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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtcgcgttctcgttgagcgctggttcatttaactttaaatttttcacag

Basic information

species Selaginella moellendorffii
transcript EFJ07923
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 5'ss of exon 10
GTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagt----tgtcgcgttctcgttgagcgctggttcatttaactttaaatttttcacag----------------------------------------
|||||||||||| ||||||||||||||||| | ||| | |  ||  | || ||||| ||||| || || ||||| |||| ||| || |||    | | ||       || ||     |  || |  |      |||||||||                                          
GTTTTCCACAAGAGGATGCCTCCTGAAGCAATAGACCTCGCTTCACGCCTTCTTCAATATTCACCGAGTCTCCGCTGCACTGCTgtgagtatattcttgctgcaattttaagtagcagaacagtagaaaagtgatttttcactactgctcacagcaggggtactgtaaaacgccccttttctta

upper sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: LOC_Os02g14130.1 (Oryza sativa), 5'ss of exon 10
GTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtcgcgttctcgttgagcg-ctggttcat-ttaacttt--aaatttttcacag----------------------------------------
 |||||||||||||||||||||| |||||| | ||| | |  ||  | || || |||||| | || |  || ||||||| |||||| |||| ||    ||   |||   | ||| ||||  | |||| |  ||    |  ||                                          
ATTTTCCACAAGCGGATGCCTCCAGAAGCAATTGACCTTGCATCACGTCTTCTCCAGTATGCACCAAATCTACGATGCACTGCCgtgagttttccatctcattttgtttgactgattcaagtcaactgttgaagccatctacctattaatgattgctccaaattattatggcattagttgtttc

upper sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: GLYMA06G42840.1 (Glycine max), 5'ss of exon 10
GTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtcgcgttctcgttgagcgctggttcatttaac---tttaaatttttcacag----------------------------------------------------------------------------------------------------------------------------------
|||||||||||||| ||||||||||||||| | ||| | |  || ||||| || || ||||| || || || || |||| ||| || ||| |       |  | |     |   |||| ||| |   |||||||       |                                                                                                                                   
GTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCGgtgagtaggatgagccatgatacctacc--ttcacttatcccctttaaataaaaggaaaacatacacaggaagaagttttgcttatattaaccttgctgtgatattatatctatattccttatggcatgttttttttatttagttaactcaattggcataattttcaccaatggcttttattatttcag

upper sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: GLYMA12G15470.1 (Glycine max), 5'ss of exon 10
GTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgt-cgcgttctcgttgagcgctggttcatttaactttaaatttttcacag-----------------------------------------------------------------------------------------------------------------------------------
|||||||||||||| ||||||||||||||| | ||| | |  || ||||| || || ||||| || || ||||| |||| ||| || ||| |   |   | |  |    | ||      ||   ||||||||       |                                                                                                                                    
GTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTCCGCTGCACTGCGgtgagtaggatgaactatgatacctcccttcacttttcccctttaaataaaaggaaaacatacacaggaaaaagtttgcttattttaaccttcttgctgtgatattatatctatattccttatggcatgttttttaatttagttaactcaattggcttaattttcactggtggcttttattatttcag

upper sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgt-------cgcgttctcgttgagcgctggttcatttaactttaaatttttcacag------------------------------------------------------------------
||||||||||||||||||||||| |||||  | ||| | |  ||  |||| ||||| || || || || || || |||| ||| ||  ||  |       |  || ||| || |  | |       ||  || |   || ||   |                                                                   
GTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCGgttggtatttctaaaccaagtactc-ttaattgttacagtggttctctctggcttctttggaccatacactgttcaatgaaggagtgaaatgttgtttttcaactgacttgtttgtttgccgtctgaag

upper sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: PP1S306_43V6.2 (Physcomitrella patens), 5'ss of exon 10
GTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtcgcgttctcgttgagcgctggttca--tttaactttaaatttttcacag-------------------------------------------
||||||||||| || ||||| ||||||||||| ||||||||||| ||||| |||||||| || || |  || || ||||| || || ||| |   | |  ||  ||   | |||| |   | | |  || |  | |                                                 
GTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCTgtgagtagcgtcatattctgtgt-tgttggtacgggtgtgatgttgagctgtgtgggtctgcgttgagtcgtggcgttctgcgaggtgccaacgaggcatt

upper sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtcgcgttctcgttgagcgctggttcatttaactttaaatttttcacag--------------------------------------------
|||||||||||||| |||||||| |||||||| ||  |||| || ||||| |||||||| || || |  || || |||||||| || |||  |  ||   |  ||  |   ||     || | |    |     ||   |                                            
GTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCTgtgagtgatgacggggtttttctgttgtgaagtgttgatcgcgcagaccatcgttggttacgatgaatctttctctctattggtgggaacaggatgttga

upper sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 5'ss of exon 10
GTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagt--tgtcgcgttctcgttgagc-gctggttcatttaactttaaa-----tttttcacag------------------------------------
||||||||||| || |||||| | |||||||||||| |||| || || ||||| ||||| ||||| |  || || ||||| || || |||  |   | ||| || |   || |  ||| | ||  |   |  |     ||  |   ||                                    
GTTTTCCACAAACGCATGCCTTCAGAAGCAGTGGACCTGGTTTCAAGACTGCTACAGTACTCCCCAAATCTGCGGTGCAACGCTgtgagtaataatgggttttcctgttgcagagggtccgttcgaagatgcaggccattgcttcaagtgtcggctgttgtatccggcattgattgatggcatt

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|169097159|gb|FE498446.1|FE498446
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169024326|gb|FE434316.1|FE434316
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169098040|gb|FE496874.1|FE496874
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTCCATCCGTTTTTTGATGAGCTCCGAGACCCGAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169061466|gb|FE469565.1|FE469565
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTCCATCCGTTTTTTGATGAGCTCCGAGACCCGAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169070550|gb|FE479827.1|FE479827
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169033662|gb|FE441902.1|FE441902
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169063978|gb|FE472789.1|FE472789
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169024325|gb|FE434315.1|FE434315
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169026298|gb|FE433389.1|FE433389
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169056816|gb|FE466433.1|FE466433
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTCCATCCGTTTTTTGATGAGCTCCGAGACCCGAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169096868|gb|FE498649.1|FE498649
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169065474|gb|FE474298.1|FE474298
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169031970|gb|FE440670.1|FE440670
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169079299|gb|FE490188.1|FE490188
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169080587|gb|FE490943.1|FE490943
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169100491|gb|FE502692.1|FE502692
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
EST: gi|169082218|gb|FE487012.1|FE487012
EST:     ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC                         CTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA
genomic: ACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACA

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: 57

GTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtc ... tttttcacagCTGGAGGCACTTGTGCATCCCTTTTTTGATGAGCTCCGAGACCCAAGCACAAGGCTACCCAATGGACGACCGTTGCCAGCCTTGTTCAACTTCAAACCAC




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCCgtaagttgtcgcgttctcgttgagcgctggttcatttaactttaaatttttcacag

- - - - - - - - - - - - - - - - - - - - - - -  GCTGCT