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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcgttatctctcgtttcatctgttcagtttataagtcgttttctacagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCA

Basic information

species Selaginella moellendorffii
transcript EFJ22392
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 23
lower sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 12
---------------------------------------------------------------------------------------------------------------------------------------------gtgagtcgttatctctcgtttcatctgttcagtttataagtcgttttcta-----cagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCA
                                                                                                                                               | |    |||  |||  |||| || |   | |  |  ||   |||  |     ||||| || ||||||||||| || ||||||||  ||||||| || |||||||| ||||||||||| || ||  || | ||| | || | ||| || || || |
gttggagcaattttcttttattcaattgctatgtaattgctattttgtttgccattgcgaagctacctattgcctattccattgagacactttgttgtgatattgtatgtggatatgctgaaattcttaattctaagctcgacgggcttgtatg-ctcagttcaactctaatgctgctctgttcctttacacatttcagCTTCTCTGGGTAAATCTAATCATGGATACACTGGGAGCTCTGGCTTTAGCAACTGAACCACCGACGGATAACCTTATGAAGAGACAGCCTGTTGGTCGAA

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 23
lower sequence: GRMZM2G340139_T01 (Zea mays), 3'ss of exon 27
----------------------------------------------gtgagtcgttatctctcgtttcatctgttcagtttataagtcgttttcta-cagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCA
                                                 | |  ||     |  |  ||  | ||  |||| ||  ||      |  ||||| |||||||| |||||||||||||| ||  | ||||| || || ||||| || |||||||| |||||| || ||||| | ||||  ||||| || || |
atatagcaaagtacttaatgtaagaccttacagggatcttgtttgctatatttcttgcaaataatgccaatttttttgtttttatctccccccttggcagCTTCTTTGGGTGAATCTTATTATGGACACACTCGGAGCTCTTGCATTAGCAACCGAACCACCAACAGACAACCTAATGAAGAGGCATCCCGTCGGTCGAA

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 23
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 26
-------------------------------gtgagtcgttatctctcgtt---tcatctgttcagtttataagtcgttttctacagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCA
                                | |    |||  ||  | |    |||      |   | |    | || |||| |||| |||||||| |||||||| ||||||||| |||||||||| ||  | || ||||||||||| || ||  || | |||||| |  | || ||||| || |
gttgactttctttttttctttctaggttatgctcatgtattaagtcaggatgagccatgatgctaaaatctgttgctttctctatagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAA

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 23
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 26
-------------------------------gtgagtcgttatctctcgtt---tcatctgttcagtttataagtcgttttctacagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCA
                                | |    |||  ||  | |   ||||    | |   | |    | || |||| |||| ||||||||||||||||| ||||||||| ||||||| || ||  | || ||||||||||| || ||  || | |||||| |  | || ||||| || |
gttgactttctttttctctttctaggttatgctcacgtattaagtcaggatgagtcatgacattaaaatctgttgctttctctatagCTTCTTTGGGTAAATCTTATCATGGATACTCTGGGAGCACTAGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGATCCCCAGTGGGTCGAA

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 23
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 28
------------------------------------------gtgagtcgttatctctcgtttcatctgttcagtttataagtcgttttctacagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCA
                                             |||  | |  ||     |            ||||   |    |  |  |||| |||||||| |||||||| ||||||||| | || || || |||||||||||||| ||||| || ||  ||||||||||| |  |||| || ||  | |
gttcgaaatagtagttttatactctctctttctcatctgcacaaaagtattcacttcagaacttggtaaaaagtcttatcccttaccta-tgtagCTCCTTTGGGTCAATCTTATAATGGATACTCTTGGGGCTCTTGCTTTAGCCACTGAGCCACCAACCGATCACTTAATGGATCGAGCGCCTGTTGGCAGAA

upper sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 23
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
---------------------------------gtgagtcgttatctctcgtttcatctgttcagtt---tataagtcgtttt--ctacagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCA
                                 |  |||  |  | | |||| |||| |||| |  |   | |       |||   ||||||| || ||||| |||||||| ||||||||| | ||||| || || || |||||||||||||| |||||  || | ||| | ||||| || || || || |
gttggtggcccacccattgctgcctcttgagttgacagttctattatgtcgtctcatttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA

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|169101664|gb|FE501208.1|FE501208
EST:     ACGTCGTGGCCGCAGCAAAGTCGAGCCAGGTTCCTCTTACTGCTGTGCAG                         CTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCC
genomic: ACGTCGTGGCCGCAGCAAAGTCGAGCCAGGTTCCTCTTACTGCTGTGCAGgtgagtcgtt ... ttttctacagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCC
EST: gi|169108170|gb|FE512543.1|FE512543
EST:     CGTCGTGGCCGCAGCAAAGTCGAGCCAGGTTCCCTCT-ACTGCTGTGCAG                         CTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCC
genomic: CGTCGTGGCCGCAGCAAAGTCGAGCCAGGTTCC-TCTTACTGCTGTGCAGgtgagtcgtt ... ttttctacagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCC
EST: gi|169075222|gb|FE484104.1|FE484104
EST:     ACGTCGTGGCCGCAGCAAAGTCGAGCCAGGTTCCTCTTACTGCTGTGCAG                         CTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCC
genomic: ACGTCGTGGCCGCAGCAAAGTCGAGCCAGGTTCCTCTTACTGCTGTGCAGgtgagtcgtt ... ttttctacagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCC

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: 42

GAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCGCAGCAAAGTCGAGCCAGGTTCCTCTTACTGCTGTGCAGgtgagtcgtt ... ttttctacagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagtcgttatctctcgtttcatctgttcagtttataagtcgttttctacagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCA
                                           tcgttttct  CT-rich tract
                                agtttataa  TA-rich tract