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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttcgacctttgacggatcttcgtgactcatactattgtcttgcagTGTTAAACTTGAGGAGGTTCAGGCTGCAAGGGATCATCTGGTAGTCTATGAACGGGAAAATGCCTTGCAGTCCATCACAGTTTTCAAACTACCTCCGGCA

Basic information

species Selaginella moellendorffii
transcript EFJ22335
intron # 4
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|169088154|gb|FE496487.1|FE496487
EST:     CCTGTCAATGACGTTTCGTCCACAACGCTGGTACTCCCTCACCGGCCGAG                         TGTTAAACTTGAGGAGGTTCAGGCTGCAAGGGATCATCTGGTAGTCTATGA
genomic: CCTGTCAATGACGTTTCGTCCACAACGCTGGTACTCCCTCACCGACCGAGgtttgttcga ... tgtcttgcagTGTTAAACTTGAGGAGGTTCAGGCTGCAAGGGATCATCTGGTAGTCTATGA
EST: gi|169062605|gb|FE470275.1|FE470275
EST:     CCTGTCAATGACGTTTCGTCCACAACGCTGGTACTCCCTCACCGACCGAG                         TGTTAAACTTGAGGAGGTTCAGGCTGCAAGGGATCATCTGGTAGTCTATGA
genomic: CCTGTCAATGACGTTTCGTCCACAACGCTGGTACTCCCTCACCGACCGAGgtttgttcga ... tgtcttgcagTGTTAAACTTGAGGAGGTTCAGGCTGCAAGGGATCATCTGGTAGTCTATGA
EST: gi|169037306|gb|FE445475.1|FE445475
EST:     CCTGTCAATGACGTTTCGTCCACAACGCTGGTACTCCCTCACCGACCGAG                         TGTTAAACTTGAGGAGGTTCAGGCTGCAAGGGATCATCTGGTAGTCTATGA
genomic: CCTGTCAATGACGTTTCGTCCACAACGCTGGTACTCCCTCACCGACCGAGgtttgttcga ... tgtcttgcagTGTTAAACTTGAGGAGGTTCAGGCTGCAAGGGATCATCTGGTAGTCTATGA
EST: gi|169026151|gb|FE435335.1|FE435335
EST:     CCTGTCAATGACGTTTCGTCCACAACGCTGGTACTCCCTCACCGACCGAG                         TGTTAAACTTGAGGAGGTTCAGGCTGCAAGGGATCATCTGGTAGTCTATGA
genomic: CCTGTCAATGACGTTTCGTCCACAACGCTGGTACTCCCTCACCGACCGAGgtttgttcga ... tgtcttgcagTGTTAAACTTGAGGAGGTTCAGGCTGCAAGGGATCATCTGGTAGTCTATGA

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), 35 (downstream exon)
Score: 6

TTATCACCAAGAGGACGGATGATACTTACAACTCCGAGCTTTATGTGTGTCCTGTCAATGACGTTTCGTCCACAACGCTGGTACTCCCTCACCGACCGAGgtttgttcga ... tgtcttgcagTGTTAAACTTGAGGAGGTTCAGGCTGCAAGGGATCATCTGGTAGTCTATGAACGGGAAAATGCCTTGCAGTCCATCACAGTTTTCAAACTACCTCCGGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgttcgacctttgacggatcttcgtgactcatactattgtcttgcagTGTTAAACTTGAGGAGGTTCAGGCTGCAAGGGATCATCTGGTAGTCTATGAACGGGAAAATGCCTTGCAGTCCATCACAGTTTTCAAACTACCTCCGGCA
                ctttgac  putative branch site (score: 6)
                                            ttgtctt  putative PPT
                                      atactatt  TA-rich tract