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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACTATGGCGGGTCATATGTCACAATGCTCAGCTCCGGCGGCCTCGTTTTTGGGATCATCAACATCGTGGGAAACTTTGGCACAGTTTTCGTTGACAACgtaagttgacatttagatccttatctgacctctagagatttgtcaactccgtacag

Basic information

species Selaginella moellendorffii
transcript EFJ26403
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26403 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: LOC_Os10g42960.1 (Oryza sativa), 5'ss of exon 2
CAACTATGGCGGGTCATATGTCACAATGCTCAGCTCCGGCGGCCTCGTTTTTGGGATCATCAACATCGTGGGAAACTTTGGCACAGTTTTCGTTGACAACgtaagt--tgacatttagatccttatctgacctctagagatttgtcaactccgtacag-------------------
|||||     || || ||  |||| ||||||||||| || || ||||| || || |||||||||||||| || |||||||| || || ||||| ||||||||| ||    | |  ||  |  |  |   |  | |   |  | ||||| |   ||||                    
CAACTTCAAGGGCTCCTACCTCACCATGCTCAGCTCGGGGGGGCTCGTCTTCGGCATCATCAACATCGTCGGCAACTTTGGAACGGTGTTCGTAGACAACgtacgtacccaaacgtacgtagtactaataattatcttggatcgtcaattaattacaagtaatttaatttgctgcag

upper sequence: EFJ26403 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: AC202439.3_FGT006 (Zea mays), 5'ss of exon 3
CAACTATGGCGGGTCATATGTCACAATGCTCAGCTCCGGCGGCCTCGTTTTTGGGATCATCAACATCGTGGGAAACTTTGGCACAGTTTTCGTTGACAACgtaagt-tgacatttagatccttatctgacctctagagatttgtcaactccgtacag--------------------------
|||||     || || ||  |||| |||||||||||||| |||||||| || || |||||||||||||| || || || ||||| || ||||| |||||||||||  || |    ||  | || | |          | |    | |  |     |                           
CAACTTCAAGGGCTCCTACCTCACCATGCTCAGCTCCGGAGGCCTCGTCTTCGGCATCATCAACATCGTCGGCAATTTCGGCACGGTCTTCGTCGACAACgtaagcctggcggcgagcacgttgtttcttgcaggatggtactacgaaccaaattaatccatttatatgtgtccgatgcgcag

upper sequence: EFJ26403 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA04G14790.1 (Glycine max), 5'ss of exon 7
CAACTATGGCGGGTCATATGTCACAATGCTCAGCTCCGGCGGCCTCGTTTTTGGGATCATCAACATCGTGGGAAACTTTGGCACAGTTTTCGTTGACAACgtaagttgacatttagatccttatctgacc-tctagagatttgtcaactccgtacag--------------------------------------------------------------------------------------
 ||  |    || || ||  | |||||||| || ||||| ||| | ||||||||||| || ||||| || ||||| |||||||| || || |||||||| |||||     ||| |||    | |||   | |||  || ||  |  | | ||                                                                                           
TAATCACAAAGGTTCTTACCTAACAATGCTAAGTTCCGGTGGCTTAGTTTTTGGGATTATAAACATTGTTGGAAATTTTGGCACTGTGTTTGTTGACAATgtaagcattaattaagagatgtgtcttttcatcttcagtttgttttatttcgagtgtcctgaatatgcaaaagttataactttgtactcttttttgttatttgggttttgttactaattattcttcaaatggggaatgcctag

upper sequence: EFJ26403 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: Vv02s0033g01370.t01 (Vitis vinifera), 5'ss of exon 6
CAACTATGGCGGGTCATATGTCACAATGCTCAGCTCCGGCGGCCTCGTTTTTGGGATCATCAACATCGTGGGAAACTTTGGCACAGTTTTCGTTGACAACgtaagttgaca--tttagatccttatctgacctctagagatttgtcaactccgtacag-------------------------
 |||||    ||||| ||| | || ||| | ||||| || || || || ||||||||||||||||| || || |||||||| || ||||| |||||||| |||||||  ||  ||| | | | || |  ||| |   | |||   ||  ||  |||                           
GAACTACAAGGGGTCTTATCTAACGATGTTGAGCTCTGGGGGGCTTGTGTTTGGGATCATCAACATTGTTGGCAACTTTGGTACTGTTTTTGTTGACAATgtaagtttccatcttttgtttcctaacctacc-cagcatattgtccatgtctctaccttcaaaaacataggtaaactttgcag

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|169053616|gb|FE462826.1|FE462826
EST:     TTGGGATCATCAACATCGTGGGAAACTTTGGCACAGTTTTCGTTGACAAC                         GGCTACTGGATGAGCGCTATAGCCGCCCGGCCTTCGTCAACTCATAAAGGT
genomic: TTGGGATCATCAACATCGTGGGAAACTTTGGCACAGTTTTCGTTGACAACgtaagttgac ... ctccgtacagGGCTACTGGATGAGCGCTATAGCCGCCCGGCCTTCGTCAACTCATAAAGGT




















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: 32 (upstream exon), 27 (downstream exon)
Score: 4

CAACTATGGCGGGTCATATGTCACAATGCTCAGCTCCGGCGGCCTCGTTTTTGGGATCATCAACATCGTGGGAAACTTTGGCACAGTTTTCGTTGACAACgtaagttgac ... ctccgtacagGGCTACTGGATGAGCGCTATAGCCGCCCGGCCTTCGTCAACTCATAAAGGTTACTTGTTGGGAGGCCTGGTCTGGTTTGCGGTCCCTTTCTCGCTGGCAA




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