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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAAAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGCAAGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaagaaccatatttccagcaagaacttgtgtgcttactgtcatttctccag

Basic information

species Selaginella moellendorffii
transcript EFJ11589
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11589 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: LOC_Os02g18550.1 (Oryza sativa), 5'ss of exon 5
CGAAAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGCAAGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaag---aaccatatttccagcaagaa--cttgtgtgcttactgtcatttctccag---------------------------------------
||| ||    ||| |  | || |  || || || ||    | ||| ||||||||||||||| ||||||| || ||||| |||||||||||| |||||||||| | |||    |  |  ||  | ||| |||   |||  |||||    || |||  ||                                          
CGAGAAGTCAACTTCAAGTATATTCCCTCTCCAAAATGTGTTCATCCGCAAGGTGAAGATCTTGAAGGCACCGAAGTTTGATCTTGGGAAGTTGATGGAGgtgaggaaccttattctcatgcctagctagatgcctttagtgctcctggttattcttctgagaaatgtattagcatggttattggctttggaatcttatt

upper sequence: EFJ11589 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM2G030915_T08 (Zea mays), 5'ss of exon 5
CGAAAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGCAAGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaagaaccatatttccagcaagaacttgtgtg----cttactgtcatttctccag---------------------
 || ||    ||  |  | ||||  || || || |||   | ||| |||||||||||||| || |||||||| |||||||||||||||||||| |||||||||||       |||   | ||   |||  ||         ||  |||| | || |                         
TGAGAAGTCTACCTCCAGCATCTTCCCACTTCAAAACGTCTTCATCCGCAAGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAGCTCATGGAGgtaattgt---tcatgcatgcaaatagattttccagactatctccctgttacttgttagcctaaaacttgttgcttctcag

upper sequence: EFJ11589 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM2G145258_T01 (Zea mays), 5'ss of exon 5
CGAAAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGCAAGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaagaaccatatttccagcaagaacttgtgtg----cttactgtcatttctccag---------------------
 || ||    ||  |  | ||||  || || || |||   | ||| |||||||||||||| || |||||||| ||||||||||||||||| || |||||||||||    |  |||   | ||   |||  ||         ||  |||| | || |                         
TGAGAAGTCTACCTCCAGCATCTTCCCACTTCAAAACGTCTTCATCCGCAAGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAACTCATGGAGgtaattgcta--catgcatgcaaatagattttccagactatctccctgttactttttatcctaaaacttgttgcttctcag

upper sequence: EFJ11589 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM2G030915_T06 (Zea mays), 5'ss of exon 5
CGAAAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGCAAGG-TGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatga--agaaccatatttccag---caagaacttgtgtgcttactgtcatttctccag------------------
 || ||    ||  |  | ||||  || || || |||   | ||| ||||||| ||||||| || |||||||| ||||||||||||||||| || |||||||||||    | |  |||      ||    |  |   | | | | |  |     || |||                    
-GAGAAGTCTACCTCCAGCATCTTCCCACTTCAAAACGTCTTCATCCGCAAGGGTGAAGATACTCAAGGCCCCCAAGTTCGATCTTGGGAAACTCATGGAGgtaattgctacatgcatgcaaatagatttaccagactatctccctgttacttgttatcctaaaacttgttgcttatcag

upper sequence: EFJ11589 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM5G863656_T01 (Zea mays), 5'ss of exon 1
CGAAAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGCAAGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaagaaccatatttccagcaagaacttgtgtgc------ttactgtcatttctccag---------------
 || ||    ||  |  | ||||  || || || |||   | ||| |||||||||||||| || | |||||| ||||| ||||| |||||| ||||||||||||| |    | | ||     | || || || | |        |  ||||  ||   | |                
TGAGAAGTCTACCTCCAGCATCTTCCCACTTCAAAACGTCTTCATCCGCAAGGTGAAGATACTCATGGCCCCCAAGTTTGATCTCGGGAAGTTGATGGAGgtaatta----ctacatgcatggaaataatttatctagacaacatccctgtagttatcctaacacgttgcttctcag

upper sequence: EFJ11589 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA20G28780.2 (Glycine max), 5'ss of exon 4
CGAAAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGCAAGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGg-----------taatgaag-------aaccatatttccagcaagaacttgtgtgct-tactgtcatttctccag-------------------------
 || || | |||  |  | || || || ||||||||    |   |||| || || ||||||||||| ||||| ||||| ||||||||||| ||||||||||           |||| |||        |   | ||  ||   |   ||  ||     || | ||  ||  | |                          
TGAGAAGGCGACATCTAGTATTTACCCTCTGCAGAATGTGTTTGTTCGTAAAGTCAAGATCCTGAAAGCCCCTAAGTTTGATCTTGGGAAACTGATGGAGgtaattttttgataataaagttcttttgatttttttctcaatcatgcctcatgaaaaatattttctgttacctaaacttggttgcccagtctgagtttgg

upper sequence: EFJ11589 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA06G11940.1 (Glycine max), 5'ss of exon 5
CGAAAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGCAAGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaagaaccatatttccagcaagaacttgtgtgcttactgtcatttctccag----------------------------------------------
 || || |  ||  |  | |||||||| || |||||    | |||||| || || ||||||||||| || |||||||| ||||||||||| ||||||||||||   |    |||| ||      ||       |   | |   ||  ||     |                                               
TGAGAAGGCAACATCTAGTATCTATCCTCTACAGAATGTGTTCATTCGTAAAGTTAAGATCCTGAAAGCTCCAAAGTTTGATCTTGGGAAACTGATGGAGgtat--attgtccattttattcaaaaatctccttacccctctggtttttatgttaataaatgaaactgttaatccatcattgtagtgctgaactgatttggg

upper sequence: EFJ11589 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA10G39050.1 (Glycine max), 5'ss of exon 5
CGAAAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGCAAGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaa--------tgaagaaccatatt-tccagcaagaacttgtgtgcttactgt--catttctccag---------------------------------
||| || |  ||  |  | || || || ||||||||    |   |||| || || ||||||||||| || || ||||| ||||||||||| |||||||||||||        | |  |||    || || ||   ||  |||  |    | |     |||   | |                                  
CGAGAAGGCAACATCTAGTATTTACCCTCTGCAGAATGTGTTTGTTCGTAAAGTCAAGATCCTGAAAGCTCCTAAGTTTGATCTTGGGAAACTGATGGAGgtaattttttaataataaacttggttgtctagtctgagtttggttttccattagaatattaaactaatacttgctttttgagaaataagttgcatgctag

upper sequence: EFJ11589 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GLYMA11G00890.1 (Glycine max), 5'ss of exon 5
CGAAAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGCAAGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaagaaccatatttccagcaagaacttgtgtgcttactgtcatt-tctccag-------------------------------------------------
 || || |  ||  |  | |||||||| || |||||    | |||||| || || |||||||| || || |||||||| |||||||| || ||||||||||||         | | |||   ||||    |  | | | ||   | ||| | || |                                                  
TGAGAAGGCAACATCTAGCATCTATCCTCTACAGAATGTGTTCATTCGTAAAGTTAAGATCCTTAAAGCTCCAAAGTTTGATCTTGGAAAACTGATGGAGgtat------gtcctttttattgcaaattttcttatacctatgtttattatgtctaatgaatgttacagtgagttcttgatttttgtagctgaatagaaagggtca

upper sequence: EFJ11589 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: Vv05s0020g03900.t01 (Vitis vinifera), 5'ss of exon 6
CGAAAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGCAAGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaagaaccatatttccagcaagaacttgtgtgcttact-gtcatttctccag-------------------------------------------
||| || |  ||| |  | ||||||||  | |||||    |||||||| || || |||||| |||| || || ||||| |||||||| ||||||||||||||| |          | |     ||      | | | || | |   |||   |  |                                            
CGAGAAGGCAACTTCAAGCATCTATCCTTTACAGAATGTGTACATTCGGAAAGTTAAGATCTTGAAAGCTCCTAAGTTTGATCTTGGAAAGCTGATGGAGgtatttttttttttaactcttttcatttgtctattttctaatttaacatacataaacattaaaccattaaaaaaaaaaacctgtcacctttttatgccaa

upper sequence: EFJ11589 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: PP1S219_50V6.1 (Physcomitrella patens), 5'ss of exon 5
CGAAAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGCAAGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaa--tgaagaaccat-atttccagcaagaacttgtgtgcttactgtcatttctccag-----------------------------------------
 || ||||  |||  ||| ||||| || || |||||||||| |||| | || ||||||||||| ||||| || |||||||| |||  |||| |||||||||||   | | ||    |  |||       | ||     ||  |   | | |||     |                                         
TGAGAAAGCAACTCAGGGCATCTACCCACTTCAGAACACTTTCATTAGGAAAGTGAAGATCCTTAAGGCTCCGAAGTTCGACCTTATGAAGTTGATGGAGgtacgttaaggagttgttgttttgcatgtggacagaactgtgtgacggctttttcaacgttttttttttttttttttttttttttttttttttttgttga

upper sequence: EFJ11589 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: PP1S92_47V6.2 (Physcomitrella patens), 5'ss of exon 5
CGAAAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGCAAGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaagaaccatatttccagcaagaacttgtgtgcttactgtcatttctccag----------------------------------------------------------------------------------------------------------------------------------------------
 ||||| |  |||   |||||||| || |||||||| || | |||  | || |||||||| |||||||| ||||||||||||||   |||||| |||||||| |           |     | || |  ||| |||   |        || ||||                                                                                                                                               
TGAAAAGGCAACTCAAGGAATCTACCCTCTGCAGAATACATTCATCAGAAAAGTGAAGATTCTGAAGGCTCCAAAGTTCGATCTGATGAAGCTCATGGAGgtgagtgttggttgaaacgtta-catgctcttttgttgctgtctaagattatccatcagcataccatcactctgtataaactgcctaattattgataacatttagtgaagctcacggctgccagataattaagaattcgttgtctctgggattctaagtccagagtgtccacttttgttcgatctcttggtttcatag

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|169069100|gb|FE476739.1|FE476739
EST:     AGGTGAAGATTCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttctccagGTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTT
EST: gi|169056435|gb|FE467014.1|FE467014
EST:     AGGTGAAGATCCTGAAGGCCCCANAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTT
genomic: AGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttctccagGTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTT
EST: gi|169104850|gb|FE508721.1|FE508721
EST:     AGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTT
genomic: AGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttctccagGTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTT
EST: gi|169029448|gb|FE436703.1|FE436703
EST:     AGGTGAAGATTCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTC
genomic: AGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttctccagGTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTT
EST: gi|169056008|gb|FE466184.1|FE466184
EST:     AGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAG                         GTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTT
genomic: AGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttctccagGTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTT

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: 134

CGAAAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGCAAGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaaga ... atttctccagGTTCATGGTGACTACAGCGAGGATACTGGCGTCAAGGTTGAGCGACCAGTTGGTGATGAAGCCGAACCGGAGGCAGCAGAGGCTGAAGTAGTCGGGGCGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAAAAAGTGACTGCGGGAATCTATCCCCTGCAGAACACTTACATTCGCAAGGTGAAGATCCTGAAGGCCCCAAAGTTCGATCTTGGGAAGCTGATGGAGgtaatgaagaaccatatttccagcaagaacttgtgtgcttactgtcatttctccag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA