Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtggaaggaaagctggtctatataaccaccctgcctgtgccttgtgtgtcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ16567
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ16567 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os02g05330.1 (Oryza sativa), 5'ss of exon 4
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtggaaggaaagctggt-ctatataaccaccctgcctgtgccttgtgtgtcgcag----------------------------------------
 |  || |||||  | || |   | || || || ||| |||| ||||||||||| ||||| || || || |||||||| ||||| ||||||||||| |||||  | |       |  |   |  | |   |  |  |  ||      |||| || |  |                                         
GTTTGACATGCTACGTCGGCAATCTCTCCGCCCAGACCACATTAAGATGTTTGTGCTGGATGAAGCTGATGAGATGCTCTCCCGTGGTTTCAAGGATCAGgtttgcttctgaccagcccattattctgctataatacctccaacagtttgtatggctgatcttttacattatgtcttctgtagtgttcatgtttgtgtaa

upper sequence: EFJ16567 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os06g48750.1 (Oryza sativa), 5'ss of exon 4
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtggaaggaaagctggtctatataac-caccctgcctgtgccttg-tgtgtcgcag-----------------------------------------
 |  || |||||  |  | |   | || || || || |||||||||||||||||||| || || || || || ||||| || || ||||||||||| ||||| ||     |    || || | | |||    ||    |  || |  ||          ||                                         
GTTTGACATGCTGCGTAGGCAGTCCCTCCGTCCTGATTACATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgttag-cattatcttagttg-tttgtattttgcatttggtttgcggtttaacactatttagactttctgagagcatgattcattaatgattgtacaattctt

upper sequence: EFJ16567 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G027995_T01 (Zea mays), 5'ss of exon 4
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaa--------ggtggaaggaaagctggtctata--taaccaccctgcctgtgccttgtg-tgtcgcag------------------------------
 |  || |||||  |  | |   | || || || ||  |||||||||||||||| || ||||| || || || ||||| || || ||||||||||| |||||||          |  |     |     |||||   | | ||   | |||||    | || |     ||                              
GTTTGACATGCTGCGTAGACAGTCCCTCCGCCCTGATAACATCAAGATGTTTGTTCTTGACGAAGCTGATGAAATGCTTTCTCGTGGTTTCAAGGATCAGgtaaacacttctattttatttctattctctctatgcttgatcatggtacctgtattctttgctagtaaagtgcagagattaagtttaaattgatttgcca

upper sequence: EFJ16567 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA17G06110.1 (Glycine max), 5'ss of exon 4
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtggaagg--aaagctggtcta-ta-taaccaccctgcctgtgccttgtgtgtcgcag-------------------------------------
 |  ||||||||  | || |   | || | ||| ||| ||||||||||||||||  |||| ||||| || || ||||| ||||| ||||||||||| ||||||   |   |    | | ||  | || || |   |||  |   | |  ||  |   |                                          
GTTTGATATGCTGCGCCGACAGTCACTTCAGCCAGACCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTCAAGGATCAGgtaccttttcaattcacaactcatttagtacttttcactttaattattactaatactttatgtttttgataagtaatgcctacacttgtctatggatttt

upper sequence: EFJ16567 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA15G18760.3 (Glycine max), 5'ss of exon 4
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtggaaggaaagctggtctatataacca-----ccctgcctg--tgccttgtgtgtcgcag----------------------------------
 |  ||||||||  |  | |   | || ||||| ||||||||||||||||||||  |||| ||||| || || ||||| ||||| ||||| || || |||||    |  ||   |   |  | |   |||  |       |||  ||  |  ||||| | |   |                                   
ATTTGATATGCTGCGCAGACAGTCACTTCGGCCAGACTACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGTGGTTTTAAAGATCAGgttctttctaaatcatattccttttgttaatgaagaattactgattggatttcttgtttatgatatgtaatgccccacgtttctgtatttttgtacattg

upper sequence: EFJ16567 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA13G16570.1 (Glycine max), 5'ss of exon 4
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtggaaggaaagctggtctatataaccaccctgcctgtgccttgtgtgtcgcag-----------------------------------------
 |  ||||||||  |  | |   | || | ||| ||  ||||||||||||||||  |||| ||||| || || ||||| ||||| ||||| ||||| ||||||   |  |    ||      ||| ||        ||  | |  |  ||    |  |                                          
GTTTGATATGCTGCGCAGACAGTCACTTCTGCCAGATCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttcactttaattattactaaatttttttgttgttttttacaagtaatacctacacttgtctacggatttttttaaattgatgtgtaaacgttcg

upper sequence: EFJ16567 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtggaaggaaagctggtctatataaccaccctgcc----tgtgccttgtgtgtcgcag------------------
||  || ||| | | | | |   | || ||  | ||| |||||||||||||||| || || || || || || ||||| ||||| |||||||||||||||||| |     |         || |  ||  |   |  |      | |  ||||  | || | |                  
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaatatttctcagtgtttcaattccattctcgttatagtttaacttgaatctcactggtttctgggttttttcag

upper sequence: EFJ16567 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtg--------gaagg--aaagctggtctatataaccacc-ctgcctgtgccttg----tgtgtcgcag----------------
 |  || ||||| ||  | |   | || || || |||| |||||||||||||||||| || || || || || ||||| ||||| ||||||||||| |||||  | |          |||    || ||   || | |    | | |||    || ||||    ||||| |                   
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatcttcttcaaagtttgaatctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaatttgcag

upper sequence: EFJ16567 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: EDP05185 (Chlamydomonas reinhardtii), 5'ss of exon 4
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgta-------------aggtg---------gaaggaaagctggtctatataaccaccctgcctgtgccttgtgtgtcgcag----------------------------------------------------------
                                       ||||||||||||   |||||||||||| || ||||||||||| |||||||||||||||||| |              || ||          |     || ||  |    |  |  |  ||| || || | || ||||||                                                            
---------------------------------------CATCAAGATGTTCACCCTGGACGAGGCCGATGAGATGCTGTCTCGCGGTTTCAAGGACCAGATCTACGACATCTTCCAGCTGCTGCCCCCCAAGCTGCAGgtgagccggctgccagcattgcatgggcttggtctgtcgcttgcaattgcttgtagaaatctgcgcggtcgacgtgggattggaaggcggcgtgattgaa

upper sequence: EFJ16567 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S77_16V6.1 (Physcomitrella patens), 5'ss of exon 3
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtggaaggaaagctggtctatataaccaccctgcctgtgccttgtgtgtcgcag-----------------------------------------
 ||||| ||| |  |  |    ||||||||  |||| | |||||||   || || ||||||||||| || |||||||| || || |||||||||||||||||  ||||        | || | |   |        |||| |   |  ||| |     |                                         
GTACGACATGTTGCGCAGGAATGCGCTGCGCGCGGATTCCATCAAGTGCTTCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtgttgttgtcgttgctgttgttgttgttgttgccaggtgccggtgagcgtttgtggagaattgtgtttggtcgtggtgggagcggtgtggatgg

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|169088590|gb|FE491502.1|FE491502
EST:     TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
genomic: TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtgga ... tgtgtcgcagATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
EST: gi|169038264|gb|FE445289.1|FE445289
EST:     TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
genomic: TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtgga ... tgtgtcgcagATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
EST: gi|169031548|gb|FE439013.1|FE439013
EST:     TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
genomic: TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtgga ... tgtgtcgcagATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
EST: gi|169065831|gb|FE474382.1|FE474382
EST:     TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
genomic: TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtgga ... tgtgtcgcagATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
EST: gi|169110549|gb|FE513647.1|FE513647
EST:     TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
genomic: TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtgga ... tgtgtcgcagATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
EST: gi|169039347|gb|FE447228.1|FE447228
EST:     TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTCC
genomic: TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtgga ... tgtgtcgcagATTTACGACATCTTCCAGCTCC
EST: gi|169062506|gb|FE469968.1|FE469968
EST:     TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
genomic: TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtgga ... tgtgtcgcagATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
EST: gi|169045543|gb|FE450736.1|FE450736
EST:     TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTCCTTCCCT
genomic: TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtgga ... tgtgtcgcagATTTACGACATCTTCCAGCTCCTTCCCT
EST: gi|169078455|gb|FE488330.1|FE488330
EST:     TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
genomic: TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtgga ... tgtgtcgcagATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
EST: gi|169056092|gb|FE465644.1|FE465644
EST:     TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
genomic: TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtgga ... tgtgtcgcagATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
EST: gi|169060700|gb|FE467438.1|FE467438
EST:     TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
genomic: TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtgga ... tgtgtcgcagATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
EST: gi|169098742|gb|FE500254.1|FE500254
EST:     TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
genomic: TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtgga ... tgtgtcgcagATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC
EST: gi|169074031|gb|FE483472.1|FE483472
EST:     TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAG                         ATTTACGACATCTTCCAGCTCCTTCCCTCCA-GGTCCAGGTGGGCCTCTTC
genomic: TTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtgga ... tgtgtcgcagATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTC

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: 123

CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtgga ... tgtgtcgcagATTTACGACATCTTCCAGCTCCTTCCCTCCAAGGTCCAGGTGGGCCTCTTCTCCGCCACAATGCCGCCCGAGGCGCTGGAGATCACCCGCAAGTTCATGA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtggaaggaaagctggtctatataaccaccctgcctgtgccttgtgtgtcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG