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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatatgaaacatgctttgttacttgtctttctcatcttttaatcaacatttaatggctaaattccatttaagtattaatgattcatctactgttttcagCTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACCTTATTCTCATTGTACTCAACTGCTCTTGTTGGACGTCTAGTTGCTTTAG

Basic information

species Glycine max
transcript GLYMA01G01340.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G01340.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G478212_T01 (Zea mays), 3'ss of exon 5
-caatatgaaacatg----ctttgttac-ttgtctttctcatcttttaatcaacatttaatggct-----aaattccatttaagtattaatga--ttcatctactgttttcagCTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACCTTATTCTCATTGTACTCAACTGCTCTTGTTGGACGTCTAGTTGCTTTAG
  | ||    |||||      |||| || |  | |   | |   | |  ||  |    | || ||         ||  |  |  | |  |||   || | |  ||| |||||||||||||| ||||| ||||| ||||||||||| ||  |    ||| |  |   ||||||  |||||||||| ||| |  | || || ||  |||   | |
gtactactgcacatggttatcttgtgacatcatttcggttaagctctgctccgctgcaagtgccttttatgtgatctgtcaacttgtccatgctcttgaacccctgatttcagCTTGTAAAGAGGCACGCAGCAGAGATTTTCACATCAATTGCCATTGCGTCGACATTCTCTCTGTACTCAACCGCTGTCATAGGGCGCCTGATTGGGCTGG

upper sequence: GLYMA01G01340.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G32080.1 (Arabidopsis thaliana), 3'ss of exon 5
caatatgaaacatgctttgttacttgtctttctcatcttttaatcaacatttaatggctaaattccatttaagtattaatgattcatctactgttttcagCTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACCTTATTCTCATTGTACTCAACTGCTCTTGTTGGACGTCTAGTTGCTTTAG
     | |||||  |      |||||| | | |  |  ||||   |||      |||  | | ||  |||   |        | | |||    | ||||||| || || ||||| ||||||||||| ||||| ||||| ||| |||| ||  |||||||  | ||||| |||||||||||||||||| |||| | |||||
----gtaaaacaaacaacaa-acttgt-tctgttttgctttagaaaac------tggtaacaatcgctttggtt--------tgcctctgtcttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAGTTTCAACGGTATTCTCGCTCTACTCCACTGCTCTTGTTGGACGTTTAGTCGGTTTAG

upper sequence: GLYMA01G01340.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0056g01690.t01 (Vitis vinifera), 3'ss of exon 5
caatatgaaacatgctttgttact---tgtctttc-tcatcttttaatcaacatttaat-ggctaaattccatttaagtattaatgattcatctactgtttt-cagCTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACCTTATTCTCATTGTACTCAACTGCTCTTGTTGGACGTCTAGTTGCTTTAG
   ||   | |||   |  | |     |||| |||  |||  |    |   | |  ||| |  |||| ||  | |     ||  |  ||  ||||   |||| ||||||||||| ||||||||||||||||||||||| ||| |||| || || ||  ||||||| ||||| ||||||||| || |||||||  |  | |  ||||
-tgtaaagagcatttatcatcaagagatgtccttcaccatagtgcgctagtcttgcaatcgagtaaactctctct-----ttcctactttctctatgatttttcagCTTGTAAAGAGGCATGCAGCTGAGATTTTCACATCTATCATTATCTCAACAATATTCTCCTTGTATTCAACTGCTTTTATTGGACGCATTCTGGGGTTAG

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|22933413|gb|BU550552.1|BU550552
EST:     TCTATGTTCAAACAAAGAAAG                         CTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACC
genomic: TCTATGTTCAAACAAAGAAAGgtaaccatct ... ctgttttcagCTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACC
EST: gi|192322157|gb|FK014053.1|FK014053
EST:     TGGGATCTGTTATTCTCTCATTTGCCTTCTCTATGTTCAAACAAAGAAAG                         CTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACC
genomic: TGGGATCTGTTATTCTCTCATTTGCCTTCTCTATGTTCAAACAAAGAAAGgtaaccatct ... ctgttttcagCTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACC
EST: gi|192322156|gb|FK014052.1|FK014052
EST:     TGGGATCTGTTATTCTCTCATTTGCCTTCTCTATGTTCAAACAAAGAAAG                         CTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACC
genomic: TGGGATCTGTTATTCTCTCATTTGCCTTCTCTATGTTCAAACAAAGAAAGgtaaccatct ... ctgttttcagCTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACC
EST: gi|14999186|gb|BI320247.1|BI320247
EST:     CTCTCATTTGCCTTCTCTATGTTCAAACAAAGAAAG                         CTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACC
genomic: CTCTCATTTGCCTTCTCTATGTTCAAACAAAGAAAGgtaaccatct ... ctgttttcagCTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatttaatggctaaattccatttaagtattaatgattcatctactgttttcagCTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACCTTATTCTCATTGTACTCAACTGCTCTTGTTGGACGTCTAGTTGCTTTAG
                            tattaat  putative branch site (score: 2)
                                             ctgttttc  putative PPT
             taaattccatttaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatatgaaacatgctttgttacttgtctttctcatcttttaatcaacatttaatggctaaattccatttaagtattaatgattcatctactgttttcagCTTGTAAAAAGGCATGCAGCTGAGATTTTCACCTCTGTCATAATTTCTACCTTATTCTCATTGTACTCAACTGCTCTTGTTGGACGTCTAGTTGCTTTAG

- - - - -acatgct
- - - - - - - - - - - - - - - - - - - - - atcaaca