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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatcgttatcttccttgctattaaacttaaactttcacaggtgtttatttattagtacttttaaacattctgactgggtaattgcttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTGGAGTGGCACTCTACTCGTTCATCAAAGCCAGGATGGAGGAAGAGAAGCG

Basic information

species Glycine max
transcript GLYMA07G32190.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G32190.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 3'ss of exon 10
gtaaatatcgttatcttccttgctattaaacttaaactttcacaggtgtttatttattagtacttttaaacattctgactgggtaattgcttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTGGAGTGGCACTCTACTCGTTCATCAAAGCCAGGATGGAGGAAGAGAAGCG
|||||| |  | |||||  || || ||  | ||     ||      |  |   | |  |  |  |    | |   |  ||       | |||| || |||||||||||||   || ||||||||||| ||||||  | |||||||||||||||||||| | ||||| ||||| || |||| |||||| || ||||| ||
gtaaatgt--tcatctttttt-ctgtttgatttgcttattgctgccttctccctaaacatcatatgcccagaagatatctaacagcgtacttctcacagGTAACAAGATTTCAACACAAACTGGTATTGGAACATGCGTTGCAATTGCTGGAGTGGCAATGTACTCTTTCATAAAGGCCAAGATGGAAGAGGAGAAACG
















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|11688177|gb|BF595853.1|BF595853
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|208047241|gb|GD844338.1|GD844338
EST:     TTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: TTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|208221029|gb|GE020699.1|GE020699
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGNTTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAAACTGGTATAGGAACAGCCATTGCAATTGCT
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCC-AAACTGGTATAGGAACAGCCATTGCAATTGCT
EST: gi|15204849|gb|BI427617.1|BI427617
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|23728678|gb|BU762399.1|BU762399
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACCAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|7691785|gb|AW759906.1|AW759906
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|14999814|gb|BI320628.1|BI320628
EST:     GAACGTACTGAAACGCGCATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|193415327|gb|FK375821.1|FK375821
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|20449753|gb|BQ253877.1|BQ253877
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|15284741|gb|BI468632.1|BI468632
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|9260012|gb|BE348159.1|BE348159
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|207826480|gb|GD798191.1|GD798191
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCA
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCA
EST: gi|31561027|gb|CD486865.1|CD486865
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|16346698|gb|BI972293.1|BI972293
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|15199917|gb|BI424075.1|BI424075
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|14011803|gb|BG726725.1|BG726725
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|6481839|gb|AW201110.1|AW201110
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|26269373|gb|CA820436.1|CA820436
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|31475923|gb|CD417951.1|CD417951
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|10237564|gb|BE806452.1|BE806452
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
EST: gi|10232365|gb|BE801253.1|BE801253
EST:     GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTG                         GTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG
genomic: GAACGTACTGAAACGTGTATTTGTGATTGGATTTTCAATTATAGTCTTTGgtaaatatcg ... cttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgtttatttattagtacttttaaacattctgactgggtaattgcttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTGGAGTGGCACTCTACTCGTTCATCAAAGCCAGGATGGAGGAAGAGAAGCG
                            ttctgac  putative branch site (score: 2)
                                          ttgcttc  putative PPT
     ttatttattagtactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatatcgttatcttccttgctattaaacttaaactttcacaggtgtttatttattagtacttttaaacattctgactgggtaattgcttcacatagGTAACAAGATTAGCACCCAAACTGGTATAGGAACAGCCATTGCAATTGCTGGAGTGGCACTCTACTCGTTCATCAAAGCCAGGATGGAGGAAGAGAAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC