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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACTGACTGTACATTCATAAGAGTTTCAGGGTCCGAGCTAGTCCAGAAATACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaatgtccatattctatcctagtatagttacgtttttctgtgttttcttag

Basic information

species Selaginella moellendorffii
transcript EFJ20576
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ04162 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA07G00420.1 (Glycine max), 5'ss of exon 5
ATACTGACTGTACATTCATAAGAGTTTCAGGGTCCGAGCTAGTCCAGAAATACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaatgtccatattctatcctagtatagttacgt-ttttctgtgttttcttag-------------------------------------------
||||||||||||||||||| || || || || || ||| |||| ||||||||||| |||||||| || || |||||  | || ||||| || ||||| |||| |  |  | |  |  |    ||||    |  |||  | ||   | ||||| | |                                             
ATACTGACTGTACATTCATCAGGGTGTCTGGTTCTGAGTTAGTTCAGAAATACATTGGAGAAGGTTCTAGAATGGTCAGGGAACTTTTTGTTATGGCCAGgt-ttattctctttacttggcttcctctattcattatctgttgattctgtttgccttacaccaaaacagaagggataaaaacaatgtcttcttggcttcat

upper sequence: EFJ04162 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 5'ss of exon 5
ATACTGACTGTACATTCATAAGAGTTTCAGGGTCCGAGCTAGTCCAGAAATACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgt------atcgtaatgtccatattctatc-ctagtatagttacgtttttctgtgttttcttag------------------------------------
| ||||||||||| |||||||||||||| || |||||||| |||||||||||||| |||||||| || || |||||  |||| ||||| || ||||||||||      || ||| |  | || ||  ||  | || || || |   |  |   |       ||                                     
ACACTGACTGTACTTTCATAAGAGTTTCTGGTTCCGAGCTTGTCCAGAAATACATTGGAGAAGGTTCTAGAATGGTCAGAGAACTTTTTGTGATGGCAAGgttagtatatggtagtccctattttaaatttcaagcatggtaatagtggttgataggaaaatatggaactgttgataagataacatcttttaacatgtcc

upper sequence: EFJ04162 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 5'ss of exon 5
ATACTGACTGTACATTCATAAGAGTTTCAGGGTCCGAGCTAGTCCAGAAATACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtat---cgtaat-gtccatattctat---cctagtatagttacgtttttctgtgttttcttag--------------------------------------
| ||||||||||| ||||| |||||||| || || ||||| |||||||||||||| |||||||| || || |||||  |||| ||||| || |||||||||| |   | |  | |||| ||||  ||    | || || || |   |  |    |||     ||                                      
ACACTGACTGTACTTTCATCAGAGTTTCTGGTTCTGAGCTGGTCCAGAAATACATTGGAGAAGGTTCTAGAATGGTCAGAGAACTTTTTGTGATGGCAAGgtttgtacatgctagtccttatttaatatttcaagcatggtaaaagtggt--aggttggaaaagatggaacttttgacacgataaatcttttacatgcccgt

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|169037547|gb|FE446288.1|FE446288
EST:     TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169065602|gb|FE475882.1|FE475882
EST:     TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169094801|gb|FE492952.1|FE492952
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTNTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169071822|gb|FE478109.1|FE478109
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169062819|gb|FE472348.1|FE472348
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169113190|gb|FE514436.1|FE514436
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169062833|gb|FE472349.1|FE472349
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169039782|gb|FE449444.1|FE449444
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169065603|gb|FE475883.1|FE475883
EST:     TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169094802|gb|FE492953.1|FE492953
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATNCTT-ATGGACGAGATTGACAGCATTGGCT
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTAT-CTTTATGGACGAGATTGACAGCATTGGCT
EST: gi|169113973|gb|FE516444.1|FE516444
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169038427|gb|FE446128.1|FE446128
EST:     TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169055186|gb|FE461060.1|FE461060
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTNTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169071823|gb|FE478110.1|FE478110
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
EST: gi|169037548|gb|FE446289.1|FE446289
EST:     TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTAT
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTAT
EST: gi|169113189|gb|FE514435.1|FE514435
EST:     TACATCGGAGAAGGGTCGAGAATGGTGCGAGAGCTTTTCGTCATGGCAAG                         AGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC
genomic: TACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTC

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), 31 (downstream exon)
Score: 23

ATACTGACTGTACATTCATAAGAGTTTCAGGGTCCGAGCTAGTCCAGAAATACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaat ... gttttcttagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTCGTCCCGTATGGAGTCTGGCAATGGCAACGGGGACAGTGAAGTGCAGAGA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACTