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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcactctatcgtcaacattaagaccaggagctcatttttttggatttctcttttctttttcttaagATTCTCATTGACAACATCAAGAACTTTGCTCCCATTATTTACACTCCTACAGTTGGTCTCGTGTGCCAGAACTACAGTGGTCTTTTCAGACGTCCGCGAG

Basic information

species Selaginella moellendorffii
transcript EFJ19450
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ19450 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT4G00570.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagcactct--atcgtcaacattaagac-caggagctcatttttttgg-atttctcttttctttttcttaagATTCTCATTGACAACATCAAGAACTTTGCTCCCATTATTTACACTCCTACAGTTGGTCTCGTGTGCCAGAACTACAGTGGTCTTTTCAGACGTCCGCGAG
|| ||   | |      | || | |    | ||    | ||| | |  |  ||      |    || |||  || |||| ||||| ||||||||  | ||||| |||||||| ||||||||||| ||||| || || || ||||||||   |||| | |  ||| | ||  |||
gtgagtctttttggctctaaatactgtcccacattgacacatctctgagacatcataactcatcttctctgcagGTTCTTATTGATAACATCAAAGATTTTGCCCCCATTATATACACTCCTACGGTTGGACTTGTTTGTCAGAACTATTCTGGTTTGTATAGAAGACCAAGAG
















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|169026052|gb|FE434469.1|FE434469
EST:     GGAGAATTCTTAACAGGCTTCATGACCGCAACGAAACTCTGTATTACAAA                         ATTCTCATTGACAACATCAAGAACTTTGCTCCCATTATTTACACTCCTACA
genomic: GGAGAATTCTTAACAGGCTTCATGACCGCAACGAAACTCTGTATTACAAAgtaagcactc ... ttttcttaagATTCTCATTGACAACATCAAGAACTTTGCTCCCATTATTTACACTCCTACA
EST: gi|169088831|gb|FE494395.1|FE494395
EST:     GGAGAATTCTTAACAGGCTTCATGACCGCAACGAAACTCTGTATTACAAA                         ATTCTCATTGACAACATCAAGAACTTTGCTCCCATTATTTACACTCCTACA
genomic: GGAGAATTCTTAACAGGCTTCATGACCGCAACGAAACTCTGTATTACAAAgtaagcactc ... ttttcttaagATTCTCATTGACAACATCAAGAACTTTGCTCCCATTATTTACACTCCTACA
EST: gi|169073338|gb|FE481102.1|FE481102
EST:     GGAGAATTCTTAACAGGCTTCATGACCGCAACGAAACTCTGTATTACAAA                         ATTCTCATTGACAACATCAAGAACTTTGCTCCCATTATTTACACTCCTACA
genomic: GGAGAATTCTTAACAGGCTTCATGACCGCAACGAAACTCTGTATTACAAAgtaagcactc ... ttttcttaagATTCTCATTGACAACATCAAGAACTTTGCTCCCATTATTTACACTCCTACA
EST: gi|169022198|gb|FE431807.1|FE431807
EST:     GGAGAATTCTTAACAGGCTTCATGACCGCAACGAAACTCTGTATTACAAA                         ATTCTCATTGACAACATCAAGAACTTTGCTCCCATTATTTACACTCCTACA
genomic: GGAGAATTCTTAACAGGCTTCATGACCGCAACGAAACTCTGTATTACAAAgtaagcactc ... ttttcttaagATTCTCATTGACAACATCAAGAACTTTGCTCCCATTATTTACACTCCTACA
EST: gi|169056297|gb|FE464107.1|FE464107
EST:     GGAGAATTCTTAACAGGCTTCATGACCGCAACGAAACTCTGTATTACAAA                         ATTCTCATTGACAACATCAAGAACTTTGCTCCCATTATTTACACTCCTACA
genomic: GGAGAATTCTTAACAGGCTTCATGACCGCAACGAAACTCTGTATTACAAAgtaagcactc ... ttttcttaagATTCTCATTGACAACATCAAGAACTTTGCTCCCATTATTTACACTCCTACA

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), 34 (downstream exon)
Score: 60

GGAAAGAACCACCAGAGATGGTCCCAGAGATATGTCCGCATTGGCGAAGTGGAGAATTCTTAACAGGCTTCATGACCGCAACGAAACTCTGTATTACAAAgtaagcactc ... ttttcttaagATTCTCATTGACAACATCAAGAACTTTGCTCCCATTATTTACACTCCTACAGTTGGTCTCGTGTGCCAGAACTACAGTGGTCTTTTCAGACGTCCGCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaacattaagaccaggagctcatttttttggatttctcttttctttttcttaagATTCTCATTGACAACATCAAGAACTTTGCTCCCATTATTTACACTCCTACAGTTGGTCTCGTGTGCCAGAACTACAGTGGTCTTTTCAGACGTCCGCGAG
                   ctcatttttttggatt  CT-rich tract
                                       ttttctttttcttaa  TA-rich tract