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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACCGCCATTCCAATGCGCTCGTCGACGTCCTTCCTCCAGAGGCGGATTCCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaattttctttcttactcttgaaggctcgtgttcttgggtctaaacacttcttactttgtttctttcag

Basic information

species Selaginella moellendorffii
transcript EFJ38338
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ38338 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 5'ss of exon 1
GCACCGCCATTCCAATGCGCTCGTCGACGTCCTTCCTCCAGAGGCGGATTCCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaattttctttcttactcttgaaggctcgtgt---tcttgggtctaaacacttcttactttgtttctttcag--------------------------
||||||||| || ||||||||||||||||| || || || |||||||| |||||||| |||||  |   |   ||||| |||||  ||||| | ||||  || ||   ||||||     | | ||   |   || ||    |||  ||  |   |  | ||       | | |  |                           
GCACCGCCACTCGAATGCGCTCGTCGACGTGCTGCCGCCCGAGGCGGACTCCAGCATCTCTCTGCTCGGATCATCGGAGAAGCCCAACGTCACTTATACGgtcag---ttttctgctggattttttctgatccgcgtgaaccttatgttgatttatctgttctagatctgcctgtaaagtgccatgtttctagttaatttaat

upper sequence: EFJ38338 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA18G05730.1 (Glycine max), 5'ss of exon 1
-GCACCGCCATTCCAATGCGCTCGTCGACGTCCTTCCTCCAGAGGCGGATTCCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaattttctttc---------ttactcttgaaggctcgtgttcttgggtc-taaacacttcttactttgtttctttcag---------------
  |||||||| ||||| |||||||||||||| ||||| || ||||| || |||||||| || ||| | |  ||||| || ||||| |||||| | ||||| || ||     ||              | | |  |   |  |  | | |     || |    | | ||   || |||||||| ||               
TCCACCGCCACTCCAACGCGCTCGTCGACGTTCTTCCGCCGGAGGCCGACTCCAGCATCTCGCTCCTCAGCCAGTCCGAGAAGCCTGACGTCACTTATAAtgtcagtttcgttaccgtggcgaaagatcatttctagggttttatttcccacaatcatgtctagtgctggtttagtttcttttagtgttgattggcaatt
















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|169033191|gb|FE441211.1|FE441211
EST:     CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAAC                         GATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
genomic: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaatt ... tttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
EST: gi|169062255|gb|FE471069.1|FE471069
EST:     CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAAC                         GATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
genomic: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaatt ... tttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
EST: gi|169109987|gb|FE511135.1|FE511135
EST:     CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAAC                         GATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
genomic: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaatt ... tttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
EST: gi|169064808|gb|FE476128.1|FE476128
EST:     CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAAC                         GATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
genomic: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaatt ... tttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
EST: gi|169100216|gb|FE502937.1|FE502937
EST:     CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAAC                         GATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
genomic: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaatt ... tttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
EST: gi|169033190|gb|FE441210.1|FE441210
EST:     CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAAC                         GATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG
genomic: CCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaatt ... tttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAG

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: 31

GCACCGCCATTCCAATGCGCTCGTCGACGTCCTTCCTCCAGAGGCGGATTCCAGCATTTCTCTCTTGACACAGTCGGAAAAGCCAGACGTCGCCTATAACgtaagaaatt ... tttctttcagGATATTGGAGGCTGTGACATCCAGAAGCAAGAAATCCGCGAGGCCGTGGAGCTTCCTCTGACGCACCACGAGCTTTACAAGCAGATTGGTATCGATCCAC




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