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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttctagtgcgtttttgtgttctccttatctagcgtttcgtttaacag

Basic information

species Selaginella moellendorffii
transcript EFJ06565
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 14
ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttctagtgc---gtttttgtgttctcc----ttatctagcgtttcgtttaacag---------------------------------
||||| || || || || |||||||| ||  | || |||||||||||||| || ||||| || || || ||||||||||| |||||||||||||| || |||| || |  |  |   ||| || |||  ||     || |||     |  || | |                                    
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCTGAACTTGATGCAAAAATGAAAAAGTTCACAGAGGACGCCATTAAATTTAAGATGGATGATAgtatgtacctgctccctgttcttatgtcttctgacgttctctgctcctatgtcttatgttttcctacctaaacactttattttctgatgcag

upper sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 11
ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttctagt---gcgtttttgtgttctccttatctagcgtttcgtttaacag-----------------------------------------
||||| || || || || |||||||| ||  | || || ||||||||||| || ||||| || || || ||||| |||||||||||||||||||| || |||| || |  ||     |||| | | ||||  | |  ||   | || ||                                               
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacctgttttctgtttctat-ttcttgtgacttattctctctttctgtgtcttctgtcaatctacctaacaccttttattttctgatgcag

upper sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 14
ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttctagtgcgtttttgtgttctccttat-ctagcgtttcgtttaacag------------------------------------------------------------
|||||| | || ||||| |||||||| || || |||||||| || ||||||||||||||||||||||| || || |||||||||||||||||||| ||||||| || |   |   | |   | |       ||  | || |    ||||  ||                                                            
ATTGATAGAATTATTGCTAAAGGAGAGGAGGCAACTGCTGAGCTAGATGCCAAGATGAAGAAATTTACTGAAGATGCCATCAAATTTAAGATGGATGACAgtatgtgcctataattctagctttaaaaacaatattggcatgatctttacaagttttatgctttcttctgtctgtagtttatagttactaatactggtgctttctttttgtag

upper sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: GLYMA07G38050.2 (Glycine max), 5'ss of exon 14
ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttctagtgcgtttttgtgttctccttatctagcgtttcgtttaacag-------------------------------------------------
|||||  | || ||||| |||||||||||||| || ||||| |||||||| |||||||| |||||||| || || || ||||||||||||||||| ||||||| ||     |    | |    |    |||  |||   ||| |||| |  |                                                 
ATTGACAGAATTATTGCTAAAGGAGAAGAAGCAACAGCTGAGCTTGATGCTAAGATGAAAAAATTTACTGAAGATGCTATCAAATTTAAGATGGATGACAgtatgtaacctttaaatataaattctggctttgctaa-atttggtttgattgatgtcgttagaaatctattttgttgtttaaattcctgtatacccataag

upper sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 14
ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttctagtgcgtttttgtgttctccttat--------ctagcgtttcgtttaacag-----------------------------------------------------------
|||||| | || ||||| |||||||| || || ||||| || ||||||||||| |||||||||||||| || || |||||||||||||||||||| ||||||| || |   ||  |   |||  |  | |||          | || |    ||||  ||                                                           
ATTGATAGAATTATTGCTAAAGGAGAGGAGGCAACTGCCGAGCTTGATGCCAAAATGAAGAAATTTACTGAAGATGCCATCAAATTTAAGATGGATGACAgtatgtacctatgactacctgttctagctttaaaaacaatattggcatgctctttacaagttttatgctttcttctgtttgtagtttagagttactaatactgatactttcttttgtag

upper sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 14
ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttctagtgcgtttttgtgttctccttatctagcgtttcgtttaacag-------------------------------------------------
|||||  | || ||||| |||||||| ||||| || ||||| |||||||| |||||||| |||||||| || || || ||||||||||||||||| ||||||| ||     |    | |  | |    |||  |||  |||  |||| |  |                                                 
ATTGACAGAATTATTGCTAAAGGAGAGGAAGCAACAGCTGAGCTTGATGCTAAGATGAAAAAATTTACTGAAGATGCTATCAAATTTAAGATGGATGACAgtatgtaacctttgaatataatttctggctttgctaaagttg-gtttgattgatgatgttaaaaatctattttgttgtttaaatttctgtatatccacaag

upper sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 14
ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttctagtgcgtttttgtgttctccttatctagcgtttcgtttaacag------------------------------------------
|||||  | |||||||| ||||||||||| || || |||||||||||||||||||||||||||||||| || || || ||  | ||||| ||||| ||||||||||    ||||  |||     | |    |        | | ||  |  |                                          
ATTGACAGAATCATTGCCAAAGGAGAAGAGGCAACGGCTGAACTTGATGCCAAGATGAAGAAATTTACTGAAGATGCAATACAGTTTAAAATGGATGACAgtaagt----gtgctatttatccctttttccaatggtaactcccttgcatgggtaatgggatgtccaaacaagatagtttttggtttgttgcag

upper sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 14
ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttctagtgcgtttttg-tgttctccttatctagcgtttcgtttaacag-----------------------------------
|||||| | |||||||| ||||||||||| || || |||||||||||||| |||||||||||||| || || || || ||  | ||||| ||||| |||||||||   |    | |   |  | ||  || |||   |   |  |  ||                                       
ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaaggg-tgtcacttacctactatttcccctattaggttgtgtgaatattgtaatgttttgataatctgttgttttatttgttgtag

upper sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 5'ss of exon 14
ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttctagtgcgtttttg-tgttctccttatctagcgtttcgtttaacag-----------------------------------
       | |||||||| ||||||||||| || || |||||||||||||| |||||||||||||| || || || || ||  | ||||| ||||| |||||||||   |    | |   |  | ||  || |||   |   |  |  ||                                       
------AGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAGTAAGGg-tgtcacttacctactatttcccctattaggttgtgtgaatattgtaatgttttgataatctgttgttttatttgttgtag

upper sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 14
ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagt----------tctagtgcgtt--tttgtgttctccttatctagcgtttcgtttaacag---------------------------------------
|| ||  | |||||||| ||||||||||| || || ||||| |||||||| ||||||||||||||||| || || |||||||||||||| ||||| || |||| ||          || || ||  |   |  |  | | ||||||||   ||     | |  |                                       
ATAGACAGGATCATTGCTAAAGGAGAAGAGGCAACAGCTGAGCTTGATGCTAAGATGAAGAAATTTACAGAAGATGCCATCAAATTTAAAATGGATGATAgtatgtggatccactatccagggctctcactcattatttacttatctacttttgaaagttatggggctaaaatataatttaacatttatcctgctttgttcag

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|169028023|gb|FE435914.1|FE435914
EST:     CAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACA                         CTGCCGAATTTTACGACTTTGATGGCAACGATGACAAG
genomic: CAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttcta ... cgtttaacagCTGCCGAATTTTACGACTTTGATGGCAACGATGACAAG
EST: gi|169061121|gb|FE470127.1|FE470127
EST:     CAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACA                         CTGCCGAATTTTACGACTTTGATGGCAACGATGACAAG
genomic: CAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttcta ... cgtttaacagCTGCCGAATTTTACGACTTTGATGGCAACGATGACAAG
EST: gi|169023478|gb|FE430076.1|FE430076
EST:     CAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACA                         CTGCCCGA-TTTTACGACTTTGATGGGCA-CGATGACAAG
genomic: CAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttcta ... cgtttaacagCTGCC-GAATTTTACGACTTTGATGG-CAACGATGACAAG

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: 11

ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttcta ... cgtttaacagCTGCCGAATTTTACGACTTTGATGGCAACGATGACAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttctagtgcgtttttgtgttctccttatctagcgtttcgtttaacag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA