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'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   		35  
 5'  3'   		36  
 5'  3'   		37  
 5'  3'   		38  
 5'  3'   		39  
 5'  3'   		40  
 5'  3'   
41  
 5'  3'   		42  
 5'  3'   		43  
 5'  3'   		44  
 5'  3'   		45  
 5'  3'   		46  
 5'  3'   		47  
 5'  3'   		48  
 5'  3'   		49  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacaactgtaatttttctatggttgattattccactgtcttcgtcttaacttcagGACTGTGGACGACTTCGATGACTGGACGAACTGGCTTTTGTATAAAGGTGGAGTCGGAGTGAAAGGAGAAGAGAGCTGGGAAGCATGGTGGGATGAAGAG

Basic information

species Selaginella moellendorffii
transcript EFJ07568
intron # 45
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 45
lower sequence: LOC_Os06g02260.1 (Oryza sativa), 3'ss of exon 8
---------------------------------------gtaagcacaactgtaatttttctatggttgattattccactgtcttcgtctt--aacttcagGACTGTGGACGACTTCGATGACTGGACGAACTGGCTTTTGTATAAAGGTGGAGTCGGAGTGAAAGGAGAAGAGAGCTGGGAAGCATGGTGGGATGAAGAG
                                       |   | | || | ||||||    |    | | | |||    |  | | | |   ||| |||||||||| || ||||| ||||||||||| || ||| |  | |||||||||||||| || || || || ||| | ||||||||| | ||||||||||| |||
agaaacttacgcttggggtagttttagagatgttcttggggctggataaat-taatttccacaattctcactcttcattggcttccatttccaaacgtcagGACTGTTGAGGACTTTGATGACTGGACAAATTGGTTACTTTATAAAGGTGGAGTTGGTGTAAAGGGGGAAAACAGCTGGGAATCTTGGTGGGATGAGGAG

upper sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 45
lower sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 11
-----------------------------gtaagcacaactgtaatttttctatggttgatt--attccactgtcttcgtcttaacttcagGACTGTGGACGACTTCGATGACTGGACGAACTGGCTTTTGTATAAAGGTGGAGTCGGAGTGAAAGGAGAAGAGAGCTGGGAAGCATGGTGGGATGAAGAG
                             |||   | || |  || || ||  |    ||||  ||| ||    ||||  | |    | |||| ||| || || |||   |||||||| || ||||| || |||  ||||||  | || || ||||||||||| ||||||||||| |||||||| ||||| 
gtaagcagccaagcattttgtgtatctatgtac-tataagttcaaattgtcattatgagattagatttcaaacccttctccct---cttagGATTGTTGAGGATTTCAGAGACTGGACAAATTGGCTGTTTTATCGAGGTGGTATTGGTGTTAAAGGAGAAGAAAGCTGGGAAGCTTGGTGGGAAGAAGAA

upper sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 45
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 45
gtaagcacaactgtaatttttctat--ggttgattattccac----tgtcttcgtcttaac-----------------ttcagGACTGTGGACGACTTCGATGACTGGACGAACTGGCTTTTGTATAAAGGTGGAGTCGGAGTGAAAGGAGAAGAGAGCTGGGAAGCATGGTGGGATGAAGAG
|||||     || |  | ||| |||   ||||| | ||        ||| |     | |||                 |||||    ||||| |||||| | || ||||| || ||||| || || | ||||||| | || ||||||||||  || |||||||||||||||||||| ||||| 
gtaagtggtgctatcttatttatatcatgttgagtgttgagtaacgtgtttctcattgaacaacaataaaattatgctttcagAGTCGTGGAGGACTTCAAAGAATGGACAAATTGGCTCTTTTACAGAGGTGGAATTGGTGTGAAAGGAGCTGAAAGCTGGGAAGCATGGTGGGAAGAAGAA

upper sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 45
lower sequence: Vv17s0000g10010.t01 (Vitis vinifera), 3'ss of exon 40
-------------------------------------------------------------------------------------------------------------------------gtaagcacaactgtaatttttctatgg---ttgattattcc-----actgtcttcgtcttaactt--------cagGACTGTGGACGACTTCGATGACTGGACGAACTGGCTTTTGTATAAAGGTGGAGTCGGAGTGAAAGGAGAAGAGAGCTGGGAAGCATGGTGGGATGAAGAG
                                                                                                                          | |  | |||| |  || |  ||       |||| |  ||     | | |     ||||| | |        |||||||||||| ||||||||||| ||||| |  |||||  | |||||||||||||| || ||||| |||||  | ||||||||| | |||||||| ||||| 
gtaagtgctgctgtatattattaactttctgtagctttcttcttttaattgtccattctgagtattattcatttgttttattagtgtagctcgctttggcttttctttttgtgttctgaatattacta-aactctgcttctcttaaaagcactgatcagccctcatgaatcttacaatcttaccatgcaataaacagGACTGTGGAGGACTTCGATGATTGGACCAGTTGGCTCCTATATAAAGGTGGAGTTGGGGTGAAGGGAGACCATAGCTGGGAATCTTGGTGGGAGGAAGAA

upper sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 45
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 43
gtaagcacaactgt----aatttttctatggttgatt-------attccactgtc--ttcgtcttaac---ttcagGACTGTGGACGACTTCGATGACTGGACGAACTGGCTTTTGTATAAAGGTGGAGTCGGAGTGAAAGGAGAAGAGAGCTGGGAAGCATGGTGGGATGAAGAG
||||| |  | | |    | ||| ||| |  | ||||        ||  | |  |  || || ||| |   || ||||||||||| |||||    || ||||| ||||||||||| || | ||||||| | ||||| || |||| ||| |||||||| || |||||||||||||| 
gtaagtatcatttttctaattttctctctcatggatttgctcatgttttattaaccatttgttttaccccttttagGACTGTGGAGGACTTTCGGGATTGGACAAACTGGCTTTTTTACAGAGGTGGAATTGGAGTTAAGGGAGGAGAAAGCTGGGAGGCTTGGTGGGATGAAGAA

upper sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 45
lower sequence: PP1S145_49V6.1 (Physcomitrella patens), 3'ss of exon 44
-------------------------------------gtaagcacaactgtaatttttctatggttgattattccactgtcttcgtctta---actt-----cagGACTGTGGACGACTTCGATGACTGGACGAACTGGCTTTTGTATAAAGGTGGAGTCGGAGTGAAAGGAGAAGAGAGCTGGGAAGCATGGTGGGATGAAGAG
                                        |      || |   || | | | ||    ||| |   |||  ||  || |   ||       ||||||||||| ||||||||||||||||||||||||| | ||  | ||||| ||  ||||||   | ||  |  | || |||||||  ||||||   || |||
gtgagcaccagagaattccttacctttgttttgttctcctactttgtctatctattctgttttgtgatctatccttttgttctcaactgatggaccctcacgcagGACTGTGGCCGACTTCGATGACTGGACGAACTGGTTATTCCACAAAGGAGGCATCGGAGACGAGGGTAAGAAAAGTTGGGAAGTCTGGTGGCTGGAGGAG

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: 21

GAACCAGCTACTTTCTCTTGTCGTTTAGCAGTTGGTTTCTGGCCATTTCGTGGATGTATGCTCCCTACTTGTTCAATCCGTCCGGCTTCGAATGGCAAAAgtaagcacaa ... ttaacttcagGACTGTGGACGACTTCGATGACTGGACGAACTGGCTTTTGTATAAAGGTGGAGTCGGAGTGAAAGGAGAAGAGAGCTGGGAAGCATGGTGGGATGAAGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaactgtaatttttctatggttgattattccactgtcttcgtcttaacttcagGACTGTGGACGACTTCGATGACTGGACGAACTGGCTTTTGTATAAAGGTGGAGTCGGAGTGAAAGGAGAAGAGAGCTGGGAAGCATGGTGGGATGAAGAG
                                           tcttaac  putative branch site (score: 21)
                                     tcttcgtctt  CT-rich tract
      tgtaatttttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcacaactgtaatttttctatggttgattattccactgtcttcgtcttaacttcagGACTGTGGACGACTTCGATGACTGGACGAACTGGCTTTTGTATAAAGGTGGAGTCGGAGTGAAAGGAGAAGAGAGCTGGGAAGCATGGTGGGATGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA