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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCTAGACAAAACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtgaacatgaactgattttcaggatgtgcactaaaattatttctttccag

Basic information

species Selaginella moellendorffii
transcript EFJ26022
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26022 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 13
AATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCTAGACAAAACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtg-aacatgaactgatt-ttcaggatgt-gcact-aaaattatttctttccag-------------------------------------------------------
  |||||||  | || ||||| || || ||||||||||| |||||||| |||||||| || ||||| || ||||| || || || ||||| ||||| |||||  ||  | |  | |   |||   |||| | | |     | ||||      |                                                        
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcag

upper sequence: EFJ26022 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 13
AATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCTAGACAAAACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtgaacatgaactgatttt---caggatgtgcactaaaattatttctttccag---------------------------------------------------------
  |||||||  | || ||||| || || |||||||| || || ||||| ||||| ||||| ||||| |||||||| || || || ||||||||||||||||| || |||     ||||     |     |  | ||| || |  |    | |                                                          
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaa-atgtgtgaatttcacataaagaataaaataagataaaataaaacaaaaaaaaggacttacaagtccatgttggtgtgaaattcattggtttttccttgttgcag
















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|169030422|gb|FE438678.1|FE438678
EST:     ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAG                         GATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT
genomic: ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtgaacatga ... ttctttccagGATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT
EST: gi|169097110|gb|FE498956.1|FE498956
EST:     ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAG                         GATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT
genomic: ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtgaacatga ... ttctttccagGATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT
EST: gi|169059061|gb|FE468206.1|FE468206
EST:     ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAG                         GATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT
genomic: ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtgaacatga ... ttctttccagGATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT
EST: gi|169019958|gb|FE431023.1|FE431023
EST:     ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAG                         GATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT
genomic: ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtgaacatga ... ttctttccagGATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT
EST: gi|169064769|gb|FE473736.1|FE473736
EST:     ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAG                         GATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT
genomic: ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtgaacatga ... ttctttccagGATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT
EST: gi|169028509|gb|FE439924.1|FE439924
EST:     ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAG                         GATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT
genomic: ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtgaacatga ... ttctttccagGATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT
EST: gi|169066441|gb|FE474664.1|FE474664
EST:     ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAG                         GATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT
genomic: ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtgaacatga ... ttctttccagGATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT
EST: gi|169097981|gb|FE498778.1|FE498778
EST:     ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAG                         GATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT
genomic: ACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtgaacatga ... ttctttccagGATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGT

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: 22 (upstream exon), 30 (downstream exon)
Score: 10

AATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCTAGACAAAACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtgaacatga ... ttctttccagGATCACTTAATGACATCTCCTGCTGAGTCTTCTGGATCAACCAGCACTGGTAACTGGCTTTTTAAAAACAAAGAACATGGAAAGGCCAGCGCTACTGCCA




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