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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgtttctagtagcttgtttccttctcgcgcgcatctcatctcacatccgctttgatccag

Basic information

species Selaginella moellendorffii
transcript EFJ21480
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ21480 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: AT1G75440.1 (Arabidopsis thaliana), 5'ss of exon 5
ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgtttctagtagcttgtttccttctcgcgcgcatctcatctcacatccgctttgatccag---------------------------------------
||||| | |||||||||||||| ||||||||||| || || || |||||||| ||||||||||| |||||||| ||||| || |  |||||   ||  ||||  |   ||   |      || | | ||   |||  ||||| | | |                                       
ATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAGgtactta-cagctcttacactcaccattaatatataaactttgatct-ctttgttgctgaagctgaaccttcgtctcgcttggcttgttttgttgcag

upper sequence: EFJ21480 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: AT5G42990.1 (Arabidopsis thaliana), 5'ss of exon 5
ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgtttctagtagcttgtttccttctcgcgcgcatc-tcatctcacatccg----ctttgatccag-------------------------------------------
||||||| ||||| || ||||| ||||| ||||| || || ||  ||||||||||||||||||| ||||| || || ||| | |  ||||||||||     ||| |  ||        | ||  |  || || || |      ||||| || |                                           
ATATTCTGTATGACTCATGGTCTCCAGCAATGACAGTGAGTTCAGTCTGCATCAGCATCCTCTCAATGCTATCAAGTTCCCCCGAAAAGgtttctac--atttgatctctcacactttgtattgttgtcacaaattcaaactttttgaccctgccacacaactcttactatgtcttattgtcgatgacaatatcag

upper sequence: EFJ21480 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: Vv18s0001g13180.t01 (Vitis vinifera), 5'ss of exon 5
ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgtttctagtagcttgt------------ttccttctcgcgcgcatctcatctcacatccgctttgatccag-----------------------------------------------------
||||||| |||||||| ||||| ||||||||||| || || || ||||| |||||||| ||||| ||| | |||||||| || || |||||||     |  ||||            ||  ||    | | | | || ||| |  |  ||||| |||                                                        
ATATTCTATATGATTCATGGTCCCCAGCCATGACAGTTAGTTCAATCTGTATCAGCATACTCTCCATGTTATCGAGCTCAACTGTGAAGgtttggttcaaattgtcaaagttttaagttttttaaacccctcctttcttcttaattttgcttttatctttttccagcctattttagtgtgagagcattactcatgagttttttcattgtgcag

upper sequence: EFJ21480 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 5'ss of exon 5
ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgtttctagt-agcttgtttcct-----tctcgcgcgcatctcatctcaca-tccgctttgatccag----------------------------------
||||| | |||||||| ||||| ||||||||||| || || || |||||||||||||| ||||| ||||| || ||||| || || ||||||  |    | |||  || ||     | ||     | ||||   ||||| | |   ||| |                                      
ATATTTTGTATGATTCTTGGTCCCCAGCCATGACAGTTAGTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAGgttcttgtccatctttcttactagcactttcatatccttctcggttcacaattcaacttggttttccttgtgctatgattcaattctctggggcaaagct

upper sequence: EFJ21480 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S193_49V6.1 (Physcomitrella patens), 5'ss of exon 5
ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgt-ttctagtagcttgt-ttccttctcgcgcgca-tctcatctcacatccgctttgatccag--------------------------------------
||||  | ||||| || ||||| ||||| ||||| || |||||||||||||||||||||||||| ||| | || || || ||||| ||||| | ||  || | ||   |  ||| | ||   | |||      | |   ||     |  ||                                      
ATATATTGTATGACTCTTGGTCACCAGCAATGACTGTGAGCTCCATCTGCATCAGCATCCTCTCTATGTTATCTAGTTCAACAGTGAAGgtatcctgttaacctgaacttgttcacacgtttaatctttggatagaaaagcgcgagtaaagaaatactacacttaatgacattgttttatgttgacttc

upper sequence: EFJ21480 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 5'ss of exon 5
ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgt--ttctagtagcttgtttcctt-ctcgcgcgcatctcatctcacatccgctttgatccag--------------------------------------
||||||| ||||| || ||||| ||||| |||||||| || || ||||||||||||||||| || ||| | || || || || || |||||  || |   || ||     ||  |   | || ||   || |    |            |                                       
ATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAGgtactttttaaagtttccacactagcctccacgtattgaattttcagtatatcgcatgtaaaaatggggactgttcttttagtgtcctgctttctaactt

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|169069479|gb|FE480563.1|FE480563
EST:     GCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG                         ATGAGGCCACCGGATAACGATCGCTACGTCCGGAACTGCCGCAACGGGCGA
genomic: GCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgtttctagta ... tttgatccagATGAGGCCACCGGATAACGATCGCTACGTCCGGAACTGCCGCAACGGGCGA
EST: gi|169058657|gb|FE466866.1|FE466866
EST:     GCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG                         ATGAGGCCACCGGATAACGATCGCTACGTCCGGAACTGCCGCAACGGGCGA
genomic: GCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgtttctagta ... tttgatccagATGAGGCCACCGGATAACGATCGCTACGTCCGGAACTGCCGCAACGGGCGA
EST: gi|169097750|gb|FE497477.1|FE497477
EST:     GCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG                         ATGAGGCCACCGGATAACGATCGCTACGTCCGGAACTGCCGCAACGGGCGA
genomic: GCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgtttctagta ... tttgatccagATGAGGCCACCGGATAACGATCGCTACGTCCGGAACTGCCGCAACGGGCGA
EST: gi|169058658|gb|FE466867.1|FE466867
EST:     GCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG                         ATGAGGCCACCGGATAACGATCGCTACGTCCGGAACTGCCGCAACGGGCGA
genomic: GCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgtttctagta ... tttgatccagATGAGGCCACCGGATAACGATCGCTACGTCCGGAACTGCCGCAACGGGCGA
EST: gi|169069480|gb|FE480564.1|FE480564
EST:     GCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG                         ATGAGGCCACCGGATAACGATCGCTACGTCCGGAACTGCCGCAACGGGCGA
genomic: GCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgtttctagta ... tttgatccagATGAGGCCACCGGATAACGATCGCTACGTCCGGAACTGCCGCAACGGGCGA
EST: gi|169096580|gb|FE499492.1|FE499492
EST:     GCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAG                         ATGAGGCCACCGGATAACGATCGCTACGTCCGGAACTGCCGCAACGGGCGA
genomic: GCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgtttctagta ... tttgatccagATGAGGCCACCGGATAACGATCGCTACGTCCGGAACTGCCGCAACGGGCGA

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), 30 (downstream exon)
Score: 26

ATATTCTCTATGATTCGTGGTCGCCAGCCATGACCGTCAGCTCCATCTGCATCAGCATCCTCTCGATGCTCTCGAGCTCCACAGTCAAGgtttctagta ... tttgatccagATGAGGCCACCGGATAACGATCGCTACGTCCGGAACTGCCGCAACGGGCGATCGCCCAAAGACACGAGGTGGTGGTTCCACGATGACAAGGTGTGAGATG




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