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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACATTGGCAAAGCACCCAAAGGCTCCAAAACCAATTGGATCATGCACGAGTATCGCCTTCTCGATTCTTCCCGCAAACACAACCTCGGAACCGCAAAGgtacacacaattacattctctagcttcccctgtttttcaagctctcactcataatttcttatgatactaaggattctgaatttgatcattgttattttaa...

Basic information

species Glycine max
transcript GLYMA06G38410.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G38410.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S117_16V6.1 (Physcomitrella patens), 5'ss of exon 2
CTACATTGGCAAAGCACCCAAAGGCTCCAAAACCAATTGGATCATGCACGAGTATCGCCTTCTCGA------------TTCTTCCCGCAAACACAACCTCGGAACCGCAAAGgtacacacaat-tacattct--ctagcttcc--------cctgtttttcaagctc-tcactcataatttctta--tgatac-taaggattctgaatt--tgatcattgttattttaa--------------
             || ||||| |||   |||||||| ||||||||||||||||||||||||   ||             ||| | | | | |||  || |||  ||     ||||   | |   |||||       | | ||         |||||   ||| |||  |  |  || ||| || |   ||||  |   |  | || |     ||     |    | |||              
------------GGCCCCCAAGGGCGAGAAAACCAACTGGATCATGCACGAGTATCGCCTTGCTGAAGGGGTGTCGCCCTCTGCTCACCATCACCGCCGCGGCTCCTTGCGGgtatgtatagcgtacatctcactcaacatcaggagtaaacctgtcgatcatgctagttgcctatgattcctgaatcgatatatgttgcctgtggaccagcgaatgacgcccgtctaattttgtggctgcag
















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|254323746|gb|GR836085.1|GR836085
EST:     TTCTCGATTCTTCCCGCAAACACAACCTCGGAACCGCAAAG                         CTTGATGATTGGGTTCTATGTCGTATCTATAAGAAGAACTCAAGTTCACAA
genomic: TTCTCGATTCTTCCCGCAAACACAACCTCGGAACCGCAAAGgtacacacaa ... tgtgatgcagCTTGATGATTGGGTTCTATGTCGTATCTATAAGAAGAACTCAAGTTCACAA
EST: gi|192302673|gb|FG996353.1|FG996353
EST:     AGTATCGCCTTCTCGATTCTTCCCGCAAACACAACCTCGGAACCGCAAAG                         CTTGATGATTGGGTTCTATGTCGTATCTATAAGAAGAACTCAAGTTCACAA
genomic: AGTATCGCCTTCTCGATTCTTCCCGCAAACACAACCTCGGAACCGCAAAGgtacacacaa ... tgtgatgcagCTTGATGATTGGGTTCTATGTCGTATCTATAAGAAGAACTCAAGTTCACAA
EST: gi|192305751|gb|FG995707.1|FG995707
EST:     AGTATCGCCTTCTCGATTCTTCCCGCAAACACAACCTCGGAACCGCAAAG                         CTTGATGATTGGGTTCTATGTCGTATCTATAAGAAGAACTCAAGTTCACAA
genomic: AGTATCGCCTTCTCGATTCTTCCCGCAAACACAACCTCGGAACCGCAAAGgtacacacaa ... tgtgatgcagCTTGATGATTGGGTTCTATGTCGTATCTATAAGAAGAACTCAAGTTCACAA
EST: gi|11274369|gb|BF324722.1|BF324722
EST:     AGTATCGCCTTCTCGATTCTTCCCGCAGACACAACCTCGGAACCGCAAAG                         CTTGATGATTGGGTTCTATGTCGTATCTATAAGAAGAACTCAAGTTCACAA
genomic: AGTATCGCCTTCTCGATTCTTCCCGCAAACACAACCTCGGAACCGCAAAGgtacacacaa ... tgtgatgcagCTTGATGATTGGGTTCTATGTCGTATCTATAAGAAGAACTCAAGTTCACAA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACATTGGCAAAGCACCCAAAGGCTCCAAAACCAATTGGATCATGCACGAGTATCGCCTTCTCGATTCTTCCCGCAAACACAACCTCGGAACCGCAAAGgtacacacaattacattctctagcttcccctgtttttcaagctctcactcataatttcttatgatactaaggattctgaatttgatcattgttattttaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctcac