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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggatatcactagtaaaaaataaatcctcaaaattattgttttacaatgatttgtcactaattatactctgtctcagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG

Basic information

species Glycine max
transcript GLYMA03G12240.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
gttggatatcactagtaaaaaataaatcctcaaaattattgttttacaatgatttgtc---actaattatactctgtctcagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG
        |   ||   ||   || ||  |||||    |  |  ||| |  ||||| |   ||   | |||| ||||  |||||||||||||| || ||||| ||  | || ||||| |||||||||||||| |||||||||||||  ||||| || |||||||||||||| |||||||
-------gtgtgtatgcaattctatattttcaaagcgttgatactacca--atttggctaaacccgtaatacactgtg-cagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG

upper sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 12
gttggatatcactagtaaaaaataaatcctcaaaattattgttttacaa--tgatttgtcactaattatactctgtctcagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG
        | | || |  ||| | | || |     | ||   ||||  |  | | |    || |    ||||||||  |||||||||||||| || ||||| ||  | || ||||| || |||||||| ||||| || ||||| | | |||| || ||||||||||||||||||||||
-------gtgagta-tgtaaagtgattctttggg-tgataaatttaagaatttaatctaaaccagaagtactctgtg-cagCTTGATGATGTGATTGATCTTGTAATACCAAGAGGTAGCAATAAGCTCGTTTCCCAGATCAAAGCAGCAACCAAGATTCCTGTTCTTGGTCATGCTG

upper sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 12
lower sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
---------gttggat-atcactagtaaaa--aataaatcctcaaaattattgttttacaatgatttgtca-----ctaa--ttatactctgtct--cagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG
         | ||  | |  |   || |    |||| ||  | ||||| ||  || ||| || ||   | |     ||||  | ||| |        |||||| |||||||||| ||||| ||  | || |||||||| |||||||| ||||| |||||||||  |||||| || || |||||||||||||||||||
acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG

upper sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G094309_T01 (Zea mays), 3'ss of exon 4
gttggatatcac-tagtaaaaaataaatcctcaaaattattgttttacaatgatttgtcactaattatactctgtctcagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG
  ||    | |  || ||  |||   ||  |   |   ||| |     ||| |      ||| || |||| || |  |||||| |||||||||| ||||| ||  | || ||||| || |||||||| ||||| |||||||||| |||||| || || |||||||||||||||||||
-gtgagcgtaatatattatgaaaatgatgattgta-ccattatgcc-taataagcctaaactcataatacactcta-cagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGTAGCAATAAGCTGGTTTCACAAATCAAGGCATCAACTAAGATCCCTGTTCTTGGTCATGCTG

upper sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G375504_T03 (Zea mays), 3'ss of exon 11
----gttggatatcactagtaaaaaataaatcctcaaaattattgttttacaatgatttgtcactaattatactctgtctcagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG
    ||   ||||  |  | ||| ||| | ||  | ||  |        |  || |      ||| || |||   | |  |||||||||||||| || ||||| ||  | || |||||||| |||||||| ||||| |||||||| | |||||| || || ||||| || |||||||| |
gtaagtgtaatatatcatgaaaataatgattctaccaatatgc------atgataagcctaaactcataatatgttcta-cagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCGCAAATCAAAGCATCAACTAAGATACCTGTCCTCGGTCATGCGG

upper sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv08s0007g01060.t01 (Vitis vinifera), 3'ss of exon 12
gttggatatcactagtaaaaaataaatcctcaaaattattgttttacaatgatttgtcactaattata-ctctgtctcagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG
|| ||     | |   |    |||  |        || |  |  ||   || ||  | |||  || ||  |||| | |||||||||||||| |||||||| ||| ||||||||||||| || || || ||||||||||||||||| ||||| ||||| |||||||||||||||||||
gtgggg----attgagattggatatgtttgatggtttttcataataggttggttattaacttgttttagttctgccccagCTTGATGATGTCATAGATCTTGTGATCCCTAGAGGCAGCAACAAACTCGTTTCTCAAATCAAGGATTCAACTAAAATCCCTGTTCTTGGTCATGCTG

upper sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ17662 (Selaginella moellendorffii), 3'ss of exon 12
gttggatatcactagtaaaaaataaatcctcaaaattattgttttacaatgatttgtcactaattatactctgtctcagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG
                                 || |||  |||     || |   ||  |  |||   |  || ||||||||| ||||| || || || ||  | || ||||| || ||||| |||||||| ||||||||||| || || ||||||||||| || || ||||| |
-------------------------------gtaactatactttcgtgctgttagctcgtttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG

upper sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ29127 (Selaginella moellendorffii), 3'ss of exon 12
gttggatatcactagtaaaaaataaatcctcaaaattattgttttacaatgatttgtcactaattatactctgtctcagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG
                                 || |||  ||||    || |   ||  |  |||   |  || ||||||||| ||||| || || || ||  | || ||||| || ||||| |||||||| ||||||||||| || || ||||||||||| || || ||||| |
-------------------------------gtaactatacttttgtgctgttagctcgtttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcctcaaaattattgttttacaatgatttgtcactaattatactctgtctcagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG
                                 cactaat  putative branch site (score: 2)
                                            ctctgtctc  putative PPT
       aaaattattgttttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggatatcactagtaaaaaataaatcctcaaaattattgttttacaatgatttgtcactaattatactctgtctcagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG