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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGTCATTTACAGTAGCAACAAGAAGCTGCTTTACAGCAACGTGAATCTGAAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgtctgtttctagttctcttttgtgagctctattaacaagcttttgtttgtcgtaatcag

Basic information

species Selaginella moellendorffii
transcript EFJ23079
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23079 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: GLYMA05G30530.1 (Glycine max), 5'ss of exon 16
CGGTCATTTACAGTAGCAACAAGAAGCTGCTTTACAGCAACGTGAATCTGAAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgt-------ctgtttctagttctcttttgtgagctctattaacaagcttttgtttgtcgtaatcag---------------------------------------------------------------------
| || ||||||||||| ||||| ||  | ||||| || || |||||||||||||| |||| |||||||||||||||||| |||||  ||||||| |||||||          || |||||| |   ||   ||   |||| |||        | ||  ||  |  |                                                                     
CTGTGATTTACAGTAGTAACAAAAAATTACTTTATAGTAATGTGAATCTGAAGGAAGTGAGTCACATGTGTCCTTTCAATTCTGCTGCTTTTCCAGACAGgtatctatgtcattgctagtt-tgacttactagagttattgacatatccccttgtgctgttcttggatcttgtacaatttaatataaaatcctttactggtgatggtactcatctacttttaataacttaaacag

upper sequence: EFJ23079 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: GLYMA08G13680.1 (Glycine max), 5'ss of exon 16
CGGTCATTTACAGTAGCAACAAGAAGCTGCTTTACAGCAACGTGAATCTGAAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgt---ctgtttctagttctctt---ttgtgagctctattaacaagcttttgtttgtcgtaatcag---------------------------------------------------------------------
| || ||||| ||||| ||||| ||  | ||||| || || |||||||||||||| |||| |||||||||||||||||| |||||  ||||||| |||||||    || |  | |||   ||   ||   ||   | || |||        | ||  ||  |  |                                                                     
CTGTAATTTATAGTAGTAACAAAAAATTACTTTATAGTAATGTGAATCTGAAGGAAGTGAGTCACATGTGTCCTTTCAATTCTGCTGCTTTTCCAGACAGgtatcttggtctttgttagtttgacttactagagttgtttacatatccccttgtgctgttcttggatcttgtacaatttaatgtaaaatcttttactggtgatgacactcatctactgttaataactgaaacag

upper sequence: EFJ23079 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: GLYMA12G08330.1 (Glycine max), 5'ss of exon 3
CGGTCATTTACAGTAGCAACAAGAAGCTGCTTTACAGCAACGTGAATCTGAAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgt---ctgtttctagttctctt---ttgtgagctctattaacaagcttttgtttgtcgtaatcag---------------------------------------------------------------------
| || ||||| ||||| ||||| ||  | ||||| || || |||||||||||||| |||| |||||||||||||||||| |||||  ||||||| |||||||    || |  | |||   ||   ||   ||   | || |||        | ||  ||  |  |                                                                     
CTGTAATTTATAGTAGTAACAAAAAATTACTTTATAGTAATGTGAATCTGAAGGAAGTGAGTCACATGTGTCCTTTCAATTCTGCTGCTTTTCCAGACAGgtatcttggtctttgttagtttgacttactagagttgtttacatatccccttgtgctgttcttggatcttgtacaatttattgtaaaatcttttactggtgatgacactcatctactgttaataactgaaacag

upper sequence: EFJ23079 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 5'ss of exon 16
CGGTCATTTACAGTAGCAACAAGAAGCTGCTTTACAGCAACGTGAATCTGAAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgtctgtttctagttctcttttgtgagctctatt----aacaagcttttgtttgtcgtaatcag------------------------
| || || || || | ||||||||||||  | |||||||||||||||||||| || || | ||| |||||||| |||||||||||  ||||||| |||||||    |  || || || | ||| |  |   ||    | |||  |    | ||  | |||| |                        
CTGTTATATATAGCAACAACAAGAAGCTATTATACAGCAACGTGAATCTGAAAGAAGTTAGTCATATGTGTCCCTTCAACTCTGCTGCTTTTCCAGACAGgtaaacta-tatttttcctctgttattttcctttgggatcaaagtacattgtggtgaaatctggctctacttctcttccattggcag

upper sequence: EFJ23079 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: AT4G05420.2 (Arabidopsis thaliana), 5'ss of exon 15
CGGTCATTTACAGTAGCAACAAGAAGCTGCTTTACAGCAACGTGAATCTGAAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgtctgtt------tctagttctcttttgtgagctctattaacaagcttttgtttgtcgtaatcag---------------------------------------------
| || || || || ||||||||||||||| | || ||||| || ||||| || || || | ||| ||||| |||||||| |||||  |||||||||||||||    |       ||   | | | ||||  | | |       |  || |  ||    ||   ||                                             
CCGTGATCTATAGCAGCAACAAGAAGCTGTTATATAGCAATGTCAATCTTAAAGAAGTTAGTCATATGTGCCCTTTCAATTCTGCTGCTTTTCCCGACAGgtacactaaacatcctctctttttcttgtcggtttttgctttgaatttctaattcctatatgaagctaagtggctctgaaatctgattctctgttctatcttatgagcag

upper sequence: EFJ23079 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 5'ss of exon 16
CGGTCATTTACAGTAGCAACAAGAAGCTGCTTTACAGCAACGTGAATCTGAAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgt-ctgtttctagttctcttttgtgagctctattaacaagcttttgtttgtcgtaatcag----------------------------------------
|||| |||||||| || ||||||||||| || |||||||| || ||| |||| || || |  |||||||| |||||||| |||||  ||||||| || |||| |  |||   |   |   ||||    | || | |      |||  ||      | |                                          
CGGTGATTTACAGCAGTAACAAGAAGCTACTCTACAGCAATGTTAATTTGAAAGAAGTCAGCCACATGTGCCCTTTCAATTCTGCTGCTTTTCCAGATAGgtaccttttgctgcctttacttgttgcttttacttattgttctttactttcttccaacgtatgcatgtgaaatcatacagaaaaaattcatttccaatga

upper sequence: EFJ23079 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: PP1S203_55V6.1 (Physcomitrella patens), 5'ss of exon 16
CGGTCATTTACAGTAGCAACAAGAAGCTGCTTTACAGCAACGTGAATCTGAAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgtctgtttctagttctct--tttgtgagctctattaacaagcttttgttt-gtcgtaatcag--------------------------------------
| || || ||||| ||||| ||||| ||  | || |||||||| ||| ||||||| || |||||||||||||| |||||||| ||||| ||||| |||||||  ||||  |     ||   |   |   |   ||   | || |   |   |  ||     |                                      
CAGTGATATACAGCAGCAATAAGAAACTTTTGTATAGCAACGTCAATTTGAAGGAAGTCAATCACATGTGTCCATTCAACTCGGCATCGTTTCCGGACAGgttcgttttcaaccacctaactaacgcaattatttcggaggcctcattccagatgtggatggcagaaagctgcatcatacgccactttcatacttcaaca

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|169023819|gb|FE429038.1|FE429038
EST:     AAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAG                         CCTGGCAATTGGAAAGGAGGGAGAGCTCACAATCGGAACGATTGATGATAT
genomic: AAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgtctgtttct ... tcgtaatcagCCTGGCAATTGGAAAGGAGGGAGAGCTCACAATCGGAACGATTGATGATAT
EST: gi|169018280|gb|FE427713.1|FE427713
EST:     AAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAG                         CCTGGCAATTGGAAAGGAGGGAGAGCTCACAATCGGAACGATTGATGATAT
genomic: AAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgtctgtttct ... tcgtaatcagCCTGGCAATTGGAAAGGAGGGAGAGCTCACAATCGGAACGATTGATGATAT
EST: gi|169058900|gb|FE468734.1|FE468734
EST:     AAGGAGGTGAATCATATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAG                         CCTGGCAATTGGAAAGGAGGGAGAGCTCACAATCGGAACGATTGATGATAT
genomic: AAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgtctgtttct ... tcgtaatcagCCTGGCAATTGGAAAGGAGGGAGAGCTCACAATCGGAACGATTGATGATAT
EST: gi|169101941|gb|FE507764.1|FE507764
EST:     AAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAG                         CCTGGCAATTGGAAAGGAGGGAGAGCTCACAATCGGAACGATTGATGATAT
genomic: AAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgtctgtttct ... tcgtaatcagCCTGGCAATTGGAAAGGAGGGAGAGCTCACAATCGGAACGATTGATGATAT
EST: gi|169104116|gb|FE507105.1|FE507105
EST:     AAGGAGGTGAATCATATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAG                         CCTGGCAATTGGAAAGGAGGGAGAGCTCACAATCGGAACGATTGATGATAT
genomic: AAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgtctgtttct ... tcgtaatcagCCTGGCAATTGGAAAGGAGGGAGAGCTCACAATCGGAACGATTGATGATAT
EST: gi|169067315|gb|FE473900.1|FE473900
EST:     AAGGAGGTGAATCATATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAG                         CCTGGCAATTGGAAAGGAGGGAGAGCTCACAATCGGAACGATTGATGATAT
genomic: AAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgtctgtttct ... tcgtaatcagCCTGGCAATTGGAAAGGAGGGAGAGCTCACAATCGGAACGATTGATGATAT
EST: gi|169079946|gb|FE489925.1|FE489925
EST:     AAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAG                         CCTGGCAATTGGAAAGGAGGGAGAGCTCACAATCGGAACGATTGATGATAT
genomic: AAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgtctgtttct ... tcgtaatcagCCTGGCAATTGGAAAGGAGGGAGAGCTCACAATCGGAACGATTGATGATAT

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), 34 (downstream exon)
Score: 15

CGGTCATTTACAGTAGCAACAAGAAGCTGCTTTACAGCAACGTGAATCTGAAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgtctgtttct ... tcgtaatcagCCTGGCAATTGGAAAGGAGGGAGAGCTCACAATCGGAACGATTGATGATATCCAGAAGCTACATATACGCACGGTGGCACTTGGGGAACACCCTCGCAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGTCATTTACAGTAGCAACAAGAAGCTGCTTTACAGCAACGTGAATCTGAAGGAGGTGAATCACATGTGTCCTTTCAACTCTGCATCTTTTCCCGACAGgtctgtttctagttctcttttgtgagctctattaacaagcttttgtttgtcgtaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG