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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacttctacatcagtagagaaaaacacaaaagttagagttaaaattattattgccaatacccttccaaatgcatctaaaagtagcattagtaattttcagGTGGAAAGTGCTGATCTTATTGCATATGGTCTCATACCCGAATTTATAGGACGATTTCCAATCTTAATTAGCTTGTCAGCTCTAACCGAAGACCAACTTA

Basic information

species Glycine max
transcript GLYMA20G35600.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 10
tacttctacatcagtagagaaaaacacaaaagttagagttaaaattattattgccaatacccttcc----aaatgcatctaaaagtagcattagtaatt----ttcagGTGGAAAGTGCTGATCTTATTGCATATGGTCTCATACCCGAATTTATAGGACGATTTCCAATCTTAATTAGCTTGTCAGCTCTAACCGAAGACCAACTTA
                |  || |  ||| |  ||   |||||   || | |   || | | | | |    |||   |||| |   | | | |      |    ||||||| || ||||| ||||| |  |||||||| || ||||| || ||| ||||||| ||||| || ||| |||| ||||||||||| || || ||||| || |
----------------gtaaacactacatagtttt--gttaagcctagtgtaaacacttctcattcctggaaagagatcttagttttggaatgccggctgcatttcagGTTGAGAGTGCCGATCTGACAGCATATGGCCTTATACCGGAGTTTGTAGGACGCTTTCCCATATTAGTTAGTTTGTCAGCTCTGACAGAGGACCAGCTCA

upper sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 10
tacttctacatcagtagagaaaaacacaaaagttagagttaaaattatt-attgccaataccct-tccaaatgcatctaaaagtagcattagta-attttcagGTGGAAAGTGCTGATCTTATTGCATATGGTCTCATACCCGAATTTATAGGACGATTTCCAATCTTAATTAGCTTGTCAGCTCTAACCGAAGACCAACTTA
   |   ||  |  || |  ||  |       ||   |  |    |    | |  | |  | || |||   | | | || || |    |   |  |||||||||| ||||||  |||||||||||||||||| |||||||| || ||||| ||||| ||||| ||  || |||| ||||||||||| || || || |||||| 
--ataaaactcccatatattaag-ctttttgcttgctgccacccctccccactctccaccctctatcctggttcttttacaaattttctctttgcattttcagGTTGAAAGTAGTGATCTTATTGCATATGGCCTCATACCAGAGTTTATTGGACGCTTTCCTATTCTAGTTAGTTTGTCAGCTCTGACTGAGGATCAACTTG
















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|193655522|gb|FK601824.1|FK601824
EST:     GAACTGGTGGAGTTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCG                         GTGGAAAGTGCTGATCTTATTGCATATGGTCTCATACCCGAATTTATAGGA
genomic: GAACTGGTGGAGTTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCGgtgagaatta ... taattttcagGTGGAAAGTGCTGATCTTATTGCATATGGTCTCATACCCGAATTTATAGGA
EST: gi|208037307|gb|GD836174.1|GD836174
EST:     GAACTGGTGGAGTTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCG                         GTGGAAAGTGCTGATCTTATTGCATATGGTCTCATACCCGAATTTATAGGA
genomic: GAACTGGTGGAGTTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCGgtgagaatta ... taattttcagGTGGAAAGTGCTGATCTTATTGCATATGGTCTCATACCCGAATTTATAGGA
EST: gi|22928880|gb|BU546019.1|BU546019
EST:     AGTTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCG                         GTGGAAAGTGCTGATCTTATTGCATATGGTCTCATACCCGAATTTATAGGA
genomic: AGTTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCGgtgagaatta ... taattttcagGTGGAAAGTGCTGATCTTATTGCATATGGTCTCATACCCGAATTTATAGGA
EST: gi|16346887|gb|BI972482.1|BI972482
EST:     GTTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCG                         GTGGAAAGTGCTGATCTTATTGCATATGGTCTCATACCCGAATTTATAGGA
genomic: GTTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCGgtgagaatta ... taattttcagGTGGAAAGTGCTGATCTTATTGCATATGGTCTCATACCCGAATTTATAGGA
EST: gi|17519864|gb|BM188906.1|BM188906
EST:     GAACTGGTGGAGTTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCG                         GTGGAAAGTGCTGATCTTATTGCATATGGTCTCATACCCGAATTTATAGGA
genomic: GAACTGGTGGAGTTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCGgtgagaatta ... taattttcagGTGGAAAGTGCTGATCTTATTGCATATGGTCTCATACCCGAATTTATAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattattgccaatacccttccaaatgcatctaaaagtagcattagtaattttcagGTGGAAAGTGCTGATCTTATTGCATATGGTCTCATACCCGAATTTATAGGACGATTTCCAATCTTAATTAGCTTGTCAGCTCTAACCGAAGACCAACTTA
                           atctaaa  putative branch site (score: 3)
                                                ttttc  putative PPT
                                        attagtaattttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacttctacatcagtagagaaaaacacaaaagttagagttaaaattattattgccaatacccttccaaatgcatctaaaagtagcattagtaattttcagGTGGAAAGTGCTGATCTTATTGCATATGGTCTCATACCCGAATTTATAGGACGATTTCCAATCTTAATTAGCTTGTCAGCTCTAACCGAAGACCAACTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- cttctac
- - - - - - - - -agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - tattgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcat