Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttgatggagccctggcctttgtagctttgctcatacgacgagactatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG

Basic information

species Selaginella moellendorffii
transcript EFJ14095
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 18
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 19
------------------------------------gtaacttgatgg---agccctggcctttgtagctttgctcatacgacgagactatgtta--cagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG
                                    | ||  | ||     |    || |||   |    |         || | |  |  |||   ||||||||||| || ||||||||||| ||||| |||||||| |||||||| |||||||| || |   ||||| |  | || |||| ||| ||||||||     
acttggatcagcaaatattctgtctgtagtagcgctggaatataattccccaagtttgtcctccatgtactgaaatgactgatgtgtgtgagttttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC-----

upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 18
lower sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 19
------------------------------------gtaacttgatggagccctggcct-ttgtagctttgctcatacgacgagact----atgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG
                                      |||       |    | || | | ||||| |      ||||  |    |    || |||||||| ||||| |||||||| ||||||||||| || |||||||||||||| |||||||| ||||   | ||||| || |||||||   ||||||||||     
caattgctgcaatcagcttcctattgttgaaacttgaaaaccattcaaatgtgtagcatgtagtagcatccaatttacgttggtgtttggcattttacagGGTACAAGTAGACCAGCACACTATCACGTCCTCTGGGACGAGAACAATTTCACTGCAGATGAGATTCAGTCTCTAACCAACAATTTGTGCTACAC-----

upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 18
lower sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 19
----------------------------------------------gtaacttgatggagccctggcctttgtagctttgctcatacgacgagactatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG
                                               | || || |  ||   |    ||||||   | |    |||    |  | || |||||||| ||||| ||||||||||| ||||| || || |||||||||||||| |||||||| ||||   | || || || ||||||| | ||||||||||     
cttctcataaccatacaaataggatattggggtagggtgtaaagaaatgacatgttaaagaa-taatatttgta---tcggatttacattaatgcaat-ttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACAC-----

upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 18
lower sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 15
---------------------------------------------gtaacttgatggagccctggcctttgtagctttgctcatacgacgagactatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG
                                              |||  || |  |    |    ||||||   |      |||    |  |||| |||||||| ||||| ||||||||||| ||||| || || |||||||||||||| |||||||| ||||   | || || || ||||||| | |||||||||| ||  
accatacaaatagggtattggtgacttgggatagggtgtaaagaactaagatgttaaaagaataatttttgta---tcagatttacattaatgctat-ttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACACGTAA-

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|169025753|gb|FE433663.1|FE433663
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169052412|gb|FE462246.1|FE462246
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169094763|gb|FE492940.1|FE492940
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169110846|gb|FE509329.1|FE509329
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169036142|gb|FE445663.1|FE445663
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169053756|gb|FE461523.1|FE461523
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169076999|gb|FE485340.1|FE485340
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169081815|gb|FE486414.1|FE486414
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGNGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169026881|gb|FE432386.1|FE432386
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169078633|gb|FE487065.1|FE487065
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169108088|gb|FE511031.1|FE511031
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169026857|gb|FE434221.1|FE434221
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169076998|gb|FE485339.1|FE485339
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169027233|gb|FE435091.1|FE435091
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169026895|gb|FE432387.1|FE432387
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169092972|gb|FE495266.1|FE495266
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169021773|gb|FE430420.1|FE430420
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
EST: gi|169077159|gb|FE484538.1|FE484538
EST:     GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG                         GGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC
genomic: GCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTC

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), 34 (downstream exon)
Score: 75

GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAGgtaacttgat ... tatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgatggagccctggcctttgtagctttgctcatacgacgagactatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG
 acttgat  putative branch site (score: 75)
                                             tatgtta  TA-rich tract