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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcctgacattgtagagactctttatcctgattattacaaatctctcatttcacaactgtttcagtaattttttttctcacttttattattaatatcagGCTGCTAATGACTGTGACCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTTGTATTATATGAAGAAGAAATTGCG

Basic information

species Glycine max
transcript GLYMA14G40270.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 17
tttcctgacattgtagagactctttatcctgattattacaaatctct-catttcacaactgtttcagtaattttttttctcacttttattattaatatcagGCTGCTAATGACTGTGACCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTTGTATTATATGAAGAAGAAATTGCG
                        |||     | |  |   || | | | || || |||| |    | |  |  | |    || |||  |||||    ||||| || ||||| ||||| || || || ||||||||||| || || ||||| |||||  | |||||||||||||||||||||
-----------------------gtattgctgtaacaattgatttatgctttccataactct----gcatatcatgtaactacctttcatatta----cagGCGGCCAATGATTGTGATCTGGAACCGGTTGCTTATGAGTTCTTTACTCAAGCATTCATCTTATATGAAGAAGAAATTGCG

upper sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM5G825524_T01 (Zea mays), 3'ss of exon 17
tttcctgacattgtagagactctttatcctgattattacaaatctctcatttcacaactgtttcagtaattttttttctcacttttattattaatatcagGCTGCTAATGACTGTGACCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTTGTATTATATGAAGAAGAAATTGCG
                        ||| ||  | ||     || |    |||   || | || |      || || ||| | | |  || || || | ||||||| |||||||||||  | || || ||||||||||| || || ||||| || ||  |||||||||||||||||||||||
-----------------------gtatgcttgtaatactgcatat----ttttgtaagtcttcct----cttattatctgattatgtttcttgat-ttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATATTATATGAAGAAGAAATTGCG

upper sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 17
lower sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 17
----------------------------------------------------------tttcctgacattgtagagactctttatcctgattattacaaatctctcatttcacaactgtttcag------------taattttttttctcacttttattattaatatcagGCTGCTAATGACTGTGACCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTTGTATTATATGAAGAAGAAATTGCG
                                                           ||  ||  ||   ||  |    || | |   ||||  ||  | | |  |  ||   | |  || |             ||| |||| ||| |  ||   | | |  | ||||| || | ||||||||| |||||||||||||||||||||||||| || || |||||| | ||||| || ||||||||||||
gtaatttatagggttagggttactattatttcgaactcagaataacgtgacttacaatattaatggaatc-cagtaatctattgttcattttatctcagtttttttgtagcaaggcagaatctgacatagcattctcaatattttgtcttatcttggat-tcatgaacagGCCGCAAGTGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTTACCCAAGCATTTATGTTATACGAGGAAGAAATTGCG

upper sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 17
tttcctgacattgtagagactctttatcctgattattacaaatctctcatttcacaa-------ctgtttcagtaattttttttctcacttttattattaata-tcagGCTGCTAATGACTGTGACCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTTGTATTATATGAAGAAGAAATTGCG
        || || | ||| ||||||   |  ||| |    |  | |   |   |||        ||||||  |||  | | ||   || || || ||| |||  |||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||  |||| ||||||||||||||||||
--------cactgaacagagtctttaatattgttactgactaggtgttggtgggcaagaattgtttgtttctctaacctgtatttataccttgatcattgataaccagGCTGCTAATGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTCATATTGTATGAAGAAGAAATTGCG

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|51335912|gb|CO979778.1|CO979778
EST:     GTGTCATCTCCTGAACTGGCCCTGAAACTGTATCTGCAATGTGCTGAG                         GCTGCTAATGACTGTGACCTTGAGCCTGTTGCTTATGAATTTTTCACTCAG
genomic: GTGTCATCTCCTGAACTGGCCCTGAAACTGTATCTGCAATGTGCTGAGgtatgcttca ... ttaatatcagGCTGCTAATGACTGTGACCTTGAGCCTGTTGCTTATGAATTTTTCACTCAG
EST: gi|14011807|gb|BG726729.1|BG726729
EST:     CTGTGTCATCTCCTGAACTGGCCCTGAAACTGTATCTGCAATGTGCTGAG                         GCTGCTAATGACTGTGACCTTGAGCCTGTTGCTTATGAATTTTTCACTCAG
genomic: CTGTGTCATCTCCTGAACTGGCCCTGAAACTGTATCTGCAATGTGCTGAGgtatgcttca ... ttaatatcagGCTGCTAATGACTGTGACCTTGAGCCTGTTGCTTATGAATTTTTCACTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatttcacaactgtttcagtaattttttttctcacttttattattaatatcagGCTGCTAATGACTGTGACCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTTGTATTATATGAAGAAGAAATTGCG
                                           tattaat  putative branch site (score: 2)
                        ttttttttctcacttt  CT-rich tract
               tttcagtaattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcctgacattgtagagactctttatcctgattattacaaatctctcatttcacaactgtttcagtaattttttttctcacttttattattaatatcagGCTGCTAATGACTGTGACCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTTGTATTATATGAAGAAGAAATTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- -cctgaca
- - - - - - - - - - - - - -cctgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - caactgt