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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtttttatttgtgttattatttactaatattctattttactgcaacttcaaaggctatttgcccttgactctgtttctgtcctcaaattaaatttcagCAAGAGCTGGCTGCTATATTTAAGAAGATTGGGGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGTATTACCCAATTGTACCCAAAG

Basic information

species Glycine max
transcript GLYMA20G32430.1
intron # 50
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 50
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 48
ttgtttttatttgtgttattatttac-taatattc-tattttactgc-----aacttcaaaggctatttgcccttgactctgtttctgtcctcaaattaaatttcagCAAGAGCTGGCTGCTATATTTAAGAAGATTGGGGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGTATTACCCAATTGTACCCAAAG
 |  | ||| |  |  | | | | || ||| |||  ||  |||||||     || ||  |  || |||     |  | | ||| | | |  | |   |   |   |||||||||| |||||| |||| ||||| ||||| || || ||||| || ||||||||||| |||||||| || || || |||||| ||||||| |||
gtagtattactgattct-taactaacataacatttgtaaattactgcttgcaaatttgtacagcaattgatgttctattttgtctttcttttgattatgggt---agCAAGAGCTTGCTGCTGTATTCAAGAAAATTGGTGACAAACAAACATGTACAATTGGTCTTTATGAACTCTACCGGATAACCCAACTGTACCCCAAG

upper sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 50
lower sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 49
ttgtttttatttgtgttattatttactaatattctattttactgcaacttcaa---aggctatttgcccttgactctgtttctgtcctcaaattaaatt----tcagCAAGAGCTGGCTGCTATATTTAAGAAGATTGGGGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGTATTACCCAATTGTACCCAAAG
     |  |  |||  | ||| |   | ||  | | |  | |     ||| |    |    | |        |  || ||| ||| |||   |     |     ||||||||||| |||||||| || ||||| ||||| || |||||||| || || ||||| || |||||||| ||||| || || ||  | |||||||||
----gtacagctgttcttttagtcgttcatgctttgtggtgcaaatgcttaagattaatacagtgatttcacatgctatttttgttctcttttgtggctatggacagCAAGAGCTTGCTGCTATTTTCAAGAAAATTGGTGACAAGCAAACATGTACCATTGGCCTCTATGAACTGTATCGGATAACTCAGCTCTACCCAAAG

upper sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 50
lower sequence: PP1S66_170V6.1 (Physcomitrella patens), 3'ss of exon 49
------------------------------ttgtttttatttgtgttattattta--ctaatattct--attttactgcaacttcaaaggc-tatttgc---------ccttgactctgtttctgtcc-tcaaattaaatttcagCAAGAGCTGGCTGCTATATTTAAGAAGATTGGGGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGTATTACCCAATTGTACCCAAAG
                              || ||| | | |||    ||| | |  ||  || |    | | | || || |||||   || ||| ||          | ||| ||  |||| |||   ||   ||   ||  |||||||||| |||||  | || |||||||| || || ||||| ||||||||||||||||| || || || |||||||| || ||  | || ||  ||
gtaagttatgcacttttcttctttacaactttttttctgtgtgtacgcttaatcaatctggtaattagaagtcttcttcagcttcatttgcatatatgtgattacaatctttggctgagtttttgttgatctcgttg--ttgtagCAAGAGCTTGCTGCAGTGTTCAAGAAGATCGGTGATAAGCAGACTTGCACAATTGGTCTTTACGAGCTTTATCGTATCACACAGCTTTATCCTCAG

upper sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 50
lower sequence: PP1S131_18V6.1 (Physcomitrella patens), 3'ss of exon 49
--------------------ttgtttttatttgtgttatt-----atttactaatattctattttactgcaacttcaaaggctat-ttgc---ccttgactctgtttctgtcctcaaattaaattt--cagCAAGAGCTGGCTGCTATATTTAAGAAGATTGGGGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGTATTACCCAATTGTACCCAAAG
                     || | ||||  |    |||       | | ||   || |  ||||| ||| ||||     |  |  |||   |||||||| ||| |   || |  |  |  | ||  ||||||||||| |||||  | ||||||||||| || || ||||| ||||| ||||||||||| ||||| ||||||||||| |||||  | || ||  ||
gtaagttttgcgctccttctatggtattatacgctgaattcatcgggtcagtagacttattgtttacagcaccttcgtgttcattactgcaatccttgactgtgtat---tctttgacctccacttggcagCAAGAGCTTGCTGCAGTGTTTAAGAAGATCGGTGATAAGCAGACTTGTACAATTGGTCTCTATGAGCTATATCGTATCACCCAGCTATATCCTCAG

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|6566294|gb|AW233969.1|AW233969
EST:     CAACCAATAATTCAGCCTCGGGCACCCATTCAGCTGATGCCCAGTTAAAG                         CAAGAGCTGGCTGCTATATTTAAGAAGATTGGGGAGAAGCAAACTTGCACA
genomic: CAACCAATAATTCAGCCTCGGGCACCCATTCAGCTGATGCCCAGTTAAAGgtatcattat ... taaatttcagCAAGAGCTGGCTGCTATATTTAAGAAGATTGGGGAGAAGCAAACTTGCACA
EST: gi|16105237|gb|BI892977.1|BI892977
EST:     CAACCAATAATTCAGCCTCGGGCACCCATTCAGCTGATGCCCAGTTAAAG                         CAAGAGCTGGCTGCTATATTTAAGAAGATTGGGGATATTTTTACTTGCACA
genomic: CAACCAATAATTCAGCCTCGGGCACCCATTCAGCTGATGCCCAGTTAAAGgtatcattat ... taaatttcagCAAGAGCTGGCTGCTATATTTAAGAAGATTGGGGAGAAGCAAACTTGCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttcaaaggctatttgcccttgactctgtttctgtcctcaaattaaatttcagCAAGAGCTGGCTGCTATATTTAAGAAGATTGGGGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGTATTACCCAATTGTACCCAAAG
                   ccttgac  putative branch site (score: 4)
                                       tcaaattaaatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtttttatttgtgttattatttactaatattctattttactgcaacttcaaaggctatttgcccttgactctgtttctgtcctcaaattaaatttcagCAAGAGCTGGCTGCTATATTTAAGAAGATTGGGGAGAAGCAAACTTGCACAATTGGTCTATATGAACTATATCGTATTACCCAATTGTACCCAAAG

- - - - -tttgtgt
- - - - - - - - - - - - - - - - - - - - -ctgcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccctt