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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCTGAAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATGAGgttgtaaacatgttctgtattaccttatttcctgttcttcagtttttgaaatgtgtggtgcaggttcttattgtttacgtattggaattttgcatttccttacttgctctgaagttacctgaatccgctcacttgttgtag

Basic information

species Glycine max
transcript GLYMA01G29470.2
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G29470.2 (Glycine max), 5'ss of exon 20
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 5'ss of exon 19
--TTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCTGAAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATGAGgttgtaaacatgttctgtattaccttatttcctgttcttcagtttttgaaatgtgtggtgcaggttcttattgtttacgtattggaattttgcatttccttacttgctctgaagttacctgaatccgctcacttgttgtag
   |||| |||||||||||||||||||||| ||||||| ||  | ||  |||| | ||| |    |||| |  |||     ||    |  || | || | ||  |  || |||||  ||||  | || | |     |  |     || ||  |         ||  |||||||  | |   |  | ||||||                                                   
ATCTGGAAAGAGGAGATGCAACAGGTTTATCTGGGCAAGGCTGTTATCTCTGATGAAGTTGTTCCATAAAA-ACCACAAT-CAGAAATGGCA-AGACgtaagaatccaa-catgta-tgtaacaactcaatg---atcttatcacttctgttaca------acattttcttatgatgtcaatgattgaatttcag------------------------------------------------

upper sequence: GLYMA01G29470.2 (Glycine max), 5'ss of exon 20
lower sequence: AT2G38280.2 (Arabidopsis thaliana), 5'ss of exon 19
TTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCTGAAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATGAGgttgtaaacatgttctgtattaccttatttcctgttcttcagtttttgaaatgtgtggtgcaggttcttattgtttacgtattggaattttgcatttccttacttgctctgaagttacctgaatccgctcacttgttgtag
       ||||||||||||||||||||| ||||||| ||  | ||  |||| | ||| |    |||| |  |||     ||    |  || | || | ||  |  || |||||  ||||  | || | |     |  |     || ||  |         ||  |||||||  | |   |  | ||||||                                                   
-------GAGGAGATGCAACAGGTTTATCTGGGCAAGGCTGTTATCTCTGATGAAGTTGTTCCATAAAA-ACCACAAT-CAGAAATGGCA-AGACGTAAGAATCCAA-CATgta-tgtaacaactcaatg---atcttatcacttctgttaca------acattttcttatgatgtcaatgattgaatttcag------------------------------------------------
















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|22928940|gb|BU546079.1|BU546079
EST:     AAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACAT---                         G-AGATAGTATCCTCAAACCCTTGCAGCGTCAGAGATGCAGGGCTGAAGAC
genomic: AAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATGAGgttgtaaaca ... cttgttgtagGTAGATAGTATCCTCAAACCCTTGCAGCGTCAGAGATGCAGGGCTGAAGAC
EST: gi|254332341|gb|GR846386.1|GR846386
EST:     AAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATGAG                         GTAGATAGTATCCTCAAACCCTTGCAGCGTCAGAGATGCAGGGCTGAAGAC
genomic: AAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATGAGgttgtaaaca ... cttgttgtagGTAGATAGTATCCTCAAACCCTTGCAGCGTCAGAGATGCAGGGCTGAAGAC
EST: gi|26267857|gb|CA818920.1|CA818920
EST:     AAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATGAG                         GTAGATAGTATCCTCAAACCCTTGCAGCGTCAGAGATGCAGGGCTGAAGAC
genomic: AAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATGAGgttgtaaaca ... cttgttgtagGTAGATAGTATCCTCAAACCCTTGCAGCGTCAGAGATGCAGGGCTGAAGAC
EST: gi|7284344|gb|AW596937.1|AW596937
EST:     ACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATGAG                         GTAGATAGTATCCTCAAACCCTTGCAGCGTCAGAGATGCAGGGCTGAAGAC
genomic: ACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATGAGgttgtaaaca ... cttgttgtagGTAGATAGTATCCTCAAACCCTTGCAGCGTCAGAGATGCAGGGCTGAAGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGAGAGAGGAGATGCAACAGGTTTATTTGGGCAAAGCCATCATTCCTGAAGTAGTAGACAAATAAGATGCCAGGGGGCATTCCTTTCATACACATGAGgttgtaaacatgttctgtattaccttatttcctgttcttcagtttttgaaatgtgtggtgcaggttcttattgtttacgtattggaattttgcatttccttacttgctctgaagttacctgaatccgctcacttgttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG