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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcttcgggctcgatttttatctcttactcactgttgtgtgggttttcttcgtcagAACAAAGCTCTTACGTGCCAACGTACACTTTCTATCATCCCCGATGGTCAGGGGCACGACTGGAACAGTGATCGTTCTCACAACACCGGATGCCCAGCGA

Basic information

species Selaginella moellendorffii
transcript EFJ23286
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23286 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA12G01920.1 (Glycine max), 3'ss of exon 2
---------------------------------gtaagttcttcgggctcgatttttatctcttactcactgttgtgtgggttttct------tcgtcagAACAAAGCTCTTACGTGCCAACGTACACTTTCTATCATCCCCGATGGTCAGGGGCACGACTGGAACAGTGATCGTTCTCACAACACCGGATGCCCAGCGA
                                  |  |    |  || | |||   ||  | |    |    |||| |   |||| |         | ||   |||  |    || || || || || ||||| ||  | || ||       || || ||||||||||| || ||||||||||| || ||||||||||| 
tctatgttatttaataattccatcaattttgttttgggcaagtgaggtttgatgaatacttatattgcttgtttgtattatttttttaaaaaaaaattagGGAAAAATTACGCCGAGCAAATGTGCAATTTCTTTCTGCACCAATCAAGGATGGGACTACTGGAACAGTTATAGTTCTCACAACTCCAGATGCCCAGCGC
















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|169050656|gb|FE457826.1|FE457826
EST:     GTAGCCATGACTGGGAGTGTCGGCAAAGATCCATTAGGCGATTTTTACAG                         AACAAAGCTCTTACGTGCCAACGTACACTTTCTATCATCCCCGATGGTCAG
genomic: GTAGCCATGACTGGGAGTGTCGGCAAAGATCCATTAGGCGATTTTTACAGgtaagttctt ... tcttcgtcagAACAAAGCTCTTACGTGCCAACGTACACTTTCTATCATCCCCGATGGTCAG
EST: gi|169051308|gb|FE459192.1|FE459192
EST:     GTAGCCATGACTGGGAGTGTCGGCAAAGATCCATTAGGCGATTTTTACAG                         AACAAAGCTCTTACGTGCCAACGTACACTTTCTATCATCCCCGATGGTCAG
genomic: GTAGCCATGACTGGGAGTGTCGGCAAAGATCCATTAGGCGATTTTTACAGgtaagttctt ... tcttcgtcagAACAAAGCTCTTACGTGCCAACGTACACTTTCTATCATCCCCGATGGTCAG

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: 21 (upstream exon), 31 (downstream exon)
Score: 4

TCTCGAACACACTCGTCGCATTAGCGAGGCTCGGGACGGGAAGGATCAACGTAGCCATGACTGGGAGTGTCGGCAAAGATCCATTAGGCGATTTTTACAGgtaagttctt ... tcttcgtcagAACAAAGCTCTTACGTGCCAACGTACACTTTCTATCATCCCCGATGGTCAGGGGCACGACTGGAACAGTGATCGTTCTCACAACACCGGATGCCCAGCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcgggctcgatttttatctcttactcactgttgtgtgggttttcttcgtcagAACAAAGCTCTTACGTGCCAACGTACACTTTCTATCATCCCCGATGGTCAGGGGCACGACTGGAACAGTGATCGTTCTCACAACACCGGATGCCCAGCGA
                        tactcac  putative branch site (score: 4)
                                          ttttcttcgtc  putative PPT
            atttttatctctta  TA-rich tract