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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGAGCCGAACAAGGGTGTGAACCCCGACGAGGCTGTGGCTTTTGGTGCTGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaagacttgtcttcttttgtaatccatctgtgctaacgcgcgtccatcgacag

Basic information

species Selaginella moellendorffii
transcript EFJ29073
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 5
AAGGAGCCGAACAAGGGTGTGAACCCCGACGAGGCTGTGGCTTTTGGTGCTGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaagacttgtcttcttttgtaatccatctg--tgctaacg--cgcgtccatcgacag------------------------------------
|||||||| ||||||||||| ||||| || |||||||| || | ||||||||| || |||||  | ||  | ||||| || ||||| |||||    ||||||  |      ||||    | |   || ||| |  |  || ||||    |||  ||||                                         
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcg----accttgatcacatacatagtcctttgggttggtaacaactgcgatcatctgtcttgcatatacttatcgtgctttgattttggtacgcag

upper sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 5
AAGGAGCCGAACAAGGGTGTGAACCCCGACGAGGCTGTGGCTTTTGGTGCTGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgta-agcaaagact---tgtcttcttttgtaatccatctgtgctaacgcgcgtccatcgacag------------------------------------
|||||||| ||||||||||| ||||| || |||||||| || |||||||| ||||| |||||  | ||||||||||| || || || |||||    ||||||   ||  |   |   |||  |||||||  |    |  ||| |       ||   |   ||                                     
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTTTGGTGCCGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAGgttcggctcatgttttttgtgctcttttgccactggtaggtgttttttttggtaagtgatcattctgcttacataagtgtgatttttgccttgatgcag

upper sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 5
AAGGAGCCGAACAAGGGTGTGAACCCCGACGAGGCTGTGGCTTTTGGTGCTGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaagacttgtcttcttttgtaatccatctgtgctaacgcgcgtccatcgacag-----------------------------------
|||||||| ||||||||||||||||| || |||||||| || |||||||| || || |||||  | ||||||||||| || || || |||||    ||||||  |       ||  ||  |  | ||         |  |    |  ||   | | ||                                    
AAGGAGCCCAACAAGGGTGTGAACCCTGATGAGGCTGTTGCCTTTGGTGCCGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgctctttcactagtgctatagctgggtgtttttttttcttgtaagtggtcatcctgcttacataagtgtgattttgccttgatgcag

upper sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 5
AAGGAGCCGAACAAGGGTGTGAACCCCGACGAGGCTGTGGCTTTTGGTGCTGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaagacttgtcttcttttgtaatccatctgtgctaacgcg-cgtccatcgacag------------------------------------
||||| || ||||||||||||||||| || |||||||| || |||||||||||||| || ||  | || ||||| || || || || || ||    |||||||    |   |   |||   |   | | | ||   || |   ||  ||    | ||                                       
AAGGAACCCAACAAGGGTGTGAACCCAGATGAGGCTGTTGCCTTTGGTGCTGCTGTACAAGGAAGCATTTTGAGTGGAGAGGGTGGTGATGAGACCAAAGgta--tcatttccattctctatcaatgaccgatagatggttgtgcatcgagtgttgatgaatggtagacatttgatatgatatttgttccatgcag

upper sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: EDP06859 (Chlamydomonas reinhardtii), 5'ss of exon 5
------------------AAGGAGCCGAACAAGGGTGTGAACCCCGACGAGGCTGTGGCTTTTGGTGCTGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCG------GCGACGA--TGTTAAAGgtaagcaaagacttgtcttcttttgtaatccatctgtgctaa--cgcgcgtccatc-gacag------------
                  |||||||| ||||||||||| |||||||| ||||| ||||| |  || || || || |||||||  ||| | ||||| ||||| |        | |||   | |||  | | | |  |||  ||        ||      |  |||  |   || |||| | |  | |||            
CGCGAGTGGTTCGGCGGCAAGGAGCCCAACAAGGGTGTCAACCCCGATGAGGCCGTGGCCTACGGCGCGGCCGTGCAGGGCGCAATCCTCAGCGGGGAAGgtgcgtgggagggcgagtggataagtggatggatggacgggtggatgggagtttctggtaggtgggagggcgtgcgtgcgtgaggcaggtgcacaaaggg

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|169098156|gb|FE499551.1|FE499551
EST:     TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAG                         GCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
genomic: TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaag ... ccatcgacagGCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
EST: gi|169080680|gb|FE487188.1|FE487188
EST:     TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAG                         GCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
genomic: TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaag ... ccatcgacagGCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
EST: gi|169115292|gb|FE517008.1|FE517008
EST:     TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAG                         GCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
genomic: TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaag ... ccatcgacagGCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
EST: gi|169079294|gb|FE490183.1|FE490183
EST:     TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAG                         GCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
genomic: TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaag ... ccatcgacagGCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
EST: gi|169044229|gb|FE452959.1|FE452959
EST:     TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAG                         GCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
genomic: TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaag ... ccatcgacagGCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
EST: gi|169082521|gb|FE490045.1|FE490045
EST:     TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAG                         GCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
genomic: TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaag ... ccatcgacagGCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
EST: gi|169021566|gb|FE432111.1|FE432111
EST:     TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAG                         GCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
genomic: TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaag ... ccatcgacagGCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
EST: gi|169037137|gb|FE444422.1|FE444422
EST:     TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAG                         GCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
genomic: TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaag ... ccatcgacagGCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
EST: gi|169068925|gb|FE477266.1|FE477266
EST:     TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAG                         GCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
genomic: TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaag ... ccatcgacagGCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
EST: gi|169029068|gb|FE437571.1|FE437571
EST:     TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAG                         GCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG
genomic: TGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaag ... ccatcgacagGCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTG

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), 35 (downstream exon)
Score: 33

AAGGAGCCGAACAAGGGTGTGAACCCCGACGAGGCTGTGGCTTTTGGTGCTGCTGTCCAGGGCGGTATCTTGAGCGGTGAAGGCGGCGACGATGTTAAAGgtaagcaaag ... ccatcgacagGCATTCTTCTCTTGGACGTTGCGCCCCTTACTCTGGGTATCGAGACCGTTGGTGGAGTGATGACCAAGCTGATCCCCAGGAACACTGTCATTCCGACCAA




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