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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agacctgataaattccaagtggtaactgaatctgcacaaatggttattatgccttgaaaaattctcggattgatgtatgcaatattttgctttcctctagGACTTGGTTCAAAGTGACAGGGATGATCCTAGCCTACCACTGGTTACTGCACCTTTTGGGCATGCCTCCCAG

Basic information

species Glycine max
transcript GLYMA10G37000.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G37000.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g34440.1 (Oryza sativa), 3'ss of exon 5
agacctgataaattccaagtggtaactgaatctgcaca--aatggttatt-----atgccttga-aaaattctcggattgatgtatgcaatattttgctttcctctagGACTTGGTTCAAAGTGACAGGGATGATCCTAGCCTACCACTGGTTACTGCACCTTTTGGGCATGCCTCCCAG
        |   ||   | | || |||   ||  | ||   ||||| ||          || || |  ||  ||   ||  || |    |||  |   | | | |  | || |  |||||   || ||||||||||| ||||||||| |||| ||||| || ||||||||||| || |||
-------ttgttttattaatcgtcacttcttccactcattgatggtcatctcaaagcatctcgatattatcttcattttcttgcaatttatacgtctttgtacacagGAACGTA-TTCAAGCGGATAGGGATGATCCAAGCCTACCATTGGTCACTGCCCCATTTGGGCATGCTTCACAG

upper sequence: GLYMA10G37000.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G43690.1 (Arabidopsis thaliana), 3'ss of exon 5
agacctgataaattccaagt--ggtaactgaatctgcacaaatggttattatgccttgaaaaattctcggattgatgt--atgcaatattttgctttcctctagGACTTGGTTCAAAGTGACAGGGATGATCCTAGCCTACCACTGGTTACTGCACCTTTTGGGCATGCCTCCCAG
  |  | ||    || | ||  | |   || |||| | |   || || |||||  |  |  | | |    | |   ||  ||| |  ||||||   |   | |||| |  ||||||   |||||||||||||| | ||| || || || |||||||| ||||| ||||||||||||
-catttcattt-ctctaggtcagctcgatggatct-ctcctttgtttcttatgtgtctattactgcctaaaatagcgttaatggataattttgtgatgaac-agGATTCAGTTCAAGCCGACAGGGATGATCCAAACCTCCCCCTAGTAACTGCACCATTTGGACATGCCTCCCAG
















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|22541168|gb|BU091011.1|BU091011
EST:     GAATGGGAGCATTGCTTTTCCTAATCTCTGCTTTACTTTCTCGAGGACTG                         GACTTGGTTCAGAGTGACAGGGATGATCC
genomic: GAATGGGAGCATTGCTTTTCCTAATCTCTGCTTTACTTTCTCGAGGACTGgtatgtttgc ... tttcctctagGACTTGGTTCAAAGTGACAGGGATGATCC
EST: gi|208128639|gb|GD927519.1|GD927519
EST:     GAATGGGAGCATTGCTTTTCCTAATCTCTGCTTTACTTTCTCGAGGACTG                         GACTTGGTTCAAAGTGACAGGGATGATCCTAGCCTACCACTGGTTACTGCA
genomic: GAATGGGAGCATTGCTTTTCCTAATCTCTGCTTTACTTTCTCGAGGACTGgtatgtttgc ... tttcctctagGACTTGGTTCAAAGTGACAGGGATGATCCTAGCCTACCACTGGTTACTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatgccttgaaaaattctcggattgatgtatgcaatattttgctttcctctagGACTTGGTTCAAAGTGACAGGGATGATCCTAGCCTACCACTGGTTACTGCACCTTTTGGGCATGCCTCCCAG
                      gattgat  putative branch site (score: 4)
                                     tattttgctttcctct  putative PPT
        ttgaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agacctgataaattccaagtggtaactgaatctgcacaaatggttattatgccttgaaaaattctcggattgatgtatgcaatattttgctttcctctagGACTTGGTTCAAAGTGACAGGGATGATCCTAGCCTACCACTGGTTACTGCACCTTTTGGGCATGCCTCCCAG

- -cctgata
- - - - - - ttccaag
- - - - - - - - - - -gtaactg
- - - - - - - - - - - - - - - - tgcacaa
- - - - - - - - - - - - - - - - - - - - - - - -tatgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtatgca