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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatctctttttctttatgttttcgctggattataaggaggcatggtattgacctttatttgcagCTGGTTCTGATGTGGTGAGCATGAAATGCAAAGCTGAGCGTCGGGACAAGGGATATGTTCTAAATGGAAACAAAATGTGGTGCACAAATGGACCTGTTGC

Basic information

species Selaginella moellendorffii
transcript EFJ09244
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ09244 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: LOC_Os05g03480.4 (Oryza sativa), 3'ss of exon 5
--------------gtatgtat-ctctttttctttatgttttcgctggatt-ataaggagg-----catggtat--tgacctttatttgcagCTGGTTCTGATGTGGTGAGCATGAAATGCAAAGCTGAGCGTCGGGACAAGGGATATGTTCTAAATGGAAACAAAATGTGGTGCACAAATGGACCTGTTGC
              || | | | || |  |  |  |    || || |||||  | ||           ||| ||    |  | || || |||||||||||||||| || || ||||| ||||||||||||      ||    || |||||  | || || || || ||||||||||| || || ||   |||
gtaagtatcatttggtctctttactgtgctgttccagtccttggcaggatttgtgagctaattccttctggcatgcctatttctactttcagCTGGTTCTGATGTTGTCAGTATGAAGTGCAAAGCTGAGAAAGTAGATGGTGGTTATGTCATTAACGGGAATAAGATGTGGTGCACCAACGGGCCATCTGC

upper sequence: EFJ09244 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GRMZM2G381051_T03 (Zea mays), 3'ss of exon 5
--------------gtatgtatctctttttctttatgttttcgctggattataagga-------ggcatggtattgacctttatttgcagCTGGTTCTGATGTGGTGAGCATGAAATGCAAAGCTGAGCGTCGGGACAAGGGATATGTTCTAAATGGAAACAAAATGTGGTGCACAAATGGACCTGTTGC
                     |  ||  |   || |  |   || | | |||||||          |  | |  |||  | || || ||||||| |||||||| || |||||||| ||||||||||||     ||||   || ||||| || ||||| || || ||||||||||| ||||| ||   |||
gtcagtaccattccaaccccgttgctgctctgttcttctccagcagtactataaggttccttctaacgcgttgctgaaatgtaatttcagCTGGCTCTGATGTCGTCAGCATGAAGTGCAAAGCTGAGAAAGTGGACGGTGGCTATGTCCTTAATGGGAATAAGATGTGGTGCACCAATGGCCCGTCTGC

upper sequence: EFJ09244 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GLYMA12G07570.1 (Glycine max), 3'ss of exon 6
-------gtatgtatctctttttctttatgtt----ttcgctggattataaggag---gcatggt-attgacctttatttgcagCTGGTTCTGATGTGGTGAGCATGAAATGCAAAGCTGAGCGTCGGGACAAGGGATATGTTCTAAATGGAAACAAAATGTGGTGCACAAATGGACCTGTTGC
       || || |  |   ||    ||| ||    || |    |||  |||||     ||  || | ||| |||| | |||||||||||||||||| || |||||||||||||| ||||| |||   ||   ||| ||||| || ||||| ||||| |||||||| || ||||| || |||||
gtaagatgtgtgaacttgaattataatatcttgcattttgagatattccaaggaatttacaaagtgaatgaacttt-tctgcagCTGGTTCTGATGTTGTCAGCATGAAATGCAAGGCTGATCGTGTAGATGGGGGCTATGTACTTAATGGGAACAAGATGTGGTGTACTAATGGGCCAGTTGC

upper sequence: EFJ09244 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 6
-------gtatgtatctctttttctttatgtt----ttcgctggattataaggaggcatggtattgacc--tttatttgcagCTGGTTCTGATGTGGTGAGCATGAAATGCAAAGCTGAGCGTCGGGACAAGGGATATGTTCTAAATGGAAACAAAATGTGGTGCACAAATGGACCTGTTGC
       || || |  |   ||    | | ||    || |    |||  |||||        | |||     || | |||||||||||||||||| || |||||||||||||| ||||| |||   ||   ||| ||||| || ||||| ||||| |||||||| || ||||| || |||||
gtaagatgtgtgaacttgaattataatgtcttgcattttgagatattccaaggactttactaagtgaataacttttctgcagCTGGTTCTGATGTTGTCAGCATGAAATGCAAGGCTGATCGTGTAGATGGGGGCTATGTACTTAATGGGAACAAGATGTGGTGTACTAATGGGCCAGTTGC

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|169061890|gb|FE470184.1|FE470184
EST:     TTGATAAGCGGGGAACACGTTGGAGCACTGGTGATGAGCGAACCGAATT                         CTGGTTCTGATGTGGTGAGCATGAAATGCAAAGCTGAGCGTCGGGACAAGG
genomic: TTGATAAGCGGGGAACACGTTGGAGCACTGGTGATGAGCGAACCGAATTgtatgtatct ... ttatttgcagCTGGTTCTGATGTGGTGAGCATGAAATGCAAAGCTGAGCGTCGGGACAAGG




















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: 34 (upstream exon), 35 (downstream exon)
Score: 24

TTGATAAGCGGGGAACACGTTGGAGCACTGGTGATGAGCGAACCGAATTgtatgtatct ... ttatttgcagCTGGTTCTGATGTGGTGAGCATGAAATGCAAAGCTGAGCGTCGGGACAAGGGATATGTTCTAAATGGAAACAAAATGTGGTGCACAAATGGACCTGTTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttatgttttcgctggattataaggaggcatggtattgacctttatttgcagCTGGTTCTGATGTGGTGAGCATGAAATGCAAAGCTGAGCGTCGGGACAAGGGATATGTTCTAAATGGAAACAAAATGTGGTGCACAAATGGACCTGTTGC
                                    tattgac  putative branch site (score: 24)
                                          cctttattt  CT-rich tract
                   attataa  TA-rich tract