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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCCAATTCTACCATCTCTTCGCCAAGGAGTTGGCTTCTCACAAGCCTCTCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAGgtaatccatttcttctctctcgctcccgcggagcagatcttacgtgtctcctttttctctctcag

Basic information

species Selaginella moellendorffii
transcript EFJ04796
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ04796 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G025242_T02 (Zea mays), 5'ss of exon 4
CATCCAATTCTACCATCTCTTCGCCAAGGAGTTGGCTTCTCACAAGCCTCTCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAGgtaatccatttcttctctctcgctcccgcggagcagatcttacgtgtctcctttttctctctcag------------------------------------
  | |  ||||||||  | || || || ||| ||||  ||||||||||||| || |||||| |||||||||| ||  | ||||| ||||| |||||||||||| | ||| || ||||   |      || |    | || | | |      || |     ||                                       
GGTTCTCTTCTACCACTTGTTTGCTAAAGAGCTGGCACCTCACAAGCCTCTTGCAAAGTTCTTGTGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAGgta-tacatatcatctcgacctgaatggccgtttggttccttcttcagcttttctgaaagctttatttatataactttgcacgagtgattctcttgatttc
















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|169109775|gb|FE511846.1|FE511846
EST:     TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAG                         GGCATTGTCATGCAAATTCTCGCATCCGCAGGCGTGATCCAGAGGCAAAAG
genomic: TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAGgtaatccatt ... tctctctcagGGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAG
EST: gi|169107369|gb|FE508290.1|FE508290
EST:     TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAG                         GGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAG
genomic: TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAGgtaatccatt ... tctctctcagGGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAG
EST: gi|169039777|gb|FE449439.1|FE449439
EST:     TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAG                         GGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAG
genomic: TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAGgtaatccatt ... tctctctcagGGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAG
EST: gi|169099932|gb|FE503420.1|FE503420
EST:     TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAG                         GGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAG
genomic: TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAGgtaatccatt ... tctctctcagGGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAG
EST: gi|169107370|gb|FE508291.1|FE508291
EST:     TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAG                         GGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAG
genomic: TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAGgtaatccatt ... tctctctcagGGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAG
EST: gi|169045407|gb|FE452264.1|FE452264
EST:     TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAG                         GGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAG
genomic: TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAGgtaatccatt ... tctctctcagGGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAG
EST: gi|169109774|gb|FE511845.1|FE511845
EST:     TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAG                         GGCATTGTCATGCAAATTCTCGCATCCGCAGGCGTGATCCAGAGGCAAAAG
genomic: TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAGgtaatccatt ... tctctctcagGGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAG
EST: gi|169045408|gb|FE452265.1|FE452265
EST:     TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAG                         GGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAG
genomic: TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAGgtaatccatt ... tctctctcagGGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAG
EST: gi|169072441|gb|FE483837.1|FE483837
EST:     TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAG                         GGCATTGTCATGCAAATTCTCGCATCCGCAGGCGTGATCCAGAGGCAAAAG
genomic: TCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAGgtaatccatt ... tctctctcagGGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAG

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), 34 (downstream exon)
Score: 7

CATCCAATTCTACCATCTCTTCGCCAAGGAGTTGGCTTCTCACAAGCCTCTCGCGAAGTTCCTGTGCATCAAGGGAGTGGTCTTTTTCTCCTTCTGGCAGgtaatccatt ... tctctctcagGGCATTGTTATGCAAATTCTCGCATCCGCAGGCATGATCCAGAAGCAAAAGAAACTCAACGTCAACCAGATCGAGGAAGCGTACCAAAACCTCTTGGTTT




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