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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatttttcttttgcgtaccaccacaagttcttaaacacttcccttgtttagTGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCAATCTTGAACGTTAACCCAGTCGATGTTGTTGCAAGGCATGTGGAACAAA

Basic information

species Selaginella moellendorffii
transcript EFJ17159
intron # 3
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|169065121|gb|FE474569.1|FE474569
EST:     ACGAGCTCGGAGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTT                         TGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
genomic: ACGAGCTCGGGGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTTgtgagtattt ... ccttgtttagTGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
EST: gi|169070813|gb|FE480649.1|FE480649
EST:     ACGAGCTCGGGGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTT                         TGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
genomic: ACGAGCTCGGGGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTTgtgagtattt ... ccttgtttagTGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
EST: gi|169049553|gb|FE457723.1|FE457723
EST:     ACGAGCTCGGAGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTT                         TGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
genomic: ACGAGCTCGGGGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTTgtgagtattt ... ccttgtttagTGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
EST: gi|169081337|gb|FE488768.1|FE488768
EST:     GCTGCGGAAGTGGACCATGAGTTT                         TGCAAGGTCTTCACCATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
genomic: GCTGCGGAAGTGGACCATGAGTTTgtgagtattt ... ccttgtttagTGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
EST: gi|169115457|gb|FE516198.1|FE516198
EST:     CGAGCTCGGGGCAGGAG-TTGTGGGAGCTGCGGAAGTGGACCATGAGTTT                         TGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
genomic: CGAGCTCGGGGCAGGAGTTTGT-GGAGCTGCGGAAGTGGACCATGAGTTTgtgagtattt ... ccttgtttagTGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
EST: gi|169045760|gb|FE451187.1|FE451187
EST:     ACGAGCTCGGGGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTT                         TGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCT
genomic: ACGAGCTCGGGGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTTgtgagtattt ... ccttgtttagTGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCT
EST: gi|169088109|gb|FE493361.1|FE493361
EST:     ACGAGCTCGGAGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTT                         TGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
genomic: ACGAGCTCGGGGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTTgtgagtattt ... ccttgtttagTGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
EST: gi|169115458|gb|FE516199.1|FE516199
EST:     ACGAGCTCGGGGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTT                         TGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
genomic: ACGAGCTCGGGGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTTgtgagtattt ... ccttgtttagTGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
EST: gi|169081338|gb|FE488769.1|FE488769
EST:     AGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTT                         TGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
genomic: AGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTTgtgagtattt ... ccttgtttagTGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
EST: gi|169088108|gb|FE493360.1|FE493360
EST:     ACGAGCTCGGAGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTT                         TGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
genomic: ACGAGCTCGGGGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTTgtgagtattt ... ccttgtttagTGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
EST: gi|169070814|gb|FE480650.1|FE480650
EST:     ACGAGCTCGGGGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTT                         TGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA
genomic: ACGAGCTCGGGGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTTgtgagtattt ... ccttgtttagTGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCA

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: 107

GCGCCGTGGATGGGGAATTGCCGGTGTTGAGAGAAATGGTGAAGCACGAGCTCGGGGCAGGAGTTTGTGGAGCTGCGGAAGTGGACCATGAGTTTgtgagtattt ... ccttgtttagTGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCAATCTTGAACGTTAACCCAGTCGATGTTGTTGCAAGGCATGTGGAACAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtatttttcttttgcgtaccaccacaagttcttaaacacttcccttgtttagTGCAAGGTCTTCAACATTGACAAGGAGATGACTGTCGATATGGTTTTCTCAATCTTGAACGTTAACCCAGTCGATGTTGTTGCAAGGCATGTGGAACAAA
                                       cacttcccttgttt  CT-rich tract
     atttttctttt  TA-rich tract