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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTGTCTTTTGCTCGACTTACTTGATGCTCCAAGCTGGCGTCCTCGGTGGAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAGgtacatacttttaccaattactgaagttacctgtaacagtgtttatctggattacag

Basic information

species Selaginella moellendorffii
transcript EFJ23975
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23975 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: LOC_Os08g23440.1 (Oryza sativa), 5'ss of exon 12
TCCTGTCTTTTGCTCGACTTACTTGATGCTCCAAGCTGGCGTCCTCGGTGGAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAGgtacatacttttacca--attactgaagttacctgtaacagtgtttatc-tggattacag----------------------------------------
|| ||  || | || ||| | ||||||||||| || ||||||||||| ||||||||||| || ||||| || || ||  | |||||  |  | ||  | ||||      | ||| |  |  | |  | ||      ||  |  |  ||| ||   |  |                                         
TCATGCTTTCTCCTTGACCTCCTTGATGCTCCTAGTTGGCGTCCTCGTTGGAAATTTCACCATTGGAGTTTATCACTTGTTGGTGCATTGCTTTGTGTTGgtatgactatatactattacaaattcattttgacacaatggcatgcatcatgagctgtaatgctttcttaggacattattttgattaaagacttctgaca

upper sequence: EFJ23975 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: AT1G30450.3 (Arabidopsis thaliana), 5'ss of exon 11
TCCTGTCTTTTGCTCGACTTACTTGATGCTCCAAGCTGGCGTCCTCGGTGGAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAGgtacatactttt--accaattactg--aagttacctgtaacagtgtttatctggattacag---------------------------------------------------------------------------------------------------------------------
|| ||| |  |||||||  | |||||||||||||| |||||||| |||||||||| |||||| |||||| ||||  |  | || ||   | | ||||||||||   | ||||  |  | | || |  ||  |  || |  |||| |   | || | | ||                                                                                                                      
TCTTGTTTCCTGCTCGATCTTCTTGATGCTCCAAGTTGGCGTCCACGGTGGAAATATCATCATTGGAGCCTTTCCTTTGTTGGAGCCTCACTTTGCATAGgtatgaaattttcaaatactcacggagaaagtgtctttcccagtctacctatgtagtccattcctatagaaattctgatttgaactaccacgtggcttcttatctcacctgaatcctgagatgtcttattacaaagccttgttgagtttttaaattattattttttctattcttgcag

upper sequence: EFJ23975 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: Vv10s0003g04530.t01 (Vitis vinifera), 5'ss of exon 11
TCCTGTCTTTTGCTCGACTTACTTGATGCTCCAAGCTGGCGTCCTCGGTGGAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAGgtacatacttttaccaattactgaagttacctgtaacagtgttt-------atctggattacag------------------------------------
|| ||  |  | || ||  | || |||||||| || |||||||| || ||||||||||| ||||||||| | || || || || ||  |  | || |||||||     | ||  || ||  |    || |  | |    | | |       |   ||| ||||                                     
TCTTGCTTCCTTCTGGATCTTCTAGATGCTCCCAGTTGGCGTCCACGATGGAAATTTCACCACTGGAGCCTCTCTCTTCTTGGAGCAGTTCTTTGTATAGgtatggtttattctcattttattccattgcagggatttatttcttgggaagagtgggaatacaatcggggcaatcattacaactgttttttagtggatac

upper sequence: EFJ23975 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: PP1S14_51V6.1 (Physcomitrella patens), 5'ss of exon 11
TCCTGTCTTTTGCTCGACTTACTTGATGCTCCAAGCTGGCGTCCTCGGTGGAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAGgtacat------acttttaccaattactgaagttacctgtaacagtgtttatctggattacag---------------------------------------
|| || |||||||| ||  | || || || || |||||||||||||| ||||||| ||||||||||||||| || ||  |||||||  |  | ||||| |||   |       ||||| ||| ||  | |   |  | ||  ||  |||   || ||  | ||                                       
TCTTGCCTTTTGCTTGAGCTTCTAGACGCGCCCAGCTGGCGTCCTCGCTGGAAATATCATCACTGGAGCTTCTCACTTGTGGGTGCGGTTCTTTGCATCGgtgagttttgtatctttttccatttttttataatttcggtg-caaagttatcctagaa-atagcgtttttttttgtctttgaagtggcataaatactcttga

upper sequence: EFJ23975 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: PP1S5_444V6.1 (Physcomitrella patens), 5'ss of exon 11
TCCTGTCTTTTGCTCGACTTACTTGATGCTCCAAGCTGGCGTCCTCGGTGGAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAGgtacatacttttaccaattactgaagttacctgta-------acagtgtttatctggattacag------------------------------------
||||||||  | || ||| | ||||| ||||| |||||||| |||||||  ||||||||||||||||| || || || || ||||||||  | |||||  |||  | || | ||    |  | | || | |  |          |  ||||   ||   || |                                     
TCCTGTCTCCTACTTGACCTTCTTGACGCTCCTAGCTGGCGACCTCGGTTTAAATTTCATCACTGGAGTTTCTCCCTTCTAGGTGCTCTCCTTTGCATCTgtaagtcctctaacttgctcataatgtgaacacttcatttgcgtacggtttgaatgagctataatttgtatttaatttagcgttagacctgacacgagaa

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|169019690|gb|FE427493.1|FE427493
EST:     GAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAG                         TTATAATGTTTTTAATATCCTGGATTTTCACAACTGTATCACTCGCGTTGG
genomic: GAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAGgtacatactt ... tggattacagTTATAATGTTTTTAATATCCTGGATTTTCACAACTGTATCACTCGCGTTGG
EST: gi|169020756|gb|FE430157.1|FE430157
EST:     GAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAG                         TTATAATGTTTTTAATATCCTGGATTTTCACAACTGTATCACTCGCGTTGG
genomic: GAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAGgtacatactt ... tggattacagTTATAATGTTTTTAATATCCTGGATTTTCACAACTGTATCACTCGCGTTGG
EST: gi|169076690|gb|FE485525.1|FE485525
EST:     GAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAG                         TTATAATGTTTTTAATATCCTGGATTTTCACAACTGTATCACTCGCGTTGG
genomic: GAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAGgtacatactt ... tggattacagTTATAATGTTTTTAATATCCTGGATTTTCACAACTGTATCACTCGCGTTGG
EST: gi|169107879|gb|FE510978.1|FE510978
EST:     GAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAG                         TTATAATGTTTTTAATATCCTGGATTTTCACAACTGTATCACTCGCGTTGG
genomic: GAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAGgtacatactt ... tggattacagTTATAATGTTTTTAATATCCTGGATTTTCACAACTGTATCACTCGCGTTGG
EST: gi|169046025|gb|FE451257.1|FE451257
EST:     GAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAG                         TTATAATGTTTTTAATATCCTGGATTTTCACAACTGTATCACTCGCGTTGG
genomic: GAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAGgtacatactt ... tggattacagTTATAATGTTTTTAATATCCTGGATTTTCACAACTGTATCACTCGCGTTGG

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), 19 (downstream exon)
Score: 5

TCCTGTCTTTTGCTCGACTTACTTGATGCTCCAAGCTGGCGTCCTCGGTGGAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAGgtacatactt ... tggattacagTTATAATGTTTTTAATATCCTGGATTTTCACAACTGTATCACTCGCGTTGGCAAGTCTCATATATTATTACGTTAGCTTGAAAGGCAAAGCAGGAGACTG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTGTCTTTTGCTCGACTTACTTGATGCTCCAAGCTGGCGTCCTCGGTGGAAATTTCATCACTGGAGCTTTTCGCTCCTGGGTGCTCTATTGTGCATAGgtacatacttttaccaattactgaagttacctgtaacagtgtttatctggattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT