Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAAGCTCAACATCGCCAATCCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgtcgcttggatctctggatggaatggtgattttgttctcttttcgtgcag

Basic information

species Selaginella moellendorffii
transcript EFJ14726
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14726 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 5'ss of exon 2
ATGAAGCTCAACATCGCCAATCCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagc-ttgtcgcttggatctctggatggaatggtgattttgttctcttttcgtgcag------------------------------------------
       ||||||||||||| || ||||| || || ||||||||| |||| || || ||||| |||||||||| ||   |    |||   |||||   | || || |||| |  |      | |||| ||                                          
------TTCAACATCGCCAACCCGACCACCGGGTGCCAGAAGAAGCTCGAGATCGATGACGACCAGAAGCTgtgagtgctcctccttctctctctctcttga-tgctgatctgttctgaaatgcgtggagatctcttgcatcgtgttaatctagcttgtccgctcggtcctt

upper sequence: EFJ14726 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA08G45770.1 (Glycine max), 5'ss of exon 2
ATGAAGCTCAACATCGCCAATCCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgtcgcttggatctctgg--atggaatg----gtgattttgttctcttttcgtgcag------------------------------------
       |||||||||| ||||||||||| ||||| ||||||||| |||| || |||||||||| ||| ||||||   | || ||    | | |    ||  |||     ||  || |  |   | || |||  |                                    
------TTCAACATCGCGAATCCCACCACTGGATGCCAGAAGAAGCTCGAGATCGACGACGATCTGAAACTgtaattatttcactcttttttttaattataaaatatttcgtatttctacttgttcttggtggtgttcgtgtgttgtgctttcaaagaaagttgatttatt

upper sequence: EFJ14726 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA18G26190.1 (Glycine max), 5'ss of exon 1
ATGAAGCTCAACATCGCCAATCCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagc----------ttgtcgcttggatctctggatg--gaat-----ggtgattttgttctcttttcgtgcag-------------------------
       |||||||||| | ||||||||| ||||| ||||||||| |||| || |||||||||||||| |||||| |          || |  |||   | | | | ||   |||      ||  || |  |   | ||||||  |                         
------TTCAACATCGCGAGTCCCACCACTGGATGCCAGAAGAAGCTCGAGATCGACGACGATCAGAAACTgtaatcacttcactctttctttctttctttttttggtgttaaatttttgagtatttctacttgttcttcgtggtgttcgtgtgttgtgctttgagagaaa

upper sequence: EFJ14726 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 5'ss of exon 2
ATGAAGCTCAACATCGCCAATCCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgtcgcttggatctctggatggaatggtgattttgttc-tcttttcgtgcag----------------------------------------------
       |||| ||||| ||||| || || ||||||||||||||| |||| ||||| ||||||||||| ||||||||||     |   ||  |    |    |  |  |  | | | | || | |   ||                                              
------TTCAATATCGCAAATCCTACTACAGGATGTCAGAAGAAGCTCGAGATTGATGACGATCAGAAACTgtaagctt-----tcaaattcccacgtttttttttcttcctatgcgttttgttgctgagaaaatgatagaaattattagttaatgttgttttaggttttttttcc

upper sequence: EFJ14726 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S253_38V6.1 (Physcomitrella patens), 5'ss of exon 2
ATGAAGCTCAACATCGCCAATCCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagc----ttgtcgcttggatctctggatggaatggtgattt-tgttctcttttcgtgcag-------------------------------------
      |||||||||||||| ||||| ||||| || ||||||||||| || || || |||||    ||||||||||     | ||   |||   | ||     |  ||  | |   ||||| | |    |                                         
------CTCAACATCGCCAACCCCACTACGGGGTGCCAGAAGAAGGTTGAGATCGATGACGACGCTAAGCTgtaagtggcttggttctttgcgaccctttgcagtctgtcggtggatgttcgcctgcaattttacgtgctctcttgttcgcgcctgcgttttgcactgctt

upper sequence: EFJ14726 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S253_7V6.1 (Physcomitrella patens), 5'ss of exon 2
ATGAAGCTCAACATCGCCAATCCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaag---cttg--tcgcttggatctctg-gatggaatggtgatt--ttgttct---cttttcgtgcag-------------------------------
      |||||||||||||| ||||||||||| || || |||||||| || || || |||||    ||||||||||   ||||  || ||  || ||||    |   | ||||  |  | | | |    ||| ||||||                                
------CTCAACATCGCCAACCCCACCACGGGGTGCCAAAAGAAGGTTGAGATCGATGACGACGCCAAGCTgtaagttgcttggttccctgcgacctcttcagtcagacggtggattgtcgctttggattttacgtgcactcttgtttatatctgcgttttgcactctttt

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|169101825|gb|FE500771.1|FE500771
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169048524|gb|FE454419.1|FE454419
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169049454|gb|FE458300.1|FE458300
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169055042|gb|FE462957.1|FE462957
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169073800|gb|FE484021.1|FE484021
EST:     GACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: GACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169112742|gb|FE515118.1|FE515118
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169075486|gb|FE482496.1|FE482496
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169074735|gb|FE483305.1|FE483305
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169056221|gb|FE464070.1|FE464070
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169102758|gb|FE503966.1|FE503966
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169058309|gb|FE465023.1|FE465023
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169049702|gb|FE457768.1|FE457768
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169064127|gb|FE472314.1|FE472314
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169065536|gb|FE474828.1|FE474828
EST:     GGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: GGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169051339|gb|FE457650.1|FE457650
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169067221|gb|FE474989.1|FE474989
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169054063|gb|FE462298.1|FE462298
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169036060|gb|FE446766.1|FE446766
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169070522|gb|FE479799.1|FE479799
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169039385|gb|FE449112.1|FE449112
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169101289|gb|FE501977.1|FE501977
EST:     GGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: GGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169035699|gb|FE446184.1|FE446184
EST:     AGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: AGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169040201|gb|FE448123.1|FE448123
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169039338|gb|FE449091.1|FE449091
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
EST: gi|169061224|gb|FE470350.1|FE470350
EST:     CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCT                         GAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT
genomic: CCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 67

ATGAAGCTCAACATCGCCAATCCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgt ... tttcgtgcagGAAAATCTTCTATGAGAAGCGCATCTCGCAAGAGGTGCCCGGAGATGGGCTCGGAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAAGCTCAACATCGCCAATCCCACCACGGGATGTCAGAAGAAGGTCGACATTGACGACGATCAGAAGCTgtaagcttgtcgcttggatctctggatggaatggtgattttgttctcttttcgtgcag

- - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC