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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacagatggttgttttagtttctcaacttgtgaatattatattgatgattttcgcaaccaagagtctattccttattatttgtgatttgtaatgagatagACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTATTACCACAGCTCAG

Basic information

species Glycine max
transcript GLYMA11G08380.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 4
gacagatggttgttttagtttctcaacttgtgaatattatattgatgattttcg--caaccaagagtctattccttattatttgt--gatttgtaatgagat-agACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTATTACCACAGCTCAG
     |  ||      ||| | |    || | ||    |  |  | ||| |||   ||||  |   ||    |||| ||  ||||   |  |    ||   | ||| ||||| ||||| || ||||| | |||||||||||||||||| || ||||||||||| | ||||
-----actgtatagcaagtgtatacctttataaaagacacttgcaagatcttcagtcaactcatgatcctggcctttttgattgtctaaccttggttgttgtcagATCTTCGAGATGACAAACAGTTTTTCATCGACCATCCTGGTGCTGTCCCTATTACCACTGTTCAG

upper sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 5
gacagatggttgttttagtttctcaacttgtgaatattatattgatgattttc--gcaaccaa-gagtctattccttattatttgtgatttgtaatgagatagACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTATTACCACAGCTCAG
   | ||   |        ||  ||   |  || ||   |||| ||| ||||     ||  ||  | | | ||   | | ||||   || |  | |||| |||| |||||||| || |||||||||| ||| |||||||||||||| || || ||  |  ||||||||
-ctaaattagtagaaggaatttgcag--taggagtaggttatttatggttttgtgataattaacaaattttttttgtctgattttcaatgttaattgagctagATCTTCGGGAAGACAAGCAGTTCTTCATAGACCATCCTGGTGCTGTGCCCATCTCTGCAGCTCAG
















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|192304826|gb|FG997036.1|FG997036
EST:     GAAGCATTATGCACCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCACCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... aatgagatagACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTA
EST: gi|6072638|gb|AW102025.1|AW102025
EST:     TCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTA
genomic: TCTGGTTGGCACAAAGCTTGgtaagcttat ... aatgagatagACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTA
EST: gi|5606072|gb|AI900170.1|AI900170
EST:     GAAGCATTATGCACCTGGTGTCCCCATTATTCTGGTTGGCACANAGCTTG                         ACCTTCGGGATGATTAGCAGTTCTGCATCGACCATTCTGGTGCCGTACCTA
genomic: GAAGCATTATGCACCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... aatgagatagACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTA
EST: gi|31309917|gb|CD395120.1|CD395120
EST:     GAAGCATTATGCACCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCACCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... aatgagatagACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTA
EST: gi|58017044|gb|CX703786.1|CX703786
EST:     GAAGCATTATGCACCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCACCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... aatgagatagACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTA
EST: gi|19054119|gb|BM732786.1|BM732786
EST:     GAAGCATTATGCTCCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATTGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCACCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... aatgagatagACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTA
EST: gi|58016803|gb|CX703545.1|CX703545
EST:     GAAGCATTATGCACCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTG                         ACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTA
genomic: GAAGCATTATGCACCTGGTGTCCCCATTATTCTGGTTGGCACAAAGCTTGgtaagcttat ... aatgagatagACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattttcgcaaccaagagtctattccttattatttgtgatttgtaatgagatagACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTATTACCACAGCTCAG
                           ttattatttgtgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacagatggttgttttagtttctcaacttgtgaatattatattgatgattttcgcaaccaagagtctattccttattatttgtgatttgtaatgagatagACCTTCGGGATGATAAGCAGTTCTGCATCGACCATCCTGGTGCCGTACCTATTACCACAGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA