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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttgattactttttttctccctctttccataatcattgctttttaattcagatatcggtattctcacattatactttttctaacagGGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCTAGGAATGGGCTATGCTACTGAAGCACTTCATTTGCCTGGAATATCTAAG

Basic information

species Glycine max
transcript GLYMA03G38530.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38530.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os01g46510.2 (Oryza sativa), 3'ss of exon 17
gtattttgattactttttttctccctctttccataatcattgctttttaattcagatatcggtattctcacattatactttttctaa----cagGGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCTAGGAATGGGCTATGCTACTGAAGCACTTCATTTGCCTGGAATATCTAAG
      |   || || || |       ||| |||  |  |  |||||| |    |  |  |  | |     | ||| |     ||||    |||||| | |||||||||  | || || ||||||||  | || || |||||||| |||||||||||||||||||||||||||||||| ||||||||||| |||
-----gtacctatttattcttagaacatttgcatcttgctgactttttgaagtgggaaatgcaaatggtgtaatattcaaaaactaatgtgcagGGCCACTAGACTTGGTCGGGAGCATCATGATGACCTGGCTCAGTTTATGCTGGGAATGGGCTATGCTACTGAAGCACTTCATTTACCTGGAATATCAAAG

upper sequence: GLYMA03G38530.1 (Glycine max), 3'ss of exon 17
lower sequence: AT5G24710.1 (Arabidopsis thaliana), 3'ss of exon 17
gtattttgattactttttttctccctctttccataatcattgctttttaattcagatatcggtattctcacattatactttttcta-acagGGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCTAGGAATGGGCTATGCTACTGAAGCACTTCATTTGCCTGGAATATCTAAG
       |  |   | | ||   | |  |  | |  | ||   |   || || ||     || || || | |  | | ||||| |   |||||||||||| ||||| |||||||| ||||| ||| | ||||| ||||||||||| ||||| || || || ||||| ||||||||||||||||||||||||
-------gtatggatatgtttctcataatctcgtgtttatg--tgagtagttaagtagctggaatccttatacaacattttttttgcgcagGGCAAGTAGGCTTGGGAGAGAACATCATGACGATCTGGCACAGTTTATGCTAGGGATGGGATACGCAACAGAAGCTCTTCATTTGCCTGGAATATCTAAG

upper sequence: GLYMA03G38530.1 (Glycine max), 3'ss of exon 17
lower sequence: EFJ13686 (Selaginella moellendorffii), 3'ss of exon 17
gtattttgattactttttttctccctctttccataatcattgctttttaattcagatatcggtattctcacattatactttttctaacagGGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCTAGGAATGGGCTATGCTACTGAAGCACTTCATTTGCCTGGAATATCTAAG
                                     | ||  | |  |    ||   |   | | |   |||| ||  |||     ||||||    || |||||| |||| |||||||| ||  | || |||||||||||||| ||||| ||||||||||||||  | ||| |||| || || || |||
----------------------------------gtacgtttttctgcatgatagtacttactttaccggcattttatgttt----gcagGGCTTTCAGGCTTGGACGAGAGCACCATGACGACCTTGCTCAATTTATGCTAGGCATGGGATATGCTACTGAAGCTTTACATCTGCCGGGCATTTCGAAG

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|207832844|gb|GD803982.1|GD803982
EST:     CGTTGCCGATGTCTTGCTGCTTATGGTGNTGCTGTTAGTGCAGTAAAATG                         GGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCT
genomic: CGTTGCCGATGTCTTGCTGCTTATGGTGATGCTGTTAGTGCAGTAAAATGgtattttgat ... tttctaacagGGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcattgctttttaattcagatatcggtattctcacattatactttttctaacagGGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCTAGGAATGGGCTATGCTACTGAAGCACTTCATTTGCCTGGAATATCTAAG
                             ttctcac  putative branch site (score: 2)
                                        tactttttct  putative PPT
        tttttaattcagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttgattactttttttctccctctttccataatcattgctttttaattcagatatcggtattctcacattatactttttctaacagGGCAAGTAGACTTGGAAGAGAACACCATGATGATTTAGCACAATTTATGCTAGGAATGGGCTATGCTACTGAAGCACTTCATTTGCCTGGAATATCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC