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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGAAGGGATGGAGCGAAAGGATGTCATGTCCAAGAACGTCTCCATCTACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtagaaatacaaaacgtatcagaagctcatgactgtgggcgtgacag

Basic information

species Selaginella moellendorffii
transcript EFJ10745
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ10745 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os10g33800.3 (Oryza sativa), 5'ss of exon 3
GAAGGAAGGGATGGAGCGAAAGGATGTCATGTCCAAGAACGTCTCCATCTACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtagaaatacaaaacgta-tcagaagctcatgactgtgggcgtgacag------------------------------------------------
|||||| || |||||  | |||||||| ||||| || || |||||||||||||| || |||||||||||||||||      ||| |||    ||   ||||||  | | | ||   ||| ||| |  | |  | |   |  ||   || |                                                   
GAAGGAGGGAATGGAAAGGAAGGATGTTATGTCAAAAAATGTCTCCATCTACAAATCCCAAGCTTCTGCTCTTGAGGCTCATGCAGCCCCTAACTGCAAGgta-tggaaatatttcaaatgtagtttgcaatttactgcaatgattgtcaagttgccagcattgctctcaccttgagtagcaatcacatgtaatgctataa

upper sequence: EFJ10745 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA02G00810.2 (Glycine max), 5'ss of exon 3
GAAGGAAGGGATGGAGCGAAAGGATGTCATGTCCAAGAACGTCTCCATCTACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaa-cgtagaaatacaaaacgt-atcagaagctca--tgactgtgggcgtgacag--------------------------------------------
 || ||||| |||||| | |||||||| ||| | |||||||||||||| |||||||| || |||||||| |||||||||  ||||||     ||   ||||| | |      ||   || | | | |     || |  ||||| |        |||                                            
AAAAGAAGGTATGGAGAGGAAGGATGTGATGACTAAGAACGTCTCCATTTACAAGTCCCAGGCTTCTGCCCTTGAAAAGCATGCTGCTGCCAACTGCAAGgtgatccctttcatctgaatcttcagccccttcttaattgactataatttctgcagtttttttatttcaacattgttttcactttctattttaaattgct

upper sequence: EFJ10745 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA10G00920.1 (Glycine max), 5'ss of exon 3
GAAGGAAGGGATGGAGCGAAAGGATGTCATGTCCAAGAACGTCTCCATCTACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtagaaatacaaaacgtatcagaagct-----catgactgtgggcgtgacag-------------------------------------------
 || ||||| |||||| | |||||||| ||| | |||||||||||||| |||||||| || |||||||| |||||||||  ||||||     ||   ||||||||        |    |    |||||  ||       ||||| |        |||                                           
AAAAGAAGGTATGGAGAGGAAGGATGTGATGACTAAGAACGTCTCCATTTACAAGTCCCAGGCTTCTGCCCTTGAAAAGCATGCTGCTGCCAACTGCAAGgtaaccccctttcatttgaatcttcagacccttcttatttgactataatttctgcagttttttatgtcaagttttttttcctttctattgttgatgcttg

upper sequence: EFJ10745 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: AT5G43330.1 (Arabidopsis thaliana), 5'ss of exon 3
GAAGGAAGGGATGGAGCGAAAGGATGTCATGTCCAAGAACGTCTCCATCTACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtagaaatacaaaacgtatcagaagctcatgactgtgggcgtga-cag-----------------------------------------------------------
||||||||| |||||| | |||||||| |||||||||||||| ||||| ||||||||||||||||||||  | || |||  ||||||     ||   ||||| |        | | || ||| ||  | | |||| |    |    | | ||                                                            
GAAGGAAGGAATGGAGAGGAAGGATGTTATGTCCAAGAACGTTTCCATTTACAAGTCTCAAGCTTCTGCCTTGGAGAAGCATGCTGCACCAAACTGCAAGgtgataagtcttttcgaatcgt-tcttatgatcattatgcagaaattaagcaagttaatctcttattttgttgtatgagatatttcatatttgctatctcttcgttttgtag

upper sequence: EFJ10745 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: AT1G04410.1 (Arabidopsis thaliana), 5'ss of exon 3
GAAGGAAGGGATGGAGCGAAAGGATGTCATGTCCAAGAACGTCTCCATCTACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtaga------aatacaaaacgtatcagaagctcatgactgtgggcgtgacag---------------------------------------------------------------------------------------------------
||| ||||| |||||| | |||||||| ||||||||||| || ||||||||||||||||| ||| ||||  | || |||  ||| ||     ||   ||||| |              |    ||  ||   |||||   ||  |     | |  | |                                                                                                   
GAAAGAAGGTATGGAGAGGAAGGATGTGATGTCCAAGAATGTTTCCATCTACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgatctgtttgctttttaagttaaatgaagccactgcatccaatcttctctgttcattggagtgtaacagatgctttgtgttctctattgggttctagtttacgactctcttgctcacacattcgctctcgttttgtcttttttttttcag

upper sequence: EFJ10745 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv07s0005g03360.t01 (Vitis vinifera), 5'ss of exon 3
GAAGGAAGGGATGGAGCGAAAGGATGTCATGTCCAAGAACGTCTCCATCTACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaa-cgtagaaatacaaaacgtatcagaagctc---atgactgtgggcgtgacag------------------------------------------------------------------------------------------------------------------------------------------
 || ||||| |||||  |||||||||| |||||||| || || |||||||||||||| || || ||||| ||||||||   ||| ||     |    |||||   |       || |    || |||    ||    |  |   |   | |||  |                                                                                                                                          
AAAAGAAGGAATGGAAAGAAAGGATGTGATGTCCAAAAATGTTTCCATCTACAAGTCCCAGGCCTCTGCACTTGAAAATCATGCAGCTGCAAATTGCAAGgtgctcacgattgtatattttgtttcaattccttgataaaatcatccacttgattgaacattgaaccaccttaatggttaccggggaatacttttacatagaattaacctgcattacttggccaatgcttctttcttttcttttgtgtttttccaatcaattttatttattattcattcattcatttatttcag

upper sequence: EFJ10745 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv07s0005g03350.t01 (Vitis vinifera), 5'ss of exon 4
GAAGGAAGGGATGGAGCGAAAGGATGTCATGTCCAAGAACGTCTCCATCTACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtagaaatacaaaacgtatcagaagctcatgactgtgggcgtgacag---------------------------------------------------------------------------------------------------------------------------------------------------
||| ||||| |||||  | || ||||| |||||||| || || ||||||||||||||||| || ||||| ||||||||   ||| ||     |    |||||   | |||  || |  | || ||  |   || |   ||      | |                                                                                                                                                      
GAAAGAAGGAATGGAAAGGAAAGATGTGATGTCCAAAAATGTTTCCATCTACAAGTCTCAGGCCTCTGCACTTGAAAATCATGCAGCTGCAAATTGCAAGgtgctgaagat-tatatcatgtttcgaattttctttcttgataaaatcatgcacttgagtgaagattgaaccaccttaatagttaccagggaatacttttacttggaagtgacccacactccttggccaatgcttctttcttttcttctgtgtttttccaatcaattttatttattattcattcattcatttatttcag

upper sequence: EFJ10745 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S235_81V6.1 (Physcomitrella patens), 5'ss of exon 3
GAAGGAAGGGATGGAGCGAAAGGATGTCATGTCCAAGAACGTCTCCATCTACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaa-----cgt-agaaataca-aaacgtatcagaagct-catgactgtgggcgtgacag----------------------------------------
 ||||| || |||||||| |||||||| |||||||| || || |||||||||||  |||| || || || |||||  ||   ||||| || || || ||||||      ||| | |||| || || ||    | | |   | | | | ||   || |                                           
CAAGGAGGGTATGGAGCGCAAGGATGTGATGTCCAAAAATGTTTCCATCTACAAAGCTCAGGCCTCAGCACTTGAGCAGCACGCTGCAAAAGATGTCAAGgtaggtgttcgtcataaattcataagcgcgatatatgtgactttattttgaatgtaaggctaaattcatgcattcacatatggtcctataattgctgtga

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|169058483|gb|FE466380.1|FE466380
EST:     ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAG                         GTTCTGGTGGTTGCTAATCCAGCCAATACAAATGCGCTGATCCTCAAGGAG
genomic: ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtaga ... ggcgtgacagGTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
EST: gi|169063460|gb|FE471462.1|FE471462
EST:     ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAG                         GTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
genomic: ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtaga ... ggcgtgacagGTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
EST: gi|169107612|gb|FE514273.1|FE514273
EST:     ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAG                         GTTCTGGTGGTTGCTAATCCAGCCAATACAAATGCGCTGATCCTCAAGGAG
genomic: ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtaga ... ggcgtgacagGTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
EST: gi|169094562|gb|FE494514.1|FE494514
EST:     ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAG                         GTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
genomic: ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtaga ... ggcgtgacagGTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
EST: gi|169071244|gb|FE477882.1|FE477882
EST:     ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAG                         GTTCTGGTGGTTGCTAATCCAGCCAATACAAATGCGCTGATCCTCAAGGAG
genomic: ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtaga ... ggcgtgacagGTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
EST: gi|169094548|gb|FE494513.1|FE494513
EST:     ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAG                         GTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
genomic: ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtaga ... ggcgtgacagGTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
EST: gi|169071243|gb|FE477881.1|FE477881
EST:     ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAG                         GTTCTGGTGGTTGCTAATCCAGCCAATACAAATGCGCTGATCCTCAAGGAG
genomic: ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtaga ... ggcgtgacagGTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
EST: gi|169029856|gb|FE441050.1|FE441050
EST:     ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAG                         GTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
genomic: ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtaga ... ggcgtgacagGTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
EST: gi|169063459|gb|FE471461.1|FE471461
EST:     ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAG                         GTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
genomic: ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtaga ... ggcgtgacagGTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
EST: gi|169062860|gb|FE472363.1|FE472363
EST:     ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAG                         GTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
genomic: ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtaga ... ggcgtgacagGTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
EST: gi|169062861|gb|FE472364.1|FE472364
EST:     ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAG                         GTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
genomic: ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtaga ... ggcgtgacagGTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG
EST: gi|169058484|gb|FE466381.1|FE466381
EST:     ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAG                         GTTCTGGTGGTTGCTAATCCAGCCAATACAAATGCGCTGATCCTCAAGGAG
genomic: ACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtaga ... ggcgtgacagGTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAG

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: 25

GAAGGAAGGGATGGAGCGAAAGGATGTCATGTCCAAGAACGTCTCCATCTACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtaga ... ggcgtgacagGTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAGTTTGCTCCTTCCATTCCTGACAAGAACATCACTTGCTTGACGAGGCTGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGAAGGGATGGAGCGAAAGGATGTCATGTCCAAGAACGTCTCCATCTACAAGTCTCAAGCTTCTGCTCTTGAAAAGTGTGCTGCCAAGGACGTGAAGgtaacgtagaaatacaaaacgtatcagaagctcatgactgtgggcgtgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC