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

gtttggatgattgattctttggttgtgtctttttggctgatttgttttccttgttggtttgcttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCCATCCCCAACCAGCAGATAATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA

Basic information

species Selaginella moellendorffii
transcript EFJ36890
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ36890 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM5G800112_T01 (Zea mays), 3'ss of exon 3
-----------------------------gtttgg--atgattgattctttggttgtgtctt-tttggctgatttgttttccttgttggtt-tgcttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCCATCCCCAACCAGCAGATAATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA
                              ||     ||   |||    | | |||   ||| ||||||  |||  |       |   ||  || ||  |  || |||| || |||||||| ||||| || || ||||||||||| || || || ||||||||||||||||| ||   ||                        
gtacttggtggtatcattgggtttcagaacttcaaccatagctgagaagtagcttgatccttgtttggcctattaatcagATGAGGATGTGGTGTTTATTGTAGATGATAAATGAGAAGCCACAGGTGATTCAGGAGTATGAATCAGGCAAGGCAATCCCCAACCAGCAGATCATTAGCA------------------------

upper sequence: EFJ36890 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 3
--------------------gtttggatgattgattctttggttgtgtctt----tttggctgatttgttttccttgttggt-----ttgcttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCCATCCCCAACCAGCAGATAATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA
                      | |    ||||||   | ||  ||  |||     |||| ||   | |||      |  |       || |   | ||| ||||||| |||||||| ||||| ||||| |||||||| || || || || || |||||||||||||| ||   |||||||||| | || |||||| | |
aaagtctatgctgttgttgtagtagttccattgatagctgggaagtagcttgatccttggttggcctctttatgagatgaggatatggtgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA

upper sequence: EFJ36890 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM5G800112_T02 (Zea mays), 3'ss of exon 3
-----------------------------gtttgg--atgattgattctttggttgtgtctt-tttggctgatttgttttccttgt-tggtttgcttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCCATCCCCAACCAGCAGATAATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA
                              ||     ||   |||    | | |||   ||| ||||||  |||  |       |  ||   || ||  |  || |||| || |||||||| ||||| || || ||||||||||| || || || ||||||||||||||||| ||   |||||||||| | || |||||| |||
gtacttggtggtatcattgggtttcagaacttcaaccatagctgagaagtagcttgatccttgtttggcctattaatcagatgaggatgtggtgtttattgtagATGATAAATGAGAAGCCACAGGTGATTCAGGAGTATGAATCAGGCAAGGCAATCCCCAACCAGCAGATCATTAGCAAGCTCGAGAGGGCCCTGGGAACCA

upper sequence: EFJ36890 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA06G42900.1 (Glycine max), 3'ss of exon 3
------------------------------gtttggatgattgattctttggttgtgtctttttggctgatttgttttccttgttggtttgcttggtc-----cagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCCATCCCCAACCAGCAGATAATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA
                                 |  || || |||   ||  || | |||| || ||  ||| |   |  |   ||   ||| | ||      ||||||||||| ||||||||||| || ||||| ||||| || || ||||| ||||| || ||||||||||||||   |||| | ||  | || || ||||| |
gtattactctcccttcagtagaattatttttaatatatcatcgatctctttatttt-tcttattagc-aattaggcattatcaatgacgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCCATTCCAAACCAGCAGATAATTGGCAAGTTGGAAAGAGCCCTTGGAGCTA

upper sequence: EFJ36890 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA06G42890.1 (Glycine max), 3'ss of exon 3
---------gtt-tggatgattgattctttggttgtgtctttttggctgatttgttttccttgttggtttgcttggtc-----cagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCCATCCCCAACCAGCAGATAATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA
         ||  |  || || | |   ||  || |  ||| || | |  || |   |  |   || | ||| | ||      ||||||||||| ||||||||||| || ||||| |||||||| || || || ||||| || ||||||||||||||   |||| | ||  | || || ||||| |
gtattgctcgtcgtatattatcggtctctttatttt-ccttattag-tatttaggcattatcaatgatgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTATGAGTCAGGGAAGGCCATTCCAAACCAGCAGATAATTAGCAAGTTGGAAAGAGCTCTTGGAGCTA

upper sequence: EFJ36890 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA12G15420.1 (Glycine max), 3'ss of exon 3
--------------------------gtttggatgattgattctttggttgtgtctttttgg-ctgatttgttttcc-------ttgttggtttgcttggtc-----cagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCCATCCCCAACCAGCAGATAATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA
                           |||| ||   | |||| ||  | || |||||||   |  | | || ||         |   || | ||| | ||      ||||||||||| ||||||||||| || ||||| ||||| || || || || ||||| || ||||||||||||||    ||| | ||  | || || ||||| |
gtattgctttcttctctgtagattttttttgaatatattattcattattggtctcttttttttcctactagtatttaggcatgatcaatgatgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGGAAGGCCATTCCAAACCAGCAGATAATTGGGAAGTTGGAAAGGGCTCTTGGAGCAA

upper sequence: EFJ36890 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT2G42680.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------gtttggatgattgattctttggttgtgtctttttggctgatttgttttcc--ttgttggtttgcttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCCATCCCCAACCAGCAGATAATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA
                | |  |||     |  | |     | | || |     | ||  |       |  ||| ||   || ||  || | ||||| |||||||| || || || ||||||||||| ||||| ||||| || ||||||||||| ||  | || ||||| ||| | ||||| ||||| |
gtatattatccttctctctatatgtcccttattattaccctattttgtaactcggttcatgacaaagtgtttgtttctttttgtgtagATCATCAATGAGAAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGCTATACCCAACCAGCAAATCCTTTCTAAGCTGGAGAGAGCGCTTGGAGCTA

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|169022561|gb|FE429445.1|FE429445
EST:     TCATCCAAGCCCGGACGGAGAAGAAACTGACACAGGCACAGCTTGCACAG                         CTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCC
genomic: TCATCCAAGCCCGGACGGAGAAGAAACTGACACAGGCACAGCTTGCACAGgtttggatga ... cttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCC
EST: gi|169078932|gb|FE486584.1|FE486584
EST:     TCATCCAAGCCCGGACGGAGAAGAAACTGACACAGGCACAGCTTGCACAG                         CTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCC
genomic: TCATCCAAGCCCGGACGGAGAAGAAACTGACACAGGCACAGCTTGCACAGgtttggatga ... cttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCC
EST: gi|169077262|gb|FE485148.1|FE485148
EST:     TCATGCAAGCCCGGACGGAGAAGAAACTGACACAGGCACAGCTTGCACAG                         CTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCGGGAAAAGCC
genomic: TCATCCAAGCCCGGACGGAGAAGAAACTGACACAGGCACAGCTTGCACAGgtttggatga ... cttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCC
EST: gi|169022560|gb|FE429444.1|FE429444
EST:     TCATCCAAGCCCGGACGGAGAAGAAACTGACACAGGCACAGCTTGCACAG                         CTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCC
genomic: TCATCCAAGCCCGGACGGAGAAGAAACTGACACAGGCACAGCTTGCACAGgtttggatga ... cttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCC

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: 66

ACGAGCGCGTTCCGACTGACCTGAAGAAGAACATCATCCAAGCCCGGACGGAGAAGAAACTGACACAGGCACAGCTTGCACAGgtttggatga ... cttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCCATCCCCAACCAGCAGATAATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttggttgtgtctttttggctgatttgttttccttgttggtttgcttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCCATCCCCAACCAGCAGATAATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA
                  ggctgat  putative branch site (score: 66)
                                         tttgctt  putative PPT
                       atttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggatgattgattctttggttgtgtctttttggctgatttgttttccttgttggtttgcttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCCATCCCCAACCAGCAGATAATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT