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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggttttaagtgacatgggaattctgtttttttgctggtttagtgaactagttctaatatgtctgccactattttttttattcgtgatttcttattgcagCTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCACATGGAACATGGAATGATTACAAGA

Basic information

species Glycine max
transcript GLYMA13G25690.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G25690.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 1
-aggttttaagtgacatgggaattctgtttttttgctggtttagtgaactagttctaatatgtctgccactattttttttattcgtgattt--cttattgcagCTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCACATGGAACATGGAATGATTACAAGA
    | || | |    ||       |     | || ||  |   |    | |||  || |||  ||    || ||  | | ||    | ||   | | ||||||||| || ||||||||||||||  ||||| ||||||||||| |||||||||||||| ||||||| ||||||||| |
acattctttaattttgtgccctaagtacccctatgttgcctgtattg-ttggttagaacatgcttg--gttacttcatgttttgactaattaattcactgcagCTTGGAGGAACTGAGAATTCTGTATATCTCGATATGCTTCGTTTGTTTGCACATGGCACATGGAGTGATTACAAAA
















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|22524489|gb|BU083300.1|BU083300
EST:     CTTCGCTCTTCGCTTTCTCCGAGATTCTCGCTCTGCCCAATCTTCTTCAG                         CTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCA
genomic: CTTCGCTCTTCGCTTTCTCCGAGATTCTCGCTCTGCCCAATCTTCTTCAGgttcctcttt ... cttattgcagCTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCA
EST: gi|22524611|gb|BU083422.1|BU083422
EST:     CTTCGCTCTTCGCTTTCTCCGAGATTCTCGCTCTGCCCAATCTTCTTCAG                         CTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCA
genomic: CTTCGCTCTTCGCTTTCTCCGAGATTCTCGCTCTGCCCAATCTTCTTCAGgttcctcttt ... cttattgcagCTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCA
EST: gi|31561921|gb|CD487759.1|CD487759
EST:     CTTCGCTCTTCGCTTTCTCCGAGATTCTCGCTCTGCCCAATCTTCTTCAG                         CTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCA
genomic: CTTCGCTCTTCGCTTTCTCCGAGATTCTCGCTCTGCCCAATCTTCTTCAGgttcctcttt ... cttattgcagCTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCA
EST: gi|18848688|gb|BM567807.1|BM567807
EST:     CTTCGCTCTTCGCTTTCTCCGAGATTCTCGCTCTGCCCAATCTTCTTCAG                         CTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCA
genomic: CTTCGCTCTTCGCTTTCTCCGAGATTCTCGCTCTGCCCAATCTTCTTCAGgttcctcttt ... cttattgcagCTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCA
EST: gi|23053053|gb|BU577544.1|BU577544
EST:     CTTCGCTCTTCGCTTTCTCCGAGATTCTCGCTCTGCCCAATCTTCTTCAG                         CTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCA
genomic: CTTCGCTCTTCGCTTTCTCCGAGATTCTCGCTCTGCCCAATCTTCTTCAGgttcctcttt ... cttattgcagCTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCA
EST: gi|19053359|gb|BM732026.1|BM732026
EST:     CTTCGCTCTTCGCTTTCTCCGAGATTCTCGCTCTGCCCAATCTTCTTCAG                         CTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCA
genomic: CTTCGCTCTTCGCTTTCTCCGAGATTCTCGCTCTGCCCAATCTTCTTCAGgttcctcttt ... cttattgcagCTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCA
EST: gi|16346940|gb|BI972535.1|BI972535
EST:     CTTCGCTCTTCGCTTTCTCCGAGATTCTCGCTCTGCCCAATCTTCTTCAG                         CTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCA
genomic: CTTCGCTCTTCGCTTTCTCCGAGATTCTCGCTCTGCCCAATCTTCTTCAGgttcctcttt ... cttattgcagCTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactagttctaatatgtctgccactattttttttattcgtgatttcttattgcagCTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCACATGGAACATGGAATGATTACAAGA
      ttctaat  putative branch site (score: 2)
                                          tttcttatt  putative PPT
                        tattttttttattcgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggttttaagtgacatgggaattctgtttttttgctggtttagtgaactagttctaatatgtctgccactattttttttattcgtgatttcttattgcagCTTGAAGCAACTGAGAATTCTGCTTATCTTGATATGCTTCGGTTGTTTGCACATGGAACATGGAATGATTACAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA