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

gtcggtggcgtttcctcttctttttttgcttatgctgattgtgttataacgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA

Basic information

species Selaginella moellendorffii
transcript EFJ19085
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 2
-----------------gtcggtggcgtttcctcttctttttttgcttatgctgattgtgtta------taacgctcgtttgc---gcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
                  |  ||     |     |       | | |  |  | |  ||   |      || ||  | || |    | |||| || || ||||| || ||||| | ||| ||||| |||||| ||||||||||||||||||||||||||||| |
gtatttagtgccagcctatttgtaaaactgtacttgtaaccgtggatggtattaacggttgaaaataaatatcgtgctttcgaatggtagGTGGCGCTAAAGTTTGAACATAGAACCAGTAAAGGATGCAACCATGGGCCTCCTTACGAATGGCAGGTTTACAA

upper sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
--gtcggtggcgtttcc----tcttctttttttgcttatgctgattgtgtta----taacgctcgtttgcgc---agGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
   |   || | | ||     | ||   || |   | ||  |   ||  |||     |||| |  ||| |     |||||||  |||| || || ||| | | |||||||||||||||||||||  ||||||| || ||||| |||||| |
gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA

upper sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 3
-------------------------------gtcgg-tggcgt-ttcctcttctttttttgc---ttatgctgattgtg-ttataacgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
                               || |  ||  || ||  |   | | |  ||     ||   || || |  ||||        | |   |||||||| || ||||| ||||| || | |||||||||||||||||||||||||||||| || ||||| || |||  
gtattattaaggattccagtttctcattaaggttgaatgaagtattaatgaacctatactgtatgatacattgttttttcttattttaactttgtttacagGTTGCACTTAAGTTTGAGCACAGAAACAGCAAAGGTTGCAACTATGGGCCTCCTTATGAGTGGCAAGTATACAG

upper sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
-----------------------------gtcggtggcgtttcctcttctttttttgcttatgctgattgtgttataacgctcgtttg--cgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
                                |   | ||||  |       | |||  | ||    |  ||   ||  ||||  |||   | |||| ||  | || || |||||||| ||||||||||| ||||| ||||| ||||| || || |||||||||||| |
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattgatgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA

upper sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA08G47680.2 (Glycine max), 3'ss of exon 2
gtcggtggcgtttcctcttctttttttgcttatgctgatt------gtgttataacgctcgtttgcg---cagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
       || | || | ||   |   || ||   |   ||      |  ||       || || | |   ||||| ||| | || || ||||| |||| ||||||||| || |||||||| ||||||||||| ||||| || ||| |
-gtaaaagcttctcttgttacctcactgtttgaacaattttctacggcattgactgattctttcgtgtttcagGTGGCTTTGAAATTTGAGCACAGGAACAGCAAAGGCTGTAACTATGGCCCTCCTTACGAGTGGCAAGTGTACAA

upper sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA18G53810.1 (Glycine max), 3'ss of exon 2
------------------gtcggtggcgtttcctcttctttttttgcttatgctgattgtgttataacgctcgtttgcg---cagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA-
                         |  |   |  || | | |    ||| | ||||||  |  |     || |||| |   ||||| ||  | || || |||||||||| ||||||||| || || ||||| ||||||||||| ||||| || ||| | 
taaaagcttctcctgttaactcactgtttgaacaattttctatggatttaagttgattgaatgtttcttatcttttgtgtttcaggTGGCATTGAAATTTGAGCATAGGAACAGCAAAGGCTGTAATTATGGCCCTCCTTACGAGTGGCAAGTATACAAG

upper sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 2
----------------------------------gtcggtg-gcgtttcctcttctttttttgcttatgctgattgtgttataacgctcgtttg--cgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
                                  ||    | | || |  | |     | |||  | ||  | |  ||   ||  ||||  |||   | |||| ||  | || || |||||||| |||||||| || ||||| ||||| ||||| || || |||||||||||| |
gtatggtgttggttagtgtgttgatatttatttggttaaagagtgtatgatttatgcatattggatttgtcgttattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAGGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA

upper sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------gtcggtg-gcgtttcctcttctttttttgcttatgctgattgtgttataa-----cgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
                                       |||        | || |  | ||   ||  ||||||| |  ||||   |      | ||   ||    |||||||||| ||||| ||||||||||||||||| |||||||||||||| |||||  | || |||||||||||| |
gtaatataactcagtctgcgtttactgctgtggaggattgtcaccataaatatcattctattagcttagttatgcttacagtgtctcacatcttcactttcttatatagGTTGCTCTAAAGTTTGAGCATAGGAGCAGCAAGGGTTGCAACTATGGTCCTCCACATGAGTGGCAGGTTTACAA

upper sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------------------------------gtcggtggcgtt----tcctcttctttttttgcttatgctgattgtgtt---ataacgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
                                                                  |    | || |     || | |  |||||    | ||     |||| ||   ||    |||||||| |||||||||  | |||||||||||| |||| || || || ||||| ||||| |||||||| || ||||||||||||  
gtattcaatttcttacaatttgttctgctctacttctttcgcagcagcatgtttggaagatactctgcatattgcatcgaggtcttgtgatttttaatgtaataagttttgtattcatattgaactcgtttgtgcagGTTGCGTTGAAGTTCGAGCATCGGAGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACAC

upper sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------gtcggtggcgtttcctcttctttttttgcttatgctgattgtgttataacgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
                                                                      |  | |    |   |  | | | | ||    | |  | || ||  |     ||||   ||||||| ||| | ||||| || ||| |||||||||| |||||||| ||||| ||||||||||| ||||| |||||| |
gtactctttactctaattcgttgaggtccggtcgtgtcgtattccgtatagtgccgagggttgtgattatttagcgagtatctttgctttgtgtctggaagtacaaactgagtcttgtt-ttcgtgctcgcagGTAGCTTTAAAGTTTGAACATCGGAGCAGCAAGGGTTGCAATTATGGTCCTCCTTACGAGTGGCAAGTTTACAA

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: 56

CTATAGGACGGATAGGAAGCTGGGGAAAGGAGGCTTTGGTCAAGTTTACGTGGGTCGGAAGTTGGGGCCTGGTGATCTAACCGGTCCAAATGCTGTAGAGgtcggtggcg ... gtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcctcttctttttttgcttatgctgattgtgttataacgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA
                                  ttataac  putative branch site (score: 56)
                                          ctcgttt  CT-rich tract
        ttcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggtggcgtttcctcttctttttttgcttatgctgattgtgttataacgctcgtttgcgcagGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG