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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATAACTGAGGCAGGTGCAAATCGTGTTCTTGCGTGTGATCTTCACTCTGGACAAAGTATGGGGTACTTCGATATTCCTGTTGATCACGTCTATGGACAGgtatgtgcgtcatatttttctcaacgtcaccattcccgtataaaatctctttgctctttcttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ24123
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24123 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GRMZM2G180863_T01 (Zea mays), 5'ss of exon 4
TATAACTGAGGCAGGTGCAAATCGTGTTCTTGCGTGTGATCTTCACTCTGGACAAAGTATGGGGTACTTCGATATTCCTGTTGATCACGTCTATGGACAGgta-tgtgcgtcatatttttctcaacgtcaccattcccgtataaaatctctttgctctttcttgcag---------------------------------
  | ||||| || |||    | |||||  |||  |||||| |||| |||   |||    |||||||||||||||||||||| |||||  | |||||||||||| |||| ||  | |  ||  || |||    ||| | ||||   ||||| |||    ||||  | |                                 
ACTTACTGAAGCTGGTAGTGACCGTGTCATTGTATGTGATATTCATTCTACGCAAGCGTTGGGGTACTTCGATATTCCTGTGGATCATATATATGGACAGgtagtgtgagttct-tcctttacagcgtt-tgatttcagtattgcatctcgttgtaaattctatctgactacgaattagtgtcatccttggtgtctgtag

upper sequence: EFJ24123 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA07G12660.1 (Glycine max), 5'ss of exon 4
TATAACTGAGGCAGGTGCAAATCGTGTTCTTGCGTGTGATCTTCACTCTGGACAAAGTATGGGGTACTTCGATATTCCTGTTGATCACGTCTATGGACAGgta-----tg--tgcgtcatatttttctca----acgtcaccattcccgtataaaatctctttg-ctctttcttgcag----------------------
 || || || ||||||||||||||||| ||||| ||||| || || ||||| ||    ||||| || || |||||||| |||||||| || ||||||||||||     ||  |  | |||||| |  | |    |    | |||    | | |||| |  ||   || ||     ||                       
AATTACAGAAGCAGGTGCAAATCGTGTACTTGCTTGTGACCTCCATTCTGGGCAGTCCATGGGCTATTTTGATATTCCAGTTGATCATGTGTATGGACAGgtaacagatgattatgccatattgtcattacaatataatagcatggaagaaaaaaaacatttaatctattaaactcaaacaaacaaacatgccttggata

upper sequence: EFJ24123 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA03G24280.2 (Glycine max), 5'ss of exon 4
TATAACTGAGGCAGGTGCAAATCGTGTTCTTGCGTGTGATCTTCACTCTGGACAAAGTATGGGGTACTTCGATATTCCTGTTGATCACGTCTATGGACAGgtatgtgcgtcatatttttct------caacgtcaccattcccgtataaaatctctttgctctttcttgcag----------------------------
 || || || ||||||||||||||||| ||||| ||||| || || ||||| ||    ||||| || || |||||||| |||||||| || ||||| ||||||   |  |  ||| |  ||       |     | |||    | ||||||    |||  ||| |    |                              
AATTACAGAAGCAGGTGCAAATCGTGTACTTGCTTGTGACCTCCATTCTGGGCAGTCCATGGGCTATTTTGATATTCCAGTTGATCATGTGTATGGCCAGgtaacggattattatgtcactagcatatagtaatagcatggaagaataaaaagcatttaatctattaaactcaaacaaacatggcttggatgtgttgtat

upper sequence: EFJ24123 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: AT2G44530.2 (Arabidopsis thaliana), 5'ss of exon 4
TATAACTGAGGCAGGTGCAAATCGTGTTCTTGCGTGTGATCTTCACTCTGGACAAAGTATGGGGTACTTCGATATTCCTGTTGATCACGTCTATGGACAGgta--------tgtgcgtcatat---ttttctcaacgtca---ccattcccgt----ataaaatctctttgctctttcttgcag-----------------------
 || ||  || | |||||| | ||||| ||||| |||||||||||||| |||||   |||||| ||||| |||||||| || ||||| || ||||| ||||||        | |   | | ||   |  ||| | | |||    | ||   ||    ||| | | ||||   ||||  || |                         
GATTACACAGTCTGGTGCAGACCGTGTCCTTGCTTGTGATCTTCACTCCGGACAGTCTATGGGCTACTTTGATATTCCAGTCGATCATGTTTATGGCCAGgtagaaaaaagtttttcttaaatgactcctctgagcatcaagttcctttttgtgaaaatagactttcttatgtcttcttttccttgtgctttaatattcatgaacag

upper sequence: EFJ24123 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: Vv15s0021g00460.t01 (Vitis vinifera), 5'ss of exon 4
TATAACTGAGGCAGGTGCAAATCGTGTTCTTGCGTGTGATCTTCACTCTGGACAAAGTATGGGGTACTTCGATATTCCTGTTGATCACGTCTATGGACAGgtatgtgcgtcatatttttc-----tcaacgtcaccattcccgtataaaat-----ctctttg--ctctttcttgcag----------------------
 || || || || |||||||| || |||||||| ||||||||||| ||||| ||   |||||| || || |||||||| |||||||| || ||||||||||||     || |||  ||       |||| ||      ||   | | |||      || || |   |||| | ||                         
CATTACAGAAGCGGGTGCAAACCGAGTTCTTGCTTGTGATCTTCATTCTGGGCAGTCTATGGGTTATTTTGATATTCCAGTTGATCATGTGTATGGACAGgtaataaggtgatagcttctagtggtcaatgtgtatgatcagatttcaaactgatgctattggggttcttccatgttatacatcagcatgactttggtgt

upper sequence: EFJ24123 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: Vv02s0012g00530.t01 (Vitis vinifera), 5'ss of exon 4
TATAACTGAGGCAGGTGCAAATCGTGTTCTTGCGTGTGATCTTCACTCTGGACAAAGTATGGGGTACTTCGATATTCCTGTTGATCACGTCTATGGACAGgta-------------------tgtgcgtcatatttttctcaacgtcaccattcccgtataaaatctctttgctctttcttgcag-----
||| ||  | ||||||||  | ||||||||||| ||||||||||| ||||| ||    ||||| ||||| ||||||||||| |||||| | ||| | ||||||                   | ||   | ||| ||| ||    ||   ||  | | || ||||  || |  | |||  ||||      
TATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGTCCATGGGTTACTTTGATATTCCTGTGGATCACATATATTGTCAGgtaattaatttttaagccattgtttgatccttatctttttctgactccatatcactgaatgaaattactgt-ttgttttgtgcacacaag

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|169064600|gb|FE471331.1|FE471331
EST:     GACAAAGTATGGGGTACTTCGATATTCCTGTTGATCACGTCTATGGACAG                         CCTGTCATTTTGGACTACCTTGCCAGCAAAATGATCTCCGCAGATGACTTA
genomic: GACAAAGTATGGGGTACTTCGATATTCCTGTTGATCACGTCTATGGACAGgtatgtgcgt ... tttcttgcagCCTGTCATTTTGGACTACCTTGCCAGCAAAATGATCTCCGCAGATGACTTA




















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), 33 (downstream exon)
Score: 24

TATAACTGAGGCAGGTGCAAATCGTGTTCTTGCGTGTGATCTTCACTCTGGACAAAGTATGGGGTACTTCGATATTCCTGTTGATCACGTCTATGGACAGgtatgtgcgt ... tttcttgcagCCTGTCATTTTGGACTACCTTGCCAGCAAAATGATCTCCGCAGATGACTTAGTAGTAGTTTCTCCAGATGTTGGTGGTGTCGCAAGAGCTCGGGCATTTG




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