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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagacatttatatcttgtctcgtggaaaaccattgattgtttcttttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGAACAAAAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTG

Basic information

species Selaginella moellendorffii
transcript EFJ30330
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 15
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 14
-----------------------gtgagagacatttatatcttgtctcgtggaaaaccattgattgtttcttttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGAACAAAAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTG
                       || | | ||| ||| |       |  |  |  | |||  | | | || | |  || ||||  ||||    ||||||||  | | |||||   | || |||   ||  |||||||||| ||||||||| |||| ||||| ||||||||||| || ||||
gttattcctaacttccctatgatgtca-atacaattaaaatcgccattttacactaacat--actatatcctgtactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTG
















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|169116507|gb|FE517532.1|FE517532
EST:     AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG                         GCATTGGAGGGATTCTATGAGCATTATGATCCGAACTTTATTTCAATCCGA
genomic: AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
EST: gi|169094896|gb|FE491630.1|FE491630
EST:     AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG                         GCATTGGAGGGATTCTATGAGCATTATGATCCGAACTTTATTTCAATCCGA
genomic: AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
EST: gi|169105223|gb|FE504895.1|FE504895
EST:     AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG                         GCATTGGAGGGATTCTATGAGCATTATGATCCGAACTTTATTTCAATCCGA
genomic: AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
EST: gi|169034854|gb|FE444043.1|FE444043
EST:     AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG                         GCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
genomic: AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
EST: gi|169075917|gb|FE482836.1|FE482836
EST:     AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG                         GCATTGGAGGGATTCTATGAGCATTATGATCCGAACTTTATTTCAATCCGA
genomic: AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
EST: gi|169058960|gb|FE467728.1|FE467728
EST:     AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG                         GCATTGGAGGGATTCTATGAGCATTATGATCCGAACTTTATTTCAATCCGA
genomic: AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
EST: gi|169116508|gb|FE517533.1|FE517533
EST:     AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG                         GCATTGGAGGGATTCTATGAGCATTATGATCCGAACTTTATTTCAATCCGA
genomic: AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
EST: gi|169055454|gb|FE465852.1|FE465852
EST:     AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG                         GCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
genomic: AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
EST: gi|169074665|gb|FE480895.1|FE480895
EST:     AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG                         GCATTGGAGGGATTCTATGAGCATTATGATCCGAACTTTATTTCAATCCGA
genomic: AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
EST: gi|169026425|gb|FE435778.1|FE435778
EST:     AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG                         GCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
genomic: AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
EST: gi|169083647|gb|FE495380.1|FE495380
EST:     AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG                         GCATTGGAGGGATTCTATGAGCATTATGATCCGAACTTTATTTCAATCCGA
genomic: AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
EST: gi|169038845|gb|FE446988.1|FE446988
EST:     AAGTATACCCAG                         GCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
genomic: AAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
EST: gi|169067637|gb|FE475314.1|FE475314
EST:     AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG                         GCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
genomic: AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
EST: gi|169047686|gb|FE454854.1|FE454854
EST:     AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG                         GCATTGGAGGGATTCTATGAGCATTATGATCCGAACTTTATTTCAATCCGA
genomic: AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
EST: gi|169045568|gb|FE452529.1|FE452529
EST:     AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAG                         GCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA
genomic: AGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGA

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: 14

GTGTTTTGGGGACTTGACAAGAAGCTTGCGCAAAGAAAGCATTTCCCTGCTGTCAACTGGCTGATATCTTATTCGAAGTATACCCAGgtgagagaca ... tttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGAACAAAAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagacatttatatcttgtctcgtggaaaaccattgattgtttcttttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGAACAAAAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTG
                                            ttttgat  putative branch site (score: 14)
                                     ttgtttctttt  CT-rich tract
      atttatatctt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagagacatttatatcttgtctcgtggaaaaccattgattgtttcttttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGAACAAAAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA