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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcctgagatttagcatttaagcttgactatttgaaaataaaccattcaagcaaccttttttttattaaacttgtaacatagttgctattacatgtcagGTACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCGTTTGATGGGCAGGAGGCTAAGCC

Basic information

species Glycine max
transcript GLYMA19G30100.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 7
-tttcctgagatttagcatttaagcttgactatttgaaaataaaccattcaagcaaccttttttttattaaacttgtaacatagttgctattacatgtcagGTACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCGTTTGATGGGCAGGAGGCTAAGCC
 |   |  |   |  ||||||   |||  | |||| ||  |     ||| |   ||  |     ||  | | | | |   || ||    | | ||| | || || ||||||||||| || ||||||||||| |||||||| ||||| ||||||||||| |||||||||||
gtaatcaaatcatctgcattt---cttttccattttaatttcgtatattgata-aatttagaacttcctcatccttttttattgt----actgcatattagATATCTTGTTCTTGCAAATATGTTGATGGAATCTGAAGTGAATCCCTTTGATGGGCAAGAGGCTAAGCC

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 7
----------tttcctgagatttagcatttaagcttgactatttgaaaataaaccat--tcaagcaaccttttttttatta-aacttgtaacatagttgct-attacatgtcagGTACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCGTTTGATGGGCAGGAGGCTAAGCC
          ||   | |  || | || ||   |    ||   |||   ||   |||    |   ||  | |     | |   |    || |||  ||  |   |     | || || ||||| |||||||| |||||||||||||||||||| ||||| |||||||| || ||||| |||||
gtacttatacttatttaaacttcaacagttcttcacttcttcctgatcttagttcataggtacataaattctagaacactgtgatacatatcatttttttttgctgtgcattagATATCTTGTCCTTGCCAATATGTTGATGGAGTCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 7
-tttcctgagatttagcatttaagcttgactatttgaaaat---aaaccattcaagcaaccttttttttattaaacttgtaacatagttgctattacatgtcagGTACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCGTTTGATGGGCAGGAGGCTAAGCC
 | | || |  | ||   || |    |  || |    || |   | | || || |  | | | |   | | || | || |    |  ||  |      | | || || ||||| |||||||| ||||||||||| |||||||| ||||| |||||||| || ||||| |||||
gtatactca--tctatacttcatttctttctgtacagaagttttagaacactctaata-catatcgataaatatatttttggttt--tttttgccgtgtattagATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------tttcctgagatttagcatttaagcttgactatttgaaaataaaccattcaagcaaccttttttttatta----aacttg--taacatagttgct-attacatgtcagGTACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCGTTTGATGGGCAGGAGGCTAAGCC
                         || ||   ||   |  |||  | |||    ||    || ||     | |||||  || || |   | |    |||||   |||||  |||    ||   ||  ||||||||| || ||||| ||||||||||||||||||||||| || || |||||||  ||||||||||| ||
gtgagtttgtttggtacgcttaaagtttcttgtatcatgagttt--gtttggagtttcagtaacaacttcctgaagcatactcttctgagtgacgagaactttgttaacaaggttttggatgggattgcagGTACCTGGTACTTGCTAACATGTTGATGGAGTCTGAAGTGAACCCATTTGATGCTCAGGAGGCTAAACC

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------------tttcctgagatttagcatttaag----cttgactatttgaaaataaaccattcaagca---accttttttttattaaacttg-----taacatagttgctattacatgt-cagGTACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCGTTTGATGGGCAGGAGGCTAAGCC
                          | |  | | |||||    ||  |    ||| ||   |    || ||       |||||   || | |   | |  | || ||     || ||  |||| |  |  |  | ||||||| | || ||||| |||||| | |||||||||||||| || || |||||||  ||||||||||| ||
gtaagtttagagtattttaaatttcttgtattaatatttattggttgcgaatacttcacagctacgtaacaacttgcaaaagcatgtacttctgagtgaagagacctggtatttatcaaggttgttgatggagttgcagGTACTTGGTGCTTGCTAACATGCTAATGGAGTCTGAAGTGAACCCATTTGATGCTCAGGAGGCTAAACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaagcaaccttttttttattaaacttgtaacatagttgctattacatgtcagGTACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCGTTTGATGGGCAGGAGGCTAAGCC
                           ttgtaac  putative branch site (score: 2)
            ttttttttattaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcctgagatttagcatttaagcttgactatttgaaaataaaccattcaagcaaccttttttttattaaacttgtaacatagttgctattacatgtcagGTACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCGTTTGATGGGCAGGAGGCTAAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
tttcctg
- - - - - - - - - - - gcttgac
- - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - -ccattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgcta