTGCTGATCATATAAAATTCGACCATGGGTACAATGCAAAG
genomic: CTCCTCAAGAACTAGATAATTTGCTTTGCGGCCGCAGGGAGTTGTGGGAGgtgatttttg ... cttactgcagGCTGAGACACTTGCTGATCATATAAAATTCGACCATGGGTACAATGCAAAG
EST: gi|208027054|gb|GD826824.1|GD826824
EST:     CTCCTCAAGAACTAGATAATTTGCTTTGCGGCCGCAGGGAGTTGTGGGAG                         GCTGAGACACTTGCTGATCATATAAAATTCGACCATGGGTACAATGCAAAG
genomic: CTCCTCAAGAACTAGATAATTTGCTTTGCGGCCGCAGGGAGTTGTGGGAGgtgatttttg ... cttactgcagGCTGAGACACTTGCTGATCATATAAAATTCGACCATGGGTACAATGCAAAG
EST: gi|120529051|gb|EH257185.1|EH257185
EST:     AGGGAGTTGTGGGAG                         GCTGAGACACTTGCTGATCATATAAAATTCGACCATGGGTACAATGCAAAG
genomic: AGGGAGTTGTGGGAGgtgatttttg ... cttactgcagGCTGAGACACTTGCTGATCATATAAAATTCGACCATGGGTACAATGCAAAG
EST: gi|207701146|gb|GD682391.1|GD682391
EST:     CTCCTCAAGAACTAGATAATTTGCTTTGCGGCCGCAGGGAGTTGTGGGAG                         GCTGAGACACTTGCTGATCATATAAAATTCGACCATGGGTACAATGCAAAG
genomic: CTCCTCAAGAACTAGATAATTTGCTTTGCGGCCGCAGGGAGTTGTGGGAGgtgatttttg ... cttactgcagGCTGAGACACTTGCTGATCATATAAAATTCGACCATGGGTACAATGCAAAG
EST: gi|254323026|gb|GR839939.1|GR839939
EST:     AGGGAGTTGTGGGAG                         GCTGAGACACTTGCTGATCATATAAAATTCGACCATGGGTACAATGCAAAG
genomic: AGGGAGTTGTGGGAGgtgatttttg ... cttactgcagGCTGAGACACTTGCTGATCATATAAAATTCGACCATGGGTACAATGCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatttagaacaaggcattgaaattaaaagttttttgtttttaatcttactgcagGCTGAGACACTTGCTGATCATATAAAATTCGACCATGGGTACAATGCAAAGAGCCCTGCCATTGTTAAT
                                           atcttac  putative branch site (score: 3)
                                            tcttact  CT-rich tract
                attgaaattaaaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatttttgcccaattatattattgcttttaatattagttaaaatattagatttagaacaaggcattgaaattaaaagttttttgtttttaatcttactgcagGCTGAGACACTTGCTGATCATATAAAATTCGACCATGGGTACAATGCAAAGAGCCCTGCCATTGTTAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG