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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttaaaatgccaatttttatctgttggtcaataactttacatgaatttaacatttttttgctgcatatatgatgtttgttttaatccttgttgcaacagAATTTGCTTGTTGATGAATTGAAGCTAGCAGAAATTGGCCCAAAATTTGAACATCATGAGGTGTTCCCTGCACGAACTAACACAGGCAAGATTTGTTT

Basic information

species Glycine max
transcript GLYMA03G33080.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33080.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0040g02540.t01 (Vitis vinifera), 3'ss of exon 5
tgttaaaatgccaatttttat-ctgttggtcaataactttacatgaatttaa--catttttttgctgcatatatgatgtttgtt--ttaatccttgttgcaacagAATTTGCTTGTTGATGAATTGAAGCTAGCAGAAATTGGCCCAAAATTTGAACATCATGAGGTGTTCCCTGCACGAACTAACACAGGCAAGATTTGTTT
     |||     ||| || |  | |  ||  ||||  |   ||   | |    ||| |   ||   |  || |  | | | ||  || ||      |  | ||||||||||  ||||||||||| ||  |||| || ||||| ||||||||||| |||||||   |||| ||||| |||||||| ||||             
-----aaacatggattattctattatatgtacataatatattatttttcttgttcatctgactgtcactgattttttctctattcctttatgtgcaattgatcagAATTTGCAGGTTGATGAATTAAATTTAGCTGACATTGGTCCAAAATTTGAGCATCATGCTATGTTTCCTGCTCGAACTAATACAG-------------
















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|208195825|gb|GD989990.1|GD989990
EST:     TCAGCATGGGAAATCCACACTGTGTAACTTTCAGTAGAGAAGGAAGCCAG                         AATTTGCTTGTTGATGAATTGAAGCTAGCAGAAATTGGCCCAAAATTTGAA
genomic: TCAGCATGGGAAATCCACACTGTGTAACTTTCAGTAGAGAAGGAAGCCAGgtctttattt ... gttgcaacagAATTTGCTTGTTGATGAATTGAAGCTAGCAGAAATTGGCCCAAAATTTGAA
EST: gi|208296980|gb|GE096576.1|GE096576
EST:     TCAGCATGGGAAATCCACACTGTGTAACTTTCAGTAGAGAAGGAAGCCAG                         AATTTGCTTGTTGATGAA
genomic: TCAGCATGGGAAATCCACACTGTGTAACTTTCAGTAGAGAAGGAAGCCAGgtctttattt ... gttgcaacagAATTTGCTTGTTGATGAA
EST: gi|193620828|gb|FK571408.1|FK571408
EST:     TCAGCATGGGGAATCCACACTGTGTAACTTTCAGTAGAGAAGGAAGCCAG                         AATTTGCTTGTTGATGAATTGAAGCTAGCAGAAATTGGGCCAAAATTTGAA
genomic: TCAGCATGGGAAATCCACACTGTGTAACTTTCAGTAGAGAAGGAAGCCAGgtctttattt ... gttgcaacagAATTTGCTTGTTGATGAATTGAAGCTAGCAGAAATTGGCCCAAAATTTGAA
EST: gi|192298876|gb|FG987621.1|FG987621
EST:     TCAGCATGGGAAATCCACACTGTGTAACTTTCAGTAGAGAAG-AAGCCAG                         AATTTGCTTGTTGATGAATTGAAGCTAGCAGAA-TTGGCCCAAA-TTTGA-
genomic: TCAGCATGGGAAATCCACACTGTGTAACTTTCAGTAGAGAAGGAAGCCAGgtctttattt ... gttgcaacagAATTTGCTTGTTGATGAATTGAAGCTAGCAGAAATTGGCCCAAAATTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaacatttttttgctgcatatatgatgtttgttttaatccttgttgcaacagAATTTGCTTGTTGATGAATTGAAGCTAGCAGAAATTGGCCCAAAATTTGAACATCATGAGGTGTTCCCTGCACGAACTAACACAGGCAAGATTTGTTT
                                  ttttaat  putative branch site (score: 3)
                                        tccttgtt  CT-rich tract
                    atatatgatgtttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttaaaatgccaatttttatctgttggtcaataactttacatgaatttaacatttttttgctgcatatatgatgtttgttttaatccttgttgcaacagAATTTGCTTGTTGATGAATTGAAGCTAGCAGAAATTGGCCCAAAATTTGAACATCATGAGGTGTTCCCTGCACGAACTAACACAGGCAAGATTTGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - aatgcca
- - - - - - - - - - tctgttg
- - - - - - - - - - - - - - - - - - - - catgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt