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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgtttgtttctgcattttcgggaattgcaggcaatattgttaacccgttggaataacag

Basic information

species Selaginella moellendorffii
transcript EFJ14291
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 5'ss of exon 7
GTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgtttgtttctgcat---tttcgggaattgcagg--caatattgttaacccgttggaataacag-----------------------------------
|| ||||| || || || ||||| || ||||| |||||||||||||||||||| ||||| ||||| ||||| || || ||  | || ||||| || ||||||  ||  |    |    |  ||   |||       | | || ||| |   |    || |  |                                   
GTGGAAGGGACAATTCAACAGCTATTTGAAGGTCATCATATGAATTATATTGAGTGCATTAATGTTGACTACAAATCTACAAGGAAAGAATCATTCTATGgtaggtgacaaggtgaaatctggaccttgtttctttattgtttttatctattcatcatgattgtagatttatcatgtattttcgtaactcttttctag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GLYMA14G04890.1 (Glycine max), 5'ss of exon 7
GTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgtttgtttctgcattttcgggaattgcaggc--aatattgttaacccgttggaataacag----------------------
||||| || || |||||| |||| || ||||| ||||||||||||||||| ||||||||||||||||||||||| || ||| ||||||| || |||||||||   ||  || |    | | |  |    ||  |||  |      ||  | || |   |                       
GTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATGAATTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcatgtacagactgaagctatgtgcttaattgtaccttgccacttgattctaatttagttttacatatacttgcag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GLYMA02G43930.1 (Glycine max), 5'ss of exon 7
GTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgtttgtttctgcattttcgggaattgcaggc--aatattgttaacccgttggaataacag----------------------
||||| || || |||||| || | || ||||| ||||||||||| ||||| ||||||||||||||||||||||| || ||| ||||||| || |||||||||   ||  || |    | | |  |  | ||  |||  |      ||  | || |   |                       
GTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGTCATTTTATGgtactttcatgtacacactgaacctatatgcttaattgtaccttgccacttgattctaatttagttttgcatatgcttgcag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GLYMA20G11300.1 (Glycine max), 5'ss of exon 7
GTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgt--ttgtttctgcattttcggg--aattgcaggcaatattgttaacccgt-tggaataacag-------------------------
||||| || || |||||  || | || ||||| || ||||||||||| ||||||||||||||||| ||||| || || ||| ||||||| || |||||||||  ||  || ||||||||      ||||  | |     || ||      | || |||   |                          
GTTGAGGGAACTATACAAAAGTTATTTGAAGGACACCATATGAATTACATTGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGTCATTTTATGgtacttccttatgcattttgaattcaattatatgtttagttcttctttgttatgtaattctaatttagtttttgcatatgcatgttag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GLYMA13G16170.1 (Glycine max), 5'ss of exon 7
GTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgt--ttgtttctgcattttcggg--aattgcaggcaatattgttaacccgttggaataacag-------------------------
||||| || ||||||||  |  | || ||||| || ||||||||||| || |||||||||||||| ||||| || || ||| ||||||| || |||||||||  ||  || ||||||||      ||||  | |   | || ||      |  | ||  |                           
GTTGAGGGAACCATACAAAAATTATTTGAAGGGCACCATATGAATTACATAGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGTCATTTTATGgtacttccttatgcattttgaattcaattatatgttttgttcttccttgttatgtatttctaatttagttttgcatatgcatgttag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GLYMA10G23680.1 (Glycine max), 5'ss of exon 3
GTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgtttgtttctgcattttcgggaattgcaggcaatattgtt----------aacccgttggaataacag--------------
|| ||||| || ||||||||  | || ||||| || |||||||| |||||||||||||| |||||||| ||||| || ||  | || ||||| ||||||||| ||  | |     ||  ||| |||    | | ||| ||          ||||   | |||||   |              
GTGGAAGGCACTATACAGCAATTGTTTGAAGGACACCATATGAACTATATTGAATGCATAAATGTGGATTATAAATCAACAAGGAAAGAATCATTTTATGgtatgcatttttgcctttagga-ttgtttactacattattgcatatcttgaaccttatagaatattggatattttattatag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 5'ss of exon 7
GTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgtttgtttctgcattttcgggaattgcag-gcaatattgttaacccgttgg--aataacag--------------------------
|| || ||||| ||||||||| | || ||||| || |||||||| |||||||||||||| |||||||||||||| || ||  |||||||||| ||||||||| ||| | |   |||||  | | |  |  | | |||   | |    ||||    |  ||                           
GTGGAGGGTACTATACAGCAGTTATTTGAAGGGCACCATATGAACTATATTGAATGCATTAATGTGGACTATAAATCAACAAGAAAGGAATCATTTTATGgtatgtatttcagttttcatggactagattgtattatctgtgatagattggtgggtttcacttgtctgtatacatatttggttacag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 5'ss of exon 7
GTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgtttgtttctgcattttcgggaattgcaggcaatattgttaacccgttggaat-aacag------------------------------------------------------------------------------------
|| || || || ||||||||| | || ||||| || |||||||| || ||||| ||||||||||||||||| || || ||  |||||||||| ||||||||| |   | |    ||   |   || ||  |  | | | ||  |  | |  || ||  |                                                                                    
GTGGAGGGGACAATACAGCAGTTGTTTGAAGGGCACCATATGAACTACATTGAGTGCATCAATGTGGACTACAAATCTACAAGAAAGGAATCATTTTATGgtattcatttttggttcaagc--ttacattctttgtagctaggcattcgctattaatgggaatgcatgatacttgaactatatatgtcctaatataaaaagaaaggaaaaaaaatgaactgcatttttatttttgcatggcag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 5'ss of exon 7
GTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgt-ttgtttctgcattttcgg--gaattgcaggcaatattgttaacccgttggaataacag------------------
|| || || || ||||||||| | || ||||| || |||||||| || ||||||||||||||||||||||| || || ||  | ||||| || |||||||||  |  || |  ||||  ||  ||| |||  |   || |||       |      || |                   
GTGGAGGGCACTATACAGCAGTTATTTGAAGGGCACCATATGAACTACATTGAATGCATCAATGTGGACTACAAATCTACAAGGAAGGAGTCATTTTATGgtacttattttatatttatggttgaaatgcctgatttagtgtctgtttttcattgcaaaataaattgtttgtgtggcag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S104_2V6.1 (Physcomitrella patens), 5'ss of exon 7
GTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgtttgtttctgcattttcgggaattgcaggcaatattgttaacccgttggaataacag---------------------------------------------------------------------------------------
|| || || || |||||  | ||||| ||||||||||||||||||||||| |||||||||||||| || | |||||||||||| ||||| || | |||||||    ||||      || |   |    | |  || ||||  ||||    || |   |                                                                                       
GTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGTCCTATTATGgtacacttct------tctgacttgattgactctaatgttgtcccgagacaacactgggcatgtggcttatcatggtcgggctttgttgatcttccgtacgctgctagatttcactttaataatatgtgaagtaaacgttggcag

