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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttgtaattaaaagtgaagtcagaaatcattttgttaaaccaagcatagccttaaagtttgacgattggttttggctttaacaatgtgtatttgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTCGCTGCTTATATTTACAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA

Basic information

species Glycine max
transcript GLYMA02G39360.1
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 26
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
atttttgtaattaaaagtgaagtcagaaatcattttgttaaaccaagcatagccttaaagtttgacgattggttttggctttaacaatgtgtatttgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTCGCTGCTTATATTTACAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
  |   |  |||| |  |||    |    | |||    | |      | |    ||  | |||||  ||   |  |||||  ||     || ||   ||| |||||||||||||  | |||||||||||| |  ||||||| || ||||||||||| ||||| ||||||||||| || |||||  |||| || |||||||
-gtaaagcgattaga--tgattgtactgcttattgatgttatttttccttttttttttattttga--ataactaatggctggaatgccttg-at---cagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 26
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
atttttgtaattaaaagtgaagtcagaaatcattt-tgttaaaccaagcatagccttaaagtttgacgattggttttggctttaacaatgtgtatttgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTCGCTGCTTATATTTACAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
  |   |  |||| |  |||    |    | |||  |||||         |    ||  | |||||  ||   |  |||||  ||     || ||   ||| |||||||||||||  | |||||||||||| |  ||||||| || ||||||||||| ||||| ||||||||||| || |||||  |||| || |||||||
-gtaaagcgattata--tgattgtactgcttattgatgttatttttccttttttattttattttga--ataactaatggctggaatgccttg-at---cagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 11
atttttgtaat-taaaagtgaagtcagaaatcattttgttaaaccaagcatagccttaaagtttgacgattggttttggctttaacaatgtgtatttgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTCGCTGCTTATATTTACAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
      ||||  ||||| | || |    |  ||    ||    | |  | || |  ||  | ||     ||  |      | |   ||| | | |  |||| |||||||||||||  | || ||||||||| |  |||| || || ||||||||||| ||||| || |||||||||||||||||| | || || |||||||
------gtaaaataaaaataaaat----agccagacagtcgtgcaattcctatcgctaccgcttttaatttaataaca--tgtgttaatttat-tgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCCATTGCTCTATCGAAGAAAGACA

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
atttttgtaattaaaagtgaagtcagaaat-cattttgttaaaccaagcatagccttaaagtt-tgacgattggttttggct---ttaacaatgtgtattt-----gcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTCGCTGCTTATATTTACAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
      |||   || ||  |  |  | | | | | |||||         || |  | |   || |    | || |||    |   ||| |  |||  ||||     |||| | |||||||||||  | |||||||||||| |  | ||||| || ||||||||||| ||||| || |||||||| ||||||||| | ||||| ||||| |
------gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcatttcttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 6
atttttgtaat-taaaagtgaagtcagaaatcattttgttaaaccaagcatagccttaaagtttgacgattggttttggctttaacaatgtgtatttgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTCGCTGCTTATATTTACAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
      ||||  ||||| | || |    |  ||    ||    | |  | || |  ||  | ||     ||  |      | |   ||| | | |  |||| |||||||||||||  | || ||||||||| |  |||| || || ||||||||||| ||||| || ||||||||||| |||||| | || || |||||||
------gtaaaataaaaataaaat----agccagacagtcgtgcaattcctatcgctaccgcttttaatttaataaca--tgtgttaatttat-tgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCGATTGCTCTATCGAAGAAAGACA

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 3
-----------------atttttgtaattaaaagtgaagtcagaaatcattttgttaaaccaagcatagccttaaagtttgacgattggttttggctttaacaatgtgtatttgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTCGCTGCTTATATTTACAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
                 | | ||| | |    | ||  |       |  | |  |    | | |||||   |||  | ||    |||   |    || |  | || | |    |||| |||||||||||||  | || ||||||||| |  | ||||| || ||||||||||| ||||| || |||||||| ||||||||| | ||||| ||||| |
gtacaaaatagccagataatcttgcagtgcctattgctgctgctgttgttgtaatcgtgcgatgcatattgttactgctttttaatttaata-acctgtgtccatttctgga-gcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 25
atttttgtaat-taaaagtgaagtcagaaatcattttgttaaaccaagcatagccttaaagtttgacgattggttttggctttaacaatgtgtatttgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTCGCTGCTTATATTTACAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
      ||||  ||||| | || |    |  ||    ||    | |  | |  |  ||  | ||     ||  |      | |   ||| | | |  |||| |||||||||||||  | || ||||||||| |  |||| || || ||||||||||| ||||| || ||||||||||| |||||| | || || |||||||
------gtaaaataaaaataaaat----agccagacagtcgtgcaattcctgtcgctaccgcttttaatttaatagca--tgtgttaatttat-tgagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATCGCCGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAGTCGATTGCTCTATCGAAGAAAGACA

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 26
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 26
atttttgtaattaaaagtgaagtcagaaatcattttgttaaaccaagcatagccttaaagtttgacgattggttttggctttaacaatgtgtatttgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTCGCTGCTTATATTTACAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
               || ||  |  ||| | ||||||||||     | |  || | | |    ||  ||     |  | | ||   ||| || |   ||| ||||||| ||||||||||| |||||||||||| | |||||||||||||| |||||||| || |||||||| || |||||||| |||||||| |||||||
------------gtgagagagatt-gaatttattttgttaatgttggta-ggcttcataagcagaacatgtacataagatctagtgatgcgtgtggacagGTTGAGAAACATGAGCTTCTGGAGATGAGGCGTATTGCTGCTTATATTTATAAGAAAGCAGGTAGATGGAAACAATCCATTGCATTGTCAAAGAAAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcatagccttaaagtttgacgattggttttggctttaacaatgtgtatttgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTCGCTGCTTATATTTACAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA
                                 ctttaac  putative branch site (score: 3)
         ttaaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttgtaattaaaagtgaagtcagaaatcattttgttaaaccaagcatagccttaaagtttgacgattggttttggctttaacaatgtgtatttgcagATTGAGAAGCATGAGCTTCTTGAGATGAGGCGTGTCGCTGCTTATATTTACAAGAAAGCTGGAAGATGGAAGCAGTCCATTGCTTTGTCAAAAAAAGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - -caagcat
- - - - - - - - - - - - - - - - - - - - - - - - - -gccttaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttttg