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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGAAAGAGACGGGATTTGTAGGTCTGAAAAACCAAGGAGCTACTTGTTACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgtaaccatctcgattttcttgctttttttacagttattcgtgttggcag

Basic information

species Selaginella moellendorffii
transcript EFJ14291
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 1
AAAGAAAGAGACGGGATTTGTAGGTCTGAAAAACCAAGGAGCTACTTGTTACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgt----aaccat---ctcgattttcttgctttttttacagttattcgtgttggcag--------------------------
||| ||||| || || |  || || ||||| |||||||||||||| ||||||||||| |||||  |||||||||| || ||  | ||||  ||| | |||||     | |||       | ||    || || |  ||  || ||         |                           
AAAAAAAGAAACAGGTTACGTTGGCCTGAAGAACCAAGGAGCTACCTGTTACATGAACTCTCTACTACAGACACTATACCATATACCATACTTCAGGAAGgtgtgagatcatgcatcataattcagagcattctagactattgtttccagaactaattgactaacttcattattttacccag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os07g06950.1 (Oryza sativa), 5'ss of exon 7
--------------------------------------------------------------AAAGAAAGAGACGGGATTTGTAGGTCTGAAAAACCAAGGAGCTACTTGTTACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgta-accatctcgattttcttgcttt----ttttacagttattcgtgttggcag-----------
                                                               || || || || || | ||| ||||||||||| ||||| |||||||| || |||||||||||| | ||||| ||||| ||  | |||| |||| |||||||| |  || | | ||| || | | |    ||||  | ||| |  | || | |            
ACTTGTATAGTGGAGGCCGAAGTTGCTGTATGTAAGGTGGTTGATTATTGGAGCTATGACTCTAAAAAGGAAACTGGTTATGTTGGTCTGAAAAATCAAGgtgctacttgctatatgaattctcttcttcagactctgtaccatattccatatttcagaaaggtacaaaatgtagttttactggttatataattttgtacttaat-atatttgtatggtgctaacag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 5
AAAGAAAGAGACGGGATTTGTAGGTCTGAAAAACCAAGGAGCTACTTGTTACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgta-accatctcgattttcttgctttttttacagttattcgtgttggcag-----------------------------
 || || || || |||| ||| ||||| || || ||||||||||| ||||| ||||| |||||| |||| |||||||| ||  | |||| |||| | |||||     |||   | ||| |     | |  |   ||  |   ||                                   
GAAAAAGGAAACAGGATATGTTGGTCTAAAGAATCAAGGAGCTACCTGTTATATGAACTCTCTTCTACAAACACTGTACCATATACCATATTTCAGGAAGgtctgagatcattactttttcctagtctacatgatttgttaagtacctgaacttaagactaattgaaatttcatcttag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G018508_T03 (Zea mays), 5'ss of exon 2
AAAGAAAGAGACGGGATTTGTAGGTCTGAAAAACCAAGGAGCTACTTGTTACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgta--accatctcgattttcttgc--tttttttacagtt--attcgtgttggcag------------------------------
 || || || || || | ||| ||||| ||||| ||||| ||||| || || |||||||||||| | ||||| ||||| ||| | |||| |||| ||||||||  | |      |||  | ||   ||  |   | | |  |   |  | |  ||                              
TAAAAAGGAAACTGGCTATGTTGGTCTTAAAAATCAAGGTGCTACCTGCTATATGAATTCTCTTCTTCAGACGCTGTACCACATCCCATATTTCAGAAAGgtacaaacgagaaaattcacatgtcattgctcccctgctcaacctgcttggatagatgcagctaactacagatatttcttgccag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA10G23680.1 (Glycine max), 5'ss of exon 1
AAAGAAAGAGACGGGATTTGTAGGTCTGAAAAACCAAGGAGCTACTTGTTACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgtaacc-------atctcgatttt-------cttgctttttttacagttattcgtgttggcag----------------
||| || || || || | ||| || |||||||| ||||||||||| ||||| |||||||||||  | || ||| |||| ||| |  | | |||||||||||| |||       || |  | |||       |||  ||||||   ||  | | |     | |                 
AAAAAAGGAAACTGGTTATGTTGGACTGAAAAATCAAGGAGCTACATGTTATATGAATTCTCTGCTTCAAACATTGTACCACATTTCTTATTTCCGAAAGgttacccagtagcatataaactttgtaaggtcttatttttttataaggaaatagctcatgtataaatttttttgttcag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: AT3G11910.2 (Arabidopsis thaliana), 5'ss of exon 5
AAAGAAAGAGACGGGATTTGTAGGTCTGAAAAACCAAGGAGCTACTTGTTACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgtaaccatctcgattttcttgctttttttac--agttattcgtg--ttggcag------------------------------------------------
||| |||||||| || ||||| || || ||||||||||| ||||| |||||||||||||||||  | |||||  | || ||| | || |  ||  |||||||      || | |||  || |||||| ||     ||| || ||  || |||                                                 
AAAAAAAGAGACAGGTTTTGTTGGACTAAAAAACCAAGGTGCTACCTGTTACATGAATTCTCTCCTGCAGACTTTATACCACATACCTTACTTTAGAAAGgttggatgcttgttttgttttctttttctatttgcttaatcatgagttcgcaaaattctagagaaagacatttgagtaatgcacccatcctttccttgtag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 5'ss of exon 5
AAAGAAAGAGACGGGATTTGTAGGTCTGAAAAACCAAGGAGCTACTTGTTACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgt---aaccatctcgattttcttgctttttttacagttattcgtgttggcag------------------------------------------
||| || ||||| || ||||| || ||||| |||||||| ||||||||||||||||||||||| ||||| || || || ||  | || | |||| |||||||    |  ||||    ||| |    || ||||   |||||  | |                                                
AAAAAAGGAGACTGGTTTTGTTGGACTGAAGAACCAAGGGGCTACTTGTTACATGAATTCTCTCTTACAAACTCTCTACCATATTCCTTATTTCAGAAAGgttaggagtatcttatatttttcttattgtttattattatttatttcaatgagtatctaaaaggaaataccttattttggactatgtatgtcag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 5'ss of exon 5
AAAGAAAGAGACGGGATTTGTAGGTCTGAAAAACCAAGGAGCTACTTGTTACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgtaacca---tctcgattttcttgctttttttac--agttattcgtgttggcag--------------------------------
|||||| ||||| || | ||| || ||||| |||||||||||||| |||||||||||||| ||| | |||||||| || ||  | || |  ||| |||||||    |   ||||  ||||| | ||||  ||      ||  |  | || |||                                 
AAAGAAGGAGACTGGTTATGTTGGACTGAAGAACCAAGGAGCTACCTGTTACATGAATTCCCTTCTTCAGACACTCTACCATATTCCTTACTTCAGAAAGgttgggaaattctcttttttcctcctttacttgtttcattgatattatttgcaagaaagcactacatttggaactgtgtatttcag

upper sequence: EFJ14291 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 5'ss of exon 5
AAAGAAAGAGACGGGATTTGTAGGTCTGAAAAACCAAGGAGCTACTTGTTACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgtaaccatc---tcgattttcttgctttttttacagtta----ttcgtgttggcag--------------------------------------------
 ||||| || || |||||||| ||  | || || ||||||||||| || ||||||||||||||  | |||||| ||||||| ||||| |  ||||| ||||| |   ||   || ||          |  ||   ||||     |  | |  |||                                             
GAAGAAGGAAACAGGATTTGTTGGGTTAAAGAATCAAGGAGCTACATGCTACATGAATTCTCTCCTCCAGACATTGTATCATCTGCCTTACTTCCGGAAGgttattttcctgtcaatacagaaatcatggttgtggttagaaccttttttcagcaactcagtttcaggagtctcggattctctttcggttcagtacttta

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|169032748|gb|FE437775.1|FE437775
EST:     ACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAG                         GCAGTATACCATATGCCAACAACGGAACATGATGTTCCATCCAGTAGTATA
genomic: ACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgtaaccatct ... gtgttggcagGCAGTATACCATATGCCAACAACGGAACATGATGTTCCATCCAGTAGTATA




















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: 29 (upstream exon), 27 (downstream exon)
Score: 10

AAAGAAAGAGACGGGATTTGTAGGTCTGAAAAACCAAGGAGCTACTTGTTACATGAATTCTCTTTTACAGACACTGTATCACCTGCCATTTTTCCGAAAGgtaaccatct ... gtgttggcagGCAGTATACCATATGCCAACAACGGAACATGATGTTCCATCCAGTAGTATACCACTGGCACTTCAAAGTTTGTTCTATAAGATCCAGTATAGCGACACGA




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