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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcaaaacttccaagttagttcttggcattttgtgctaactatcctatattatagAACTGGTATCACAGCAGGCAAAGCAGCAGGAATGAAAGTAGTGGCTGTTCCGTCTCTGCCATCCAAGGCCTCACGTCATTTGTACGCATCTGCTGACCAC

Basic information

species Selaginella moellendorffii
transcript EFJ22483
intron # 5
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|169075504|gb|FE482514.1|FE482514
EST:     AGCCGCTGCCTTGTCATCGAAGACTCTCC                         AACTGGTATCACAGCAGGCAAAGCAGCAGGAATGAAAGTAGTGGCTGTTCC
genomic: AGCCGCTGCCTTGTCATCGAAGACTCTCCgtaagttcaa ... tatattatagAACTGGTATCACAGCAGGCAAAGCAGCAGGAATGAAAGTAGTGGCTGTTCC
EST: gi|169027651|gb|FE434840.1|FE434840
EST:     AAACAACTCGATGCCACTCCAAGCCGCTGCCTTGTCATCGAAGACTCTCC                         AACTGGTATCACAGCAGGCAAAGCAGCAGGAATGAAAGTAGTGGCTGTTCC
genomic: AAACAACTCGATGCCACTCCAAGCCGCTGCCTTGTCATCGAAGACTCTCCgtaagttcaa ... tatattatagAACTGGTATCACAGCAGGCAAAGCAGCAGGAATGAAAGTAGTGGCTGTTCC
EST: gi|169075505|gb|FE482515.1|FE482515
EST:     AAACAACTCGATGCCACTCCAAGCCGCTGCCTTGTCATCGAAGACTCTCC                         AACTGGTATCACAGCAGGCAAAGCAGCAGGAATGAAAGTAGTGGCTGTTCC
genomic: AAACAACTCGATGCCACTCCAAGCCGCTGCCTTGTCATCGAAGACTCTCCgtaagttcaa ... tatattatagAACTGGTATCACAGCAGGCAAAGCAGCAGGAATGAAAGTAGTGGCTGTTCC

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: 34 (upstream exon), 30 (downstream exon)
Score: 13

ATTCTTGGAGGCCGCTAAACAACTCGATGCCACTCCAAGCCGCTGCCTTGTCATCGAAGACTCTCCgtaagttcaa ... tatattatagAACTGGTATCACAGCAGGCAAAGCAGCAGGAATGAAAGTAGTGGCTGTTCCGTCTCTGCCATCCAAGGCCTCACGTCATTTGTACGCATCTGCTGACCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaaaacttccaagttagttcttggcattttgtgctaactatcctatattatagAACTGGTATCACAGCAGGCAAAGCAGCAGGAATGAAAGTAGTGGCTGTTCCGTCTCTGCCATCCAAGGCCTCACGTCATTTGTACGCATCTGCTGACCAC
                                 tgctaac  putative branch site (score: 13)
                                       ctatcct  CT-rich tract
                                        tatcctatattata  TA-rich tract