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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtgctcgttttctcgatttctcttctcccgaatttcatacattttctcttggtagTGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCTTCATGGGATACAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAA

Basic information

species Selaginella moellendorffii
transcript EFJ30452
intron # 1
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|70671032|gb|DN839609.1|DN839609
EST:     ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAG                         TGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCT
genomic: ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAGgtatgtgtgc ... ctcttggtagTGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCT
EST: gi|169062675|gb|FE470345.1|FE470345
EST:     ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAG                         TGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCT
genomic: ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAGgtatgtgtgc ... ctcttggtagTGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCT
EST: gi|169099960|gb|FE503448.1|FE503448
EST:     ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAGGTAG                      
genomic: ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGC-AA---AGgtatgtgtgc ... ctcttgg
EST: gi|70670339|gb|DN838916.1|DN838916
EST:     ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAG                         TGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCT
genomic: ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAGgtatgtgtgc ... ctcttggtagTGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCT
EST: gi|169074641|gb|FE481196.1|FE481196
EST:     ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAG                         TGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCT
genomic: ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAGgtatgtgtgc ... ctcttggtagTGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCT
EST: gi|169036555|gb|FE444126.1|FE444126
EST:     ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAG                         TGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCT
genomic: ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAGgtatgtgtgc ... ctcttggtagTGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCT
EST: gi|169054887|gb|FE463491.1|FE463491
EST:     ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAG                         TGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCT
genomic: ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAGgtatgtgtgc ... ctcttggtagTGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCT
EST: gi|169063852|gb|FE471207.1|FE471207
EST:     ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAG                         TGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCT
genomic: ATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAGgtatgtgtgc ... ctcttggtagTGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCT

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), 35 (downstream exon)
Score: 73

GAGCGCGGCGCCGCCATGAGCCACCGGAAGTTCGAGCATCCCCGGCATGGATCTCTGGGCTTCCTTCCCAGGAAGCGTGCCCAGCGCCATCGCGGCAAAGgtatgtgtgc ... ctcttggtagTGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCTTCATGGGATACAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctcgttttctcgatttctcttctcccgaatttcatacattttctcttggtagTGAAATCCTTCCCTCGGGATGATCCTACGAAGAAGCCCCATTTGACAGCCTTCATGGGATACAAGGCCGGCATGACTCATATCGTCCGGGAGGTCGAGAA
                                       cattttctctt  CT-rich tract
                              aatttcatacatttt  TA-rich tract