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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatacatcttcttctacttgatattcaactgacctctagatgttctacagGAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGACTGGCATTTCGACCATCGACGTTATGAACTCCATAGCCCGAGGTCAGAA

Basic information

species Selaginella moellendorffii
transcript EFJ11911
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 6
--------------------gtgatacatcttcttctact-tgatattcaactgacctctagatgttc----------------tacagGAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGACTGGCATTTCGACCATCGACGTTATGAACTCCATAGCCCGAGGTCAGAA
                     | || |||    ||  | | || | |  | |  |    ||||| ||                 | ||||||| || ||||| || || ||||| || ||||| |||||||||||||||||||| || || || || || |||||||| || || ||||| ||||||||
gtaggtgctagctgcttttgattattcataagatttgattatggtgtaaatcaaatgcttagattttgacatcgggtttgctggtgcagGAAGTTCTATCAATCCCAGTGAACGAACATACCCTGAAGAAATGATTCAGACTGGGATATCTACAATTGATGTTATGAATTCTATTGCCCGTGGTCAGAA
















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|169049346|gb|FE458244.1|FE458244
EST:     TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTATCTAGACATTTCTG                         GAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
genomic: TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTGgtgatacatc ... tgttctacagGAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
EST: gi|169092669|gb|FE496263.1|FE496263
EST:     TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTG                         GAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
genomic: TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTGgtgatacatc ... tgttctacagGAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
EST: gi|169108146|gb|FE512519.1|FE512519
EST:     TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTG                         GAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
genomic: TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTGgtgatacatc ... tgttctacagGAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
EST: gi|169035381|gb|FE444319.1|FE444319
EST:     TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTG                         GAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
genomic: TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTGgtgatacatc ... tgttctacagGAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
EST: gi|169036846|gb|FE443832.1|FE443832
EST:     CGATCTTGGCAGAAGCTTACCTAGACATTTCTG                         GAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
genomic: CGATCTTGGCAGAAGCTTACCTAGACATTTCTGgtgatacatc ... tgttctacagGAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
EST: gi|169104894|gb|FE509038.1|FE509038
EST:     TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTG                         GAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
genomic: TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTGgtgatacatc ... tgttctacagGAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
EST: gi|169049517|gb|FE458740.1|FE458740
EST:     TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTG                         GAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
genomic: TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTGgtgatacatc ... tgttctacagGAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
EST: gi|169059085|gb|FE468230.1|FE468230
EST:     TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTG                         GAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
genomic: TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTGgtgatacatc ... tgttctacagGAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
EST: gi|169088665|gb|FE491525.1|FE491525
EST:     TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTATCTAGACATTTCTG                         GAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
genomic: TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTGgtgatacatc ... tgttctacagGAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
EST: gi|169057426|gb|FE465730.1|FE465730
EST:     TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTATCTAGACATTTCTG                         GAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA
genomic: TATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTGgtgatacatc ... tgttctacagGAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGA

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), 31 (downstream exon)
Score: 19

CCGGTGTCCATAGATATGCTCGGTAGAATCTTTAATGGTTCTGGGAAGCCTATCGATAACGGGCCCCCGATCTTGGCAGAAGCTTACCTAGACATTTCTGgtgatacatc ... tgttctacagGAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGACTGGCATTTCGACCATCGACGTTATGAACTCCATAGCCCGAGGTCAGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatacatcttcttctacttgatattcaactgacctctagatgttctacagGAAGCTCCATCAACCCAAGCGAACGTACGTACCCGGAAGAAATGATTCAGACTGGCATTTCGACCATCGACGTTATGAACTCCATAGCCCGAGGTCAGAA
                               aactgac  putative branch site (score: 19)
                         ttgatatt  TA-rich tract