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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGCCGTGTTCTTGCGCAGAATCTTTCGATCCCCTGGATCCAAACGGCAACATCACGATCAAGTGGGATGTAATGAGCTGGTCCGCGGATGGCTATGTCgtaagttctcgggatccctctcttccacacacatttcttccgaaatttcgagttctttctctctttcacggcctctaacccgggatttcttcttctctag

Basic information

species Selaginella moellendorffii
transcript EFJ11028
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11028 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os10g35460.1 (Oryza sativa), 5'ss of exon 2
CATGCCGTGTTCTTGCGCAGAATCTTTCGATCCCCTGGATCCAAACGGCAACATCACGATCAAGTGGGATGTAATGAGCTGGTCCGCGGATGGCTATGTCgtaagttctcgggatccctctcttccacacacatttcttccgaaatttcgagttctttctct-ctttcacggcctctaacccgggatttcttcttctctag-------
                    |  |||  ||| |||||||||||||||||||||||||||| || |||||||| |||   ||| |  | ||||||||||  ||||||    | |          | |||  |||| ||| ||   ||||     ||   || | | || ||    |||    |   | | | |||  |  |        
--------------------ATGCTTATGATTCCCTGGATCCAAACGGCAACATCACGATAAAATGGGATGTGATGCAATGGACTCCTGATGGCTATGCTgtaagtagcggtggcag------tacaccaacatctctacctttattttcgtctcaacctgtacatttacactatcttgttct--actacctctaataaaaaaatata

upper sequence: EFJ11028 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA18G50770.1 (Glycine max), 5'ss of exon 2
CATGCCGTGTTCTTGCGCAGAATCTTTCGATCCCCTGGATCCAAACGGCAACATCACGATCAAGTGGGATGTAATGAGCTGGTCCGCGGATGGCTATGTCgtaagttctcgggatccctctcttccacacacatttcttccgaaatttcgagttctttctctctttcacggcctctaacccgggatttcttcttctctag-
                       | | ||||||  ||||||||||||| ||||| |||||||| ||||||||  ||   ||| |  | ||||||||||| ||||||  |    |   | || ||          |  || | |     ||     |  |      |        |||       |       ||  |    
---------------------TGCGTACGATCCTTTGGATCCAAACGGAAACATAACGATCAAATGGGATGTTGTGTCATGGACACCAGATGGCTATGTAGtaagtaatacaaacttcactgttatttgttttatattttctaggccacggaaaatcccaagaaatagatagacctagttgtcaaaggtgcattgacagat

upper sequence: EFJ11028 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 5'ss of exon 2
CATGCCGTGTTCTTGCGCAGAATCTTTCGATCCCCTGGATCCAAACGGCAACATCACGATCAAGTGGGATGTAATGAGCTGGTCCGCGGATGGCTATGTCgtaagt-----------tctcgggatccctctcttcca--cacacatttcttccgaaatttcgagttctttctctctttcacggcctctaacccgggatttcttcttctctag---------------------------------
                    || | | |||| | || |||||| | || || ||||| |||||||||||||||||||||||| |  | ||||| ||||| ||||||              |   ||   |   || ||       |  |  | | |   | |   | | ||  | | |  | ||  || |        |   || || |||||                                 
--------------------AAGCCTACGATTCGCTTGATCCAGAGGGAAATATCACCATCAAGTGGGATGTAATGAGCTGGACTCCAGATGGTTATGTTgtaagtaaaatattaaactacaaaatattttgattgcaatagtgaaccttgttcaagcatccacttgcctttgcccatgaatggattccacttacatttcaattgttttctagttatgatctaatctttttattcatgttgggcag

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|169103315|gb|FE508865.1|FE508865
EST:     ACATCACGATCAAGTGGGATGTAATGAGCTGGTCCGCGGATGGCTATGTC                         GCACTGGTGACCATGTACAACTACCAGCAATACCGCCACATCGAGACGCCC
genomic: ACATCACGATCAAGTGGGATGTAATGAGCTGGTCCGCGGATGGCTATGTCgtaagttctc ... tcttctctagGCACTGGTGACCATGTACAACTACCAGCAATACCGCCACATCGAGACGCCC
EST: gi|169077320|gb|FE485622.1|FE485622
EST:     ACATCACGATCAAGTGGGATGTAATGAGCTGGTCCGCGGATGGCTATGTC                         GCACTGGTGACCATGTACAACTACCAGCAATACCGCCACATCGAGACGCCC
genomic: ACATCACGATCAAGTGGGATGTAATGAGCTGGTCCGCGGATGGCTATGTCgtaagttctc ... tcttctctagGCACTGGTGACCATGTACAACTACCAGCAATACCGCCACATCGAGACGCCC
EST: gi|169051201|gb|FE460269.1|FE460269
EST:     GATCAAGTGGGATGTAATGAGCTGGTCCGCGGATGGCTATGTC                         GCACTGGTGACCATGTACAACTACCAGCAATACCGCCACATCGAGACGCCC
genomic: GATCAAGTGGGATGTAATGAGCTGGTCCGCGGATGGCTATGTCgtaagttctc ... tcttctctagGCACTGGTGACCATGTACAACTACCAGCAATACCGCCACATCGAGACGCCC

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), 32 (downstream exon)
Score: 49

CATGCCGTGTTCTTGCGCAGAATCTTTCGATCCCCTGGATCCAAACGGCAACATCACGATCAAGTGGGATGTAATGAGCTGGTCCGCGGATGGCTATGTCgtaagttctc ... tcttctctagGCACTGGTGACCATGTACAACTACCAGCAATACCGCCACATCGAGACGCCCGGATGGACACTGGGATGGACTTGGGCCAAGAAGGAAGTGATTTGGGGAA




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