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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctctgtcactaatgttttcattgttgatattgatgtattacagatgattttatgtaagattactttgcttatgattggtattctctgtccaatatctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTCGCTGCTTCTGAAAATGATGGTGCTATAT

Basic information

species Glycine max
transcript GLYMA09G34830.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G34830.1 (Glycine max), 3'ss of exon 14
lower sequence: AT1G31810.1 (Arabidopsis thaliana), 3'ss of exon 14
gtattctctgtcactaatgttttcattgttgatattgatgtattacagatgattttatgtaagattactttgcttatgattggtattctctgtccaatatctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTCGCTGCTTCTGAAAATGATGGTGCTATAT
                 | |  |  || || ||  | |    ||      | ||  |  |     |   ||||   || ||  | |  | | |  || ||  ||||| || | ||| | |||||||||||||||||||| | || ||||||  | || || |||||||||||||||   ||||| |||||||||||||| || |
----------------gtatgcttgttattcatggttac---ttctgtgagcttccaccttcttgtttattgcacctgctttat-tcttttcttaaaaatgcagATTGAATTGAAAACGTTGGCTGAAGAAATGCAAGCGGCGACTAAAGGCCTTGAAAAGGTTGAGCAAGAACTCATGGCTTCAGAAAATGATGGTGCAATTT

upper sequence: GLYMA09G34830.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv02s0033g01360.t01 (Vitis vinifera), 3'ss of exon 14
--------------------gtattctctgtcactaatgttttcattgttgatattgatgtattacag------atgattt-tatgtaagattactt--tgcttatgattggtattctctgtccaat-atctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTCGCTGCTTCTGAAAATGATGGTGCTATAT
                    ||||| ||   | |   | ||| | | |||  | || |  | | |||       ||   || | |||| | || |||  || || | ||   | ||   |  ||| | | | |||||||| | ||| | ||||| || |||||||||||||||||||||||| | || || ||||||||||||||| |||| || |  |||||||||||||| |
gtatgcttaacatgtcaaaagtattgtcc-ccgcagctctttgcttagtttgt-ttaacttgtaacaacattccatagcttatctgtatggtttcttgttggttcttatccattttgcattcccattgaacaagATTCAATTGAAATCTTTGGCCGAGGAAATGCAAGCTGTGAGTAAAGGTCTTGAAAAGGTTGAGCAAGAACTCACTGCCTCGGTGAATGATGGTGCTATCT

upper sequence: GLYMA09G34830.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S13_282V6.2 (Physcomitrella patens), 3'ss of exon 14
gtattctctgtcactaatgttttcattgttgatattgatgtattacagatgatttta---tgtaagattac-tttgcttat--gattggtattctctgtccaatatctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTCGCTGCTTCTGAAAATGATGGTGCTATAT
       |||||  ||   ||   ||||||   |  ||| |  |||||      |||   || | |||||   ||||  |   |||      | | ||    ||    |||||||||| ||  ||||||| || ||||||||||| ||||| || ||| |||||||||| || |||||  | |||   || || ||||||||| ||  ||
------actgtc--taggcttgcgattgttacaa--gatatgatacagcaaccattagcctgcatgattaaacttgccaactcgatctaacatatgtggtggattctcagATTCAACTGAAGTCATTGGCAGAGGAAATGCAAGCAGTGAGCAAGGGTCTAGAGAAAGTGGAACAAGAGATTGCTATGTCAGAGAATGATGGTCCTGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattttatgtaagattactttgcttatgattggtattctctgtccaatatctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTCGCTGCTTCTGAAAATGATGGTGCTATAT
                                    ttctctgtcc  CT-rich tract
     ttatgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctctgtcactaatgttttcattgttgatattgatgtattacagatgattttatgtaagattactttgcttatgattggtattctctgtccaatatctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTCGCTGCTTCTGAAAATGATGGTGCTATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT