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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgactattcgtaagcttgagtgtttacactttttgcaacagATATCAAGACTTATCTTCACAAACAATGGTCTGGGCTTATTAGCGCTCGCTTCTAGTGCAGTTCACAAGGTTTGGAAATGGTCTCGCAATCCACTTGGAA

Basic information

species Selaginella moellendorffii
transcript EFJ37833
intron # 18
splice site 3'
intron type U2

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|169031531|gb|FE438996.1|FE438996
EST:     CCTCTCATTGTCGTGCATTAAAGCTACCAGATACTCTACCAGCAAGCAAG                         ATATCAAGACTTATCTTCACAAACAATGGTCTGGGCTTATTAGCGCTCGCT
genomic: CCTCTCATTGTCGTGCATTAAAGCTACCAGATACTCTACCAGCAAGCAAGgtacttgact ... tttgcaacagATATCAAGACTTATCTTCACAAACAATGGTCTGGGCTTATTAGCGCTCGCT
EST: gi|169048259|gb|FE456246.1|FE456246
EST:     CCTCTCATTGTCGTGCATTAAAGCTACCAGATACTCTACCAGCAAGCAAG                         ATATCAAGACTTATCTTCACAAACAATGGTCTGGGCTTATTAGCGCTCGCT
genomic: CCTCTCATTGTCGTGCATTAAAGCTACCAGATACTCTACCAGCAAGCAAGgtacttgact ... tttgcaacagATATCAAGACTTATCTTCACAAACAATGGTCTGGGCTTATTAGCGCTCGCT
EST: gi|169026734|gb|FE436308.1|FE436308
EST:     CCTCTCATTGTCGTGCATTAAAGCTACCAGATACTCTACCAGCAAGCAAG                         ATATCAAGACTTATCTTCACAAACAATGGTCTGGGCTTATTAGCGCTCGCT
genomic: CCTCTCATTGTCGTGCATTAAAGCTACCAGATACTCTACCAGCAAGCAAGgtacttgact ... tttgcaacagATATCAAGACTTATCTTCACAAACAATGGTCTGGGCTTATTAGCGCTCGCT
EST: gi|169110734|gb|FE514183.1|FE514183
EST:     CCTCTCATTGTCGTGCATTAAAGCTACCAGATACTCTACCAGCAAGCAAG                         ATATCAAGACTTATCTTCACAAACAATGGTCTGGGCTTATTAGCGCTCGCT
genomic: CCTCTCATTGTCGTGCATTAAAGCTACCAGATACTCTACCAGCAAGCAAGgtacttgact ... tttgcaacagATATCAAGACTTATCTTCACAAACAATGGTCTGGGCTTATTAGCGCTCGCT

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: 29 (upstream exon), 35 (downstream exon)
Score: 5

AACTACAGACGACTCAAACAAACTGTGGAAGCTAACTGAAATTGTGGAACCCTCTCATTGTCGTGCATTAAAGCTACCAGATACTCTACCAGCAAGCAAGgtacttgact ... tttgcaacagATATCAAGACTTATCTTCACAAACAATGGTCTGGGCTTATTAGCGCTCGCTTCTAGTGCAGTTCACAAGGTTTGGAAATGGTCTCGCAATCCACTTGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacttgactattcgtaagcttgagtgtttacactttttgcaacagATATCAAGACTTATCTTCACAAACAATGGTCTGGGCTTATTAGCGCTCGCTTCTAGTGCAGTTCACAAGGTTTGGAAATGGTCTCGCAATCCACTTGGAA
           acttgac  putative branch site (score: 5)
                                        cacttttt  putative PPT
                                         acttttt  TA-rich tract