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|169082131|gb|FE486470.1|FE486470
EST:     TGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATG                         ATTTGCAGCTTGATGTAAAAGGCTGCAAGGATGTTTATGCGTCGTTTGATA
genomic: TGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgtttgtttct ... ggaataacagATTTGCAGCTTGATGTAAAAGGCTGCAAGGATGTTTATGCGTCGTTTGATA
EST: gi|169031425|gb|FE437135.1|FE437135
EST:     TGAATGCATCAATGTGGACTACAAGTCCACTCGAAAGGAATCTTTTTATG                         ATTTGCAGCTTGATGTAAAAGGCTGCAAGGATGTTTATGCGTCGTTTGATA
genomic: TGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgtttgtttct ... ggaataacagATTTGCAGCTTGATGTAAAAGGCTGCAAGGATGTTTATGCGTCGTTTGATA
EST: gi|169032748|gb|FE437775.1|FE437775
EST:     TGAATGCATCAATGTGGACTACAAGTCCACTCGAAAGGAATCTTTTTATG                         ATTTGCAGCTTGATGTAAAAGGCTGCAAGGATGTTTATGCGCCGTTTGATA
genomic: TGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgtttgtttct ... ggaataacagATTTGCAGCTTGATGTAAAAGGCTGCAAGGATGTTTATGCGTCGTTTGATA

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: 31 (upstream exon), 32 (downstream exon)
Score: 9

GTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgtttgtttct ... ggaataacagATTTGCAGCTTGATGTAAAAGGCTGCAAGGATGTTTATGCGTCGTTTGATAAATACGTCGAGGTAGAGAAGCTCGAAGGGGATAACAAGTATCATGCTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAATCTTTTTATGgtttgtttctgcattttcgggaattgcaggcaatattgttaacccgttggaataacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA