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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttagtcaatatgaagagaaaatgggcagtttcatttaaattatgtagtttcttttattcctttcgtttgagatgttaacatttactttcacattacagATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCTTTTCAAGGTTGCTCAG

Basic information

species Glycine max
transcript GLYMA09G37610.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 23
acttagtcaatatga-agagaaaatgggcagtttcatttaaattatgtagtttcttttattcctttcgt---ttgagatgttaacatttactttcacattacagATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCTTTTCAAGGTTGCTCAG---------------------------------
  ||| ||    | | | |   ||||  |    | |||| ||||||| |   || ||||   || || |     |     |  |  |      | ||||| ||||||||| ||| |||||||||| |||||||| || ||||| ||||| ||||||||||| ||||||||                                  
cattattcttccttatatatctaatgtac----ttatttgaattatgaaagatcatttacatctgtcatgaaccgcacaatctaagtgctgaattacattgcagATATGACCTCCTGCATAATGCACATCTTAACCTTGAAGGTTTGGAAGAGCTTTTCAAAGTTGCTCAAGTAAGGAACCTTAACGTTCTGTACTTCCATTTG

upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 23
acttagtcaatatga-agagaaaatgggcagtttcatttaaattatgtagtttcttttattcctttcgt---ttgagatgttaacatttactttcacattacagATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCTTTTCAAGGTTGCTCAG
  ||| ||    | | | |   ||||  |    | |||| ||||||| |   || ||||   || || |     |     |  |  |      | ||||| ||||||||| ||| |||||||||| |||||||| || ||||| ||||| ||||||||||| |||||||| 
cattattcttccttatatatctaatgtac----ttatttgaattatgaaagatcatttacatctgtcatgaaccgcacaatctaagtgctgaattacattgcagATATGACCTCCTGCATAATGCACATCTTAACCTTGAAGGTTTGGAAGAGCTTTTCAAAGTTGCTCAA

upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G022997_T01 (Zea mays), 3'ss of exon 3
------acttagtcaatatgaagagaaaatgggcagtttcatttaaattatgtagtttcttttattcctttcgtttgagatgttaacatttacttt-cacattacagATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCTTTTCAAGGTTGCTCAG
      |    |||  | | || | || |||  || || |||   ||||||     | |    ||||  || |  |   |     | | | |      | ||| ||| ||||| || ||||||||||||||||| |||||  | || ||||| ||||| ||||| |||||||| 
ttgttgatgatgtctttcttaaaa-aatatgaacatttacat---aattatagtaataca---attctgttggcatataactcctaaactaatggagtaaattgcagGTATGACCTTTTGCATAATGCTCATCTCAATCTTAAGGGTTTGGAAGAGCTATTCAAAGTTGCTCAA

upper sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 23
acttagtcaatatgaagagaaaatgggcagtttcatttaaattatgtagtttcttttattcctttcgtttgagatgttaacattta--ctttcacattacagATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCTTTTCAAGGTTGCTCAG
   |  || ||    | | ||  |      | | || | | |  | || | |  | |  |    | | ||| | | || |   ||   ||  ||  | ||||||||||||||||||| ||||| ||||||||||||||||   |||||||||||||||| |||||||||
-agtgttctattaacaaaaaagctccttgctcttatatgagtccttta-tgttctatgctaacattgcttgtgcttttgattgttgacctgccaattcacagATATGATCTCTTGCACAATGCACATCTTAATCTAGAAGATCTGGATGAGCTTTTCAAAGTTGCTCAG

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|120531780|gb|EH259913.1|EH259913
EST:     GCGTTTTGACATCACCCAAATTCCTGATGTCTATGATTCATGCAA                         ATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCT
genomic: GCGTTTTGACATCACCCAAATTCCTGATGTCTATGATTCATGCAAgtaagttatt ... cacattacagATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCT
EST: gi|10237535|gb|BE806423.1|BE806423
EST:     GCGTTTTGACATCACTCAAATTCCTGATGTCTATGATTCATGCAA                         ATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCT
genomic: GCGTTTTGACATCACCCAAATTCCTGATGTCTATGATTCATGCAAgtaagttatt ... cacattacagATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCT
EST: gi|19348846|gb|BM893378.1|BM893378
EST:     GCGTTTTGACATCACCCAAATTCCTGATGTCTATGATTCATGCAA                         ATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCT
genomic: GCGTTTTGACATCACCCAAATTCCTGATGTCTATGATTCATGCAAgtaagttatt ... cacattacagATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCT
EST: gi|15203141|gb|BI425909.1|BI425909
EST:     GCGTTTTGACATCACTCAAATTCCTGATGTCTATGATTCATGCAA                         ATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCT
genomic: GCGTTTTGACATCACCCAAATTCCTGATGTCTATGATTCATGCAAgtaagttatt ... cacattacagATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagtttcttttattcctttcgtttgagatgttaacatttactttcacattacagATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCTTTTCAAGGTTGCTCAG
                             tgttaac  putative branch site (score: 2)
                                     tttactttc  CT-rich tract
                               ttaacatttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttagtcaatatgaagagaaaatgggcagtttcatttaaattatgtagtttcttttattcctttcgtttgagatgttaacatttactttcacattacagATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCTTTTCAAGGTTGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - tatgaag
- - - - - - - - - - - - - - - - - - - - - tatgtag