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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgaatccacatcgtttcgttacgaaacttactttcgcttcttctgttcatagATTCCGAGCACGGAGATTGATAAGTCGGCCAATGACAAGTTTTTCTTTCATTGGGATCAAGACTCCAAGCAGTTCACG

Basic information

species Selaginella moellendorffii
transcript EFJ15163
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|169113991|gb|FE516462.1|FE516462
EST:     GGCAGTATCTCCTCTTCGCGGCCGAGCCTTACGAGATTATCGCCTTCAAG                         ATTCCGAGCACGGAGATTGATAAGTCGGCCAATGACAAGTTTTTCTTTCAT
genomic: GGCAGTATCTCCTCTTCGCGGCCGAGCCTTACGAGATTATCGCCTTCAAGgtaatgaatc ... ctgttcatagATTCCGAGCACGGAGATTGATAAGTCGGCCAATGACAAGTTTTTCTTTCAT
EST: gi|169113992|gb|FE516463.1|FE516463
EST:     GGCAGTATCTCCTCTTCGCGGCCGAGCCTTACGAGATTATCGCCTTCAAG                         ATTCCGAGCACGGAGATTGATAAGTCGGCCAATGACAAGTTTTTCTTTCAT
genomic: GGCAGTATCTCCTCTTCGCGGCCGAGCCTTACGAGATTATCGCCTTCAAGgtaatgaatc ... ctgttcatagATTCCGAGCACGGAGATTGATAAGTCGGCCAATGACAAGTTTTTCTTTCAT
EST: gi|169045847|gb|FE453081.1|FE453081
EST:     GGCAGTATCTCCTCTTCGCGGCCGAGCCTTACGAGATTATCGCCTTCAAG                         ATTCCGAGCACGGAGATTGATAAGTCGGCCAATGACAAGTTTTTCTTTCAT
genomic: GGCAGTATCTCCTCTTCGCGGCCGAGCCTTACGAGATTATCGCCTTCAAGgtaatgaatc ... ctgttcatagATTCCGAGCACGGAGATTGATAAGTCGGCCAATGACAAGTTTTTCTTTCAT

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: 30 (upstream exon), 30 (downstream exon)
Score: 12

CCGTTTGATGTCCTCGTTTGAGCAGAAGCTGGAACCGAACGAAAAGGAGTGGCAGTATCTCCTCTTCGCGGCCGAGCCTTACGAGATTATCGCCTTCAAGgtaatgaatc ... ctgttcatagATTCCGAGCACGGAGATTGATAAGTCGGCCAATGACAAGTTTTTCTTTCATTGGGATCAAGACTCCAAGCAGTTCACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgaatccacatcgtttcgttacgaaacttactttcgcttcttctgttcatagATTCCGAGCACGGAGATTGATAAGTCGGCCAATGACAAGTTTTTCTTTCATTGGGATCAAGACTCCAAGCAGTTCACG
                           aacttac  putative branch site (score: 12)
                             cttactttcgcttctt  CT-rich tract
                          aaactta  TA-rich tract