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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ22392
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 22
lower sequence: LOC_Os08g40530.1 (Oryza sativa), 5'ss of exon 11
GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagat--------aacagc---ttttggtgcgagtctgaaggatcgaaattcttgcag----------------------------------------
|| ||||| ||||| |||||||||||   |||||| || || ||||||||||| || |||||||||||  |||||||||||||  |||| ||||| |||||  | |        ||||     || |||      |   || ||  || | | |  |                                          
GCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAGgtttgtttttccccgaacaaactattctggaataccttctaatgaaggataatgtcactaagcaaacaccatggaattcctcataccctcacactaaatt

upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 22
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 5'ss of exon 9
GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagataac----agcttt----tggtgcgagtctgaaggatcgaaattcttgcag-----------------------
|| || || |||||| | ||||| |||||||| || || || || |||||||||||||| || || |||||||||||||| ||||| || ||||| ||||| ||  ||     |||||     |  | |     | |   | | ||   |||                           
GCAGACATTGGTCTTGCTATGGGTATCCAAGGAACAGAAGTAGCTAAAGAAAGCTCAGATATAATTATTCTGGATGACAATTTTGCTTCAGTTGTAAAGgttagggaagttggagcttaataatcttacacaattaatttaacaaatgccttaacatttatccatatgtaacgttctag

upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 22
lower sequence: GRMZM5G893864_T01 (Zea mays), 5'ss of exon 5
GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagataacagcttttgg----tgcgagtctgaaggatcgaaattcttgcag-------------------------------------------
|| ||||| |||||||| |||||||||||||| || || || |||||||| ||||||||||| ||||||||||||||||| ||| | |||||||| |||||  |    |   |||| |    |  |  |||  |  ||       | |||                                             
GCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTAGCCAAAGAGAGCTCAGACATAATAATTCTGGATGACAATTTTTCTTCTGTTGTGAAGgtttggc--ctatttttagaatctaaggatcttgataatacgcgcacatgcctaatacaacgttgtcttacatgttctttatcttttatattctag

upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 22
lower sequence: GRMZM2G340139_T01 (Zea mays), 5'ss of exon 26
GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagat--aacagcttttg-gtgcgagtctgaaggatcgaaattct-tgcag-----------------------------------------------
|||||||| |||||||||||||| ||   ||| || || || ||||| ||||||||||||||||||||  |||||||  ||||  | ||||| |||||||| |  |     | |||    |    || |      | | |||||   ||                                                  
GCTGATATAGGTCTTTCAATGGGAATATCAGGAACAGAAGTTGCCAAGGAAAGCTCAGACATTATAATCTTGGATGATGACTTCACCTCTGTGGTCAAGgttatcttctgtaacttcaaagcataaggcattctaaccaaaatttgatgtgtcccagtatactttcgtcacagcatgcatgatgcctttgcttatcggc

upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 22
lower sequence: GRMZM2G132712_T03 (Zea mays), 5'ss of exon 27
GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagata---acagcttttggtgcgagtctga--------aggatcgaaattcttgcag----------------------------------------
|| ||||| |||||||||||||||||    ||||| || || || ||||||||||| |||||||||||  |||||||  ||||  | || |||||||||||  | |    | |  | |    | |   || |        || |  ||  ||||| |                                          
GCCGATATAGGTCTTTCAATGGGCATTTCCGGGACAGAAGTTGCTAAAGAAAGCTCTGACATTATAATCTTGGATGATGACTTCACGTCAGTTGTCAAGgtttgtttggtagaattatccaagaggacctaactgagttcagcactgattttctttccttgtaaaaaataattccacttgtttggagttcacacattga

upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 22
lower sequence: GLYMA07G00630.2 (Glycine max), 5'ss of exon 25
GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagataacagctt---ttggtgcgagtctgaaggatcgaaattcttgcag------------------------------------------------
|||||||| |||||||| |||||||||||||| || || || || |||||||||||||| |||||||| || || || ||||||||||| || || |||||| |    |   ||       |   || ||     ||   | |   | | |                                                
GCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAGgtaggtgttctatttaatacattctcaggcttggatatgatattgtcttccgtttcctgtatcttctcctagtaaattgttgggtaatcaacgctcccac

upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 22
lower sequence: GLYMA15G00340.1 (Glycine max), 5'ss of exon 27
GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagataacag-cttttggtgcgagtctg--aaggatcgaaattcttgcag------------------------------------------------
|| ||||| |||||||| |||||||||||||| || || || || |||||||| ||||| ||||||||  ||||||| ||||||||||| || || |||||||| |    | |||||  |  | |||||  |  | |  |   | |  ||                                                 
GCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAGgtaagcttgttgtcttttttttggtgtctgtcattggtacatgatttcacatgctcaacttaagaacttatatacatttctttggcaatgatttgcctag

upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 22
lower sequence: GLYMA13G44990.1 (Glycine max), 5'ss of exon 27
GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagataacagctt-ttggtgcgagtctgaaggat-cgaaattcttgcag-------------------------------------------------
|| ||||| |||||||| |||||||||||||| || || || || |||||||| ||||| ||||||||  ||||||| ||||||||||| || || |||||||| |      || ||      ||  || |  ||  |    ||||                                                     
GCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAGgtaagcttgttatttattcacttaagcatgtattatatggttgtctttttttggtgtctgtcattggtacaatttcacatgctcaacttagaagttataa

upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 22
lower sequence: GLYMA08G23760.1 (Glycine max), 5'ss of exon 28
GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagataacagctt---ttggtgcgagtctgaaggatcgaaattcttgcag------------------------------------------------
|| ||||| |||||||| |||||||||   || || || || || |||||||||||||| |||||||| || || |||||||||||||| || || |||||| |    |   ||    |  |   || ||   | ||   | |   | | |                                                
GCAGATATTGGTCTTTCTATGGGCATCTCCGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGACAACTTTGCATCAGTAGTAAAGgtaggtgttctatttaatatattctcagccttgggtatgatattgtcttccgtttcctgtatcttctcctagtaaaaagttattacttcattttccattg

upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 22
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 5'ss of exon 27
GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaaga-----taacagcttttggtgcgag--tctgaaggatcgaaattcttgcag---------------------------------------------------------------------------------------------------------------------------------------
|| ||||| |||||  ||||||| |||||||| ||||| || || || ||||  |||||||| || ||  ||||||||||||||| ||| ||||| |||||  |      ||  | |    | | | |   ||| |   |   |  | |||   |                                                                                                                                       
GCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAGgtttgtatccttagaaaccaaggattcaaatttcttataaaagaagctcctttttgatactcttctgttgcgtgatacttttggaatttcttttcctcgtaaatgtcctcctttgggctttggggctatttgtgatctttttaattatcctgaattagatatccattttaataatcgtctcattcctatag

upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 22
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 27
GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaag-ataa--cagcttttggtgcgagtctgaaggatcgaaattcttgcag-------------------------------------------------
|| ||||| ||||| || |||||||| ||||| || || || || ||||||||||||||||| || ||  ||||||| |||||||| || ||||| ||||| ||  |||   | |  ||  || ||||     |  | |  | | ||| ||                                                 
GCAGATATAGGTCTCTCTATGGGCATTCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGACATCATTATCTTGGATGATAACTTTGCCTCAGTTGTAAAGgttagtgtaagcaaaccatttatgtgagtaaattgtcttgggaat-ttgtagttatgattctaccttgttatatttaaaacaaaaatactgtcaatccttt

upper sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 22
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 28
GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagataacagcttttggtgcgagtctgaaggatcgaaatt---cttgcag------------------------------------------------
|| ||||| |||||| ||||||||||   ||| || ||||| || ||||| ||||| ||||| || ||  |||||||||| ||||| || ||||||||||| ||        || |      | | | |  |||| | |       || |                                                 
GCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAGgttagtctgtgcattgtaagagtattttaagtgatcaatagcaaatatgtaaatgactgcaactcccacaaatgaatgttttcatccaatcttgaacaaa

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|169101664|gb|FE501208.1|FE501208
EST:     AAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG                         GTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAG
genomic: AAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagataac ... attcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAG
EST: gi|169108170|gb|FE512543.1|FE512543
EST:     AAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG                         GTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAG
genomic: AAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagataac ... attcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAG
EST: gi|169075222|gb|FE484104.1|FE484104
EST:     AAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG                         GTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAG
genomic: AAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagataac ... attcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAG

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), 34 (downstream exon)
Score: 45

GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagataac ... attcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcag

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