Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG

Basic information

species Selaginella moellendorffii
transcript EFJ22392
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 11
--------------------------------------------------gtaagataacagcttttggtgcgagtctga-aggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
                                                   |   ||      |    |   |  | | | | | |     |  ||  ||||||| ||||||||  |||| || ||||| ||||||||||| || |||||||| ||||| ||||| |||||||  || || ||  | || || || || |
ctatttttggttacagaaaccccttctaattttttggttacataaactccttctaattgagattcaaagcatggatttaacaagtttctgttctttttagGTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAGTTTCAGCTTACTGTTAATGTTGCCGCACTCGTGATTAATGTTGTTGCAG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 9
----------------------------------gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
                                   |||  |||||  |       |   | |  |      |  ||||   |||| || ||||||||||| || || ||||| ||||| || |||||||| || |||||||| |||||||||||||  || ||  |  |||| || || || |
gttagggaagttggagcttaataatcttacacaattaatttaacaaatgccttaacatttatccatatgtaacgttct---agGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GRMZM2G340139_T01 (Zea mays), 3'ss of exon 26
------------------------------------------------gtaagataacagcttttg-gtgcgagtctgaaggatcgaaatt--cttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
                                                 |  |   | |  ||| | |||  | | |  |   |  || |   |||||||||||| || ||||| ||||| || ||||| |||||||| ||||||||||||||||| || ||||| ||||||| ||| || ||| | || ||  | || |
gattttatacttcacttgctttgagtgtacctaacggttatttataacatctgtctagacttttagagtgtaaatgtttattttaaaattctccttgcagGTTGTTCGATGGGGCCGGTCTGTTTATGCAAATATTCAAAAGTTTATCCAGTTCCAACTTACTGTTAATGTTGCTGCCCTAGTTATAAATGTGATTGCTG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
                                                  ||| | |||    | |     |  |||  |   |  | |||||   |||| || ||||||||||| || || ||||| ||||| || |||||||| ||||||||||| || ||||||||||  || || ||  |||| || || || |
gtttggcctatttttagaatctaaggatcttgataatacgcgcacatgcctaatacaacgttgtcttacatgt-tctttatcttttatattct---agGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 28
--------------------------------------------------gtaagataaca-gcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
                                                   |     |||  |   || |||  ||  |      ||    ||  || ||||||| |||||||| || || || ||||| ||||||||||| ||||||||||||||||| || || ||||||| ||| || ||  | || || ||||| |
gggttttggcttaaggagagatttatttcaccaagacacgtgtcctatggattgctcaacctgtaatttgtgtaagatttctatttcattctttgtgtagGTTGTCCGCTGGGGCCGCTCTGTATATGCAAATATTCAGAAATTTATCCAGTTCCAGCTTACAGTTAATGTTGCTGCTCTTGTAATAAATGTTGTGGCAG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 27
----------------------------------------------gtaagataacagcttttggt-gcgagtctgaaggatcga----aattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
                                                |  | |  ||| ||  |  |    |||||    |  |    | ||  || ||||||| |||||||| || || || ||||| ||||||||||| ||||| ||||||||||| ||||| ||||| | ||| || ||  | || || |||||||
gattttggcttcatcttggattaagagataaatttatttcatggagacacaacacgagcattcagcagattatctgagatgtgtagttcactttgtgtagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAGCTCACTGTTAATGTAGCTGCTCTTGTAATAAATGTTGTGGCCG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 27
-------------------------------------------gtaagataaca--gcttttggtgcgagtctgaaggat-cgaaattct-----tgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
                                           |  | | ||||      ||  |  || | |  | |||  | | ||||     || ||||||| |||||||| || || || ||||| ||||||||||| ||||| |||||||| || ||||| ||||||| ||| || ||  | || || ||||| |
cacggattgatcttggattgagaagagataaatttatttcgtggagacacaacacgagcattcataagattatctaagatgtgtagttctctttgtgtagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAACTCACTGTTAATGTTGCTGCTCTTGTAATAAATGTAGTGGCAG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 25
---------------------------------------------------------------------------------------------------------------------------gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
                                                                                                                            |   |  ||| ||  || ||  | |        ||   ||  ||| |||||||  | ||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| || |||||||| |  || || ||  | || || || || |
gttagtactactttgagatattttaatttgttctgttttttgtcattagtagaagtagaaatgcactttttgaatactgattgtacaatgagaggtttatatagaattgaggtgcattgaatatttgaagcacaactgatgatgacaatt--gtttttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATAAATGTTGTTGCTG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 25
-----------------------------------------------------------------------------------------------------------------------gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
                                                                                                                        |   |  ||| ||  || ||  | |     |  ||   ||  ||| |||||||  | ||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| || |||||||| |  || || ||  | || || || || |
gtttgtactactttgagatatttttatttgttctgttttttgccattagtagtggaaatgcactttttgaacactgattgtacaatgagaggtttatatagaagtgaggtgcatttaatattgaagcacaactgatgatgacaatt--gtgtttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATTAATGTTGTTGCTG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 25
--------------------------------------------gta-agataacagcttttggtgcgagtctgaaggatcgaa---attctt---gcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
                                             ||  |||  |   | |||      ||||||    || |    ||||||   | ||||||| || ||||| || || || ||||| ||||||||||| ||||||||||| ||||| || || ||||||| ||| || ||  | || || ||||| |
gttttggcttaaggagagatttatttcaccaagacacatgtatcctatggattgctcatcttgtaatttgtctgagatgtctatttcattctttgtgtagGTTGTCCGATGGGGCCGCTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTCACGGTTAATGTTGCTGCTCTTGTAATAAATGTTGTGGCAG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 28
------------------------------------------gtaagataacagcttttggtgcgagtctgaagga--tcgaaattcttgc--------agGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
                                           | |  | |  | ||   |    |||   |  |   |  || ||||| |        |||||||    ||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| || || ||| | |  || || | | | || || || || |
aggtgtatcccatagcctgatattattttatgtaagctgattatgaattgat-gtttgaagcataagtggtactgcctttcaatttctttcgccaattcagGTTGTCAAATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTCAATATAGCAGCACTTGCTATAAATGTTGTTGCTG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 26
------------------------------------------gtaagataacagcttttggtgcgagtctgaagga--tcgaaattcttg--------cagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
                                             |  | |  | ||   | |  |||   |  |   |  || |||||         ||||||||    ||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| || || ||| | |  || || | | | || || || || |
gtgtatcctatagcccgagatattattttatgtaagctgattacgaattgat-gtttgaagcgtaagtggtactgcctttcaatttcttttgccaattcagGTTGTCAAATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTCAATATAGCAGCACTTGCTATAAATGTTGTTGCTG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: AT5G57110.1 (Arabidopsis thaliana), 3'ss of exon 27
-------------------------------------------------------------------------------------------------------------------------------------------------------gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
                                                                                                                                                        |   |  |    ||        | | ||  |      |  |  |  ||||||| || ||||| || || ||||||||||| ||||||||||| ||||| || ||||| || || ||||| |  || || ||  | || || || || |
gtttattcaaattcacttttttctactttatagattcatttgttggataaaggtctgcaagacacataaatccctacttcaatagattttttttgtgaatccatgtatactatgtgtagatccaagaatgcatttttcgtaactgaatttgttgctactaagtattccaaccttaatttgtggtgatatatattatatagGTTGTTCGATGGGGGCGATCAGTGTATGCCAACATTCAGAAGTTCATCCAATTTCAGCTCACAGTCAATGTCGCCGCTCTCGTAATTAATGTTGTAGCTG

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 27
--------------------------------------------gtaa--gataacagcttttggtgcgagtctgaaggatcgaaattcttgc-----agGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
                                            ||||   |||        |||||    |   ||   |     || ||||     ||||||| |||||||| || || || ||||| |||||||| || ||||||||||||||||| ||||| |||||||  || ||  || | || || || ||  
ttgccatgtatgcatttatgaagaggcttatttgaaaattcccagtaattcatatttatacctggtgtatatgacaattttatttgtttttgccatgtagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAGTTCCAGCTCACTGTTAATGTTGCAGCTCTTATTATAAATGTTGTTGCAT

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: PP1S8_288V6.1 (Physcomitrella patens), 3'ss of exon 27
----------------------------------------------------------------------------------------------------------------------gtaagataacagcttttg---gtgcgagtctgaaggatcgaaattcttgc----------agGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
                                                                                                                         || ||  || ||||    | |   ||    | |   ||  ||  ||           ||||||| |||||||| || ||||| |||||||| ||||||||||| || || || || |||||||| ||||||   || ||     ||||  | || ||  
gttcgattcgatcagtcattcctctaatctagagttcctcatgttcagctttgtaacccaatcgcatagccgttgtatactttgcacgtccgttagtgaaggtacttactttttagttaatagttagtaggttttctctggggatgtacttatgtctgacgtttctgttctgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAATTTCAACTGACTGTCAATGTTACGGCTCTTACCATCAATTTTGTCGCAT

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




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
         agataac  putative branch site (score: 45)
                                              ttcttgc  putative PPT
       taagataa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA