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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCACgtgagtgattcaaagctcctcttagcttgtgagtttgtaatcctgtgcttcttcatgtgtgcag

Basic information

species Selaginella moellendorffii
transcript EFJ20301
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: LOC_Os10g42110.1 (Oryza sativa), 5'ss of exon 6
GTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCACgtgag--tgattcaaagctcctcttagcttgtgag-tttgtaatcctgtgcttcttcatgtgtgcag---------------------------------
| ||||| |   |||||||||| || ||||| ||||| || ||||| ||||||||| | || ||||||||||| ||||| ||||| ||  |  |  || ||| |    |||  ||   ||  | | ||   | | |||||| | | |    |                                  
GCAGAGTCATCGCCGAGAGTGTGATATATAGCTATGGAACAGTTCTTTTGGATCTTTTGAGTGGGAAGCACATACCTCCTAGCCATgtatgcttcgtttaaatccttacttttctcaagaaatatatatatcagcgcttctccttatcattactctcatatcctggataacactgcatctgtattt

upper sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GRMZM2G169080_T01 (Zea mays), 5'ss of exon 6
GTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCACgtgag--tgattcaaagctcctctt--agcttgtgagtttgtaatc-ctgtgcttcttcatgtgtgcag-------------------------------
| |||||||  ||||||||||| || ||||| ||||| ||||| || ||||||||| | ||||| || ||||||||||| || || ||  |  | |||      | |||    ||  | |   | || |||| ||  ||   | | ||  |   |                               
GCAGAGTAATTCCCGAGAGTGTGATATATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgtatgcttcatttgctttttctcaagaagaatatatttctggaatctcttagcaattccctgcattttggtacaatgtttgcaatgatggactgctgtgt

upper sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GRMZM2G054634_T02 (Zea mays), 5'ss of exon 6
GTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCACgtgagtgattcaaagctcctctt-----agcttgtgagtttgtaatcctgtgcttcttcatgtgtgcag---------------------------------
| |||||||  || |||||||| || ||||| ||||| ||||| || ||||||||| | ||||| || ||||||||||| || || ||   || |||   |||  | ||     ||  | ||  | || |||         |    |   ||||                                  
GCAGAGTAATTCCGGAGAGTGTGATCTATAGCTATGGAACTGTCCTGTTGGATCTTTTGAGCGGAAAACACATTCCTCCTAGTCATgta--tgcttccttgctttttttcaagaagaatatgtttctggaatatctcttagcaatttccttgcatcacactgccttttggtacaatgtttgtgatgat

upper sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GLYMA05G06140.1 (Glycine max), 5'ss of exon 6
GTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCACgtgagt-gattcaaagctcctcttagcttgtgagtt--tgtaatcctgtgcttcttcatgtgtgcag---------------------------------
| ||  |||  || |||||||| || || |||||||| ||||||||  |||||||||| || || ||||| |||||||||||||| ||  || |  |   | |       ||  | ||  ||  | |||   |||||||  |  | | |   |                                 
GCAGGATAATCCCAGAGAGTGTGATCTACAGTTATGGAACTGTTCTTCTGGATCTTCTAAGTGGCAAGCATATTCCTCCAAGCCATgtatgttgcgttctaacaaaatccagtctctgcattcatataagaatgtgctttatgctttattttgtttcataaggcattataagcattctatgttacc

upper sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GLYMA17G16420.1 (Glycine max), 5'ss of exon 6
GTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCACgtgagtg--attcaaagctcctcttagcttgtgagtt--tgtaatcctgtgcttcttcatgtgtgcag---------------------------------
| ||  |||  || |||||||| || || |||||||| ||||||||  |||||||| | || || |||||||||||||||||||| ||  ||    ||| |||    | | ||  | ||  ||  | |||     |||||  |  | | | | |                                 
GCAGGATAATCCCAGAGAGTGTGATCTACAGTTATGGAACTGTTCTTCTGGATCTTTTAAGTGGCAAGCACATTCCTCCAAGCCATgtatgttgcgttctaagaaaat-tcagtctctgcattcatataagaacatgctttatgttttattctgtttcataagacatgataagcattctatgttacc

upper sequence: EFJ20301 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: AT1G50990.1 (Arabidopsis thaliana), 5'ss of exon 5
GTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCACgtgagtgattcaaagc--tcctcttagcttgtgagtttgta-atcctgtgcttct----tcatgtgtgcag---------------------
|||   |||  || ||||||||| | |  || | ||| ||  |||| |||||||||||||| ||||| |||||||||||||| || ||||||||   |||    ||   ||| ||||  | || ||      | |  |||     | | ||||                         
GTACGTTAATTCCAGAGAGTGTTGTCTTCAGCTTTGGGACGTTTCTTTTGGATCTTCTTAGTGGGAAACACATTCCTCCAAGTCATgtgagtgacaaaaattcatctagttaccttgcaaattggtttggtttctatttccaaaatgacgtgtcttttattgcactctctttattcag

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|169075974|gb|FE480982.1|FE480982
EST:     GTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCAC                         GCTTTAGATTTGATACGTGGGAAGAACATTTTGATGCTTATGGACTCATAC
genomic: GTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCACgtgagtgatt ... atgtgtgcagGCTTTAGATTTGATACGTGGGAAGAACATTTTGATGCTTATGGACTCATAC
EST: gi|169097974|gb|FE498771.1|FE498771
EST:     GTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCAC                         GCTTTAGATTTGATACGTGGGAAGAACATTTTGATGCTTATGGACTCATAC
genomic: GTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCACgtgagtgatt ... atgtgtgcagGCTTTAGATTTGATACGTGGGAAGAACATTTTGATGCTTATGGACTCATAC
EST: gi|169082053|gb|FE490565.1|FE490565
EST:     GTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCAC                         GCTTTAGATTTGATACGTGGGAAGAACATTTTGATGCTTATGGACTCATAC
genomic: GTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCACgtgagtgatt ... atgtgtgcagGCTTTAGATTTGATACGTGGGAAGAACATTTTGATGCTTATGGACTCATAC

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: 30 (upstream exon), 35 (downstream exon)
Score: 18

GTAGAGTAACACCCGAGAGTGTTATTTATAGTTATGGTACTGTTCTCTTGGATCTTCTTAGCGGGAAGCACATTCCTCCAAGCCACgtgagtgatt ... atgtgtgcagGCTTTAGATTTGATACGTGGGAAGAACATTTTGATGCTTATGGACTCATACCTGGAAGGCCAGTTTTCCAACGACGATGGAACCGAGCTCGTGCGGTTAG




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