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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttttaacaattaatgacttaatggcactggcatgcaaatgttcaaaattaatggggttatacctttgtccaatgcatggtacaatgtattattgcagGTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTTGCATTGCCGGATAGGATTCAAGCTATCCCAGATGGGACCCCTGCAGCAT

Basic information

species Glycine max
transcript GLYMA03G33680.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33680.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0040g02130.t01 (Vitis vinifera), 3'ss of exon 2
cttttttaacaattaatgacttaatggcactggcatgcaa-atgttcaaaattaatggggttatacctttgtccaatgcatgg-tacaatgtatt---attgcagGTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTTGCATTGCCGGATAGGATTCAAGCTATCCCAGATGGGACCCCTGCAGCAT
  |      |||||  ||    | |    ||||   |    || |||    ||  |    |  || || ||   ||| ||||  |   |   | |     ||||||| || ||||||||| || ||||| ||||||| |||||||||||||  |||||||||||||||||||| ||||| || ||||||||| |  |  | ||| 
--tcccattcaatttctg-tacattctttctggttcgttttattttctctcttttttccatc-tatctatgaa-aatacatgaatctgactcaattgggctgcagGTTAAAGGGCTTTCAACAGAAGAACTTGCTGCTCGTAATGATTTGGTCCTTGCATTGCCGGATAGGATCCAAGCAATACCAGATGGGGCTGCAACTGCAC
















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|9987448|gb|BE661556.1|BE661556
EST:     CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAG                         GTAAAGGGGCTTTCATCACAAGAATTTGCTGCC-GTAATGATTTGGCTCTT
genomic: CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAGgttggaacta ... attattgcagGTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
EST: gi|7588839|gb|AW704626.1|AW704626
EST:     CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAG                         GTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
genomic: CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAGgttggaacta ... attattgcagGTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
EST: gi|19053265|gb|BM731932.1|BM731932
EST:     TGGCTATGAAAAAG                         GTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
genomic: TGGCTATGAAAAAGgttggaacta ... attattgcagGTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
EST: gi|192310641|gb|FK001065.1|FK001065
EST:     CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAG                         GTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
genomic: CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAGgttggaacta ... attattgcagGTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
EST: gi|151393190|gb|EV263065.1|EV263065
EST:     CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAG                         GTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
genomic: CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAGgttggaacta ... attattgcagGTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
EST: gi|18039839|gb|BM308133.1|BM308133
EST:     CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAG                         GTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
genomic: CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAGgttggaacta ... attattgcagGTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
EST: gi|151404741|gb|EV274555.1|EV274555
EST:     CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAG                         GTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
genomic: CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAGgttggaacta ... attattgcagGTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
EST: gi|192294446|gb|FG987375.1|FG987375
EST:     CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAG                         GTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
genomic: CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAGgttggaacta ... attattgcagGTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
EST: gi|7589461|gb|AW705234.1|AW705234
EST:     CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAG                         GTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT
genomic: CTAGGTTGTTGGAGGAGGTTCCCAAGTTGCAGAGATTGGCTATGAAAAAGgttggaacta ... attattgcagGTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaattaatggggttatacctttgtccaatgcatggtacaatgtattattgcagGTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTTGCATTGCCGGATAGGATTCAAGCTATCCCAGATGGGACCCCTGCAGCAT
   aattaat  putative branch site (score: 3)
                                     tacaatgtattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttttaacaattaatgacttaatggcactggcatgcaaatgttcaaaattaatggggttatacctttgtccaatgcatggtacaatgtattattgcagGTAAAGGGGCTTTCATCACAAGAATTTGCTGCCCGTAATGATTTGGCTCTTGCATTGCCGGATAGGATTCAAGCTATCCCAGATGGGACCCCTGCAGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - gcatgca
- - - - - - - - - - - - - - - - - - - - - - - aaaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - tggggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatggt