Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTGTTGCCGGTGCTTCCAAGCTCTTGGCAAACACCCTCTACTCCTACCGTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctgttatcttttcttgtttccatctcgccattcccaagttttcttctcacgtctcgtgatttgatccag

Basic information

species Selaginella moellendorffii
transcript EFJ25863
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ25863 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: LOC_Os06g06030.1 (Oryza sativa), 5'ss of exon 4
TTCTGTTGCCGGTGCTTCCAAGCTCTTGGCAAACACCCTCTACTCCTACCGTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgta----tgggctgt-tatcttttctt----gtttccatctc----gccattcccaagttttcttctcacgtctcgtgatttgatccag
 ||| |||| |||||||| ||||| ||||| |||| ||| |||||||||||||| ||||| ||||| || || || ||||| ||||| ||||| || | |||       | ||   |  ||||  ||    || |  |  |     ||  |   | | | |     | | || |  |   | |||| ||
CTCTATTGCTGGTGCTTCAAAGCTTTTGGCCAACATCCTGTACTCCTACCGTGGGATGGGACTGTCAATTGGTACAATGATTGCTGGATGGGATGAGAAGgtgaattcagcctacatgcctttgattagaagtcttaagtttatgtgctgtgtgctactctatacttaatgtgttctatctcgatctag

upper sequence: EFJ25863 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S2_300V6.1 (Physcomitrella patens), 5'ss of exon 4
TTCTGTTGCCGGTGCTTCCAAGCTCTTGGCAAACACCCTCTACTCCTACCGTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctgttatcttttcttgtttccatctcgccattcccaagttttcttctcacgtctcgt--gatttgatccag------------------------
||| ||  | || ||||| ||| |  | ||||||||||||||||| ||| | || |||||||||| |||||| || ||||| |||||||||||||||||||||   | | |||    ||||   |   ||    |   |   | || || ||      |  | |  ||    ||| ||                        
TTCAGTGACTGGAGCTTCAAAGTTGCTTGCAAACACCCTCTACTCATACAGAGGAATGGGTCTGTTCATGGGCACTATGATTGCTGGCTGGGACGAAACGgtacaagttcttaggacttctaagtg--atgctcctgatgtgaggtcttatttgttgataacattggaaaccatcaaggatgacttcacgactttggacagc

upper sequence: EFJ25863 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S39_347V6.1 (Physcomitrella patens), 5'ss of exon 4
TTCTGTTGCCGGTGCTTCCAAGCTCTTGGCAAACACCCTCTACTCCTACCGTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctgtt-----atcttttcttgtttccatctcgccattcccaa-gttttcttctcacgtctcgtgatttgatccag------------------
||| ||  | || ||||| ||| |  | ||||| ||||| ||||| ||  | || |||||||| || ||||| || ||||| ||||||||||||||||||||||    |  |     |    ||   |    |  || || ||   ||| |  || ||   |   ||   ||  | | |                     
TTCAGTGACTGGAGCTTCAAAGTTGCTTGCAAATACCCTTTACTCATATAGAGGAATGGGTCTATCTATGGGCACTATGATTGCTGGCTGGGACGAAACGgtatttttttcttaaatagtaatttacgcaatcgacttgctatatacaatgaattttttaaaaagctttagagctaagcttacgactttctacaagaaag

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|70669750|gb|DN838327.1|DN838327
EST:     GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACG                         GGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
genomic: GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctg ... tttgatccagGGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
EST: gi|70670787|gb|DN839364.1|DN839364
EST:     GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACG                         GGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
genomic: GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctg ... tttgatccagGGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
EST: gi|169066324|gb|FE473000.1|FE473000
EST:     GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACG                         GGGCCCGCTCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
genomic: GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctg ... tttgatccagGGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
EST: gi|169047645|gb|FE454813.1|FE454813
EST:     GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACG                         GGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
genomic: GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctg ... tttgatccagGGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
EST: gi|169066323|gb|FE472999.1|FE472999
EST:     GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACG                         GGGCCCGCTCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
genomic: GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctg ... tttgatccagGGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
EST: gi|169062114|gb|FE469173.1|FE469173
EST:     GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACG                         GGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
genomic: GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctg ... tttgatccagGGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
EST: gi|169038991|gb|FE447732.1|FE447732
EST:     GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACG                         GGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
genomic: GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctg ... tttgatccagGGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
EST: gi|169053896|gb|FE460987.1|FE460987
EST:     GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACG                         GGGCCCGCTCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
genomic: GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctg ... tttgatccagGGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
EST: gi|70669328|gb|DN837905.1|DN837905
EST:     GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACG                         GGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
genomic: GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctg ... tttgatccagGGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
EST: gi|169062115|gb|FE469174.1|FE469174
EST:     GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACG                         GGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
genomic: GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctg ... tttgatccagGGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
EST: gi|169019358|gb|FE427668.1|FE427668
EST:     GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACG                         GGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
genomic: GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctg ... tttgatccagGGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
EST: gi|169106278|gb|FE507992.1|FE507992
EST:     GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACG                         GGGCCCGCTCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
genomic: GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctg ... tttgatccagGGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
EST: gi|169019357|gb|FE427667.1|FE427667
EST:     GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACG                         GGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
genomic: GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctg ... tttgatccagGGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
EST: gi|169047646|gb|FE454814.1|FE454814
EST:     GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACG                         GGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT
genomic: GTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctg ... tttgatccagGGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACT

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), 30 (downstream exon)
Score: 18

TTCTGTTGCCGGTGCTTCCAAGCTCTTGGCAAACACCCTCTACTCCTACCGTGGCATGGGTCTGTCCATGGGAACCATGATCGCTGGCTGGGACGAAACGgtatgggctg ... tttgatccagGGCCCCGCGCTCTTTTACGTTGATAGCGAAGGTGGAAGAACGAAAGGAACTCTTTTCTCCGTTGGCTCTGGGTCTACTTACGCTTACGGCATTCTCGACA




<











<


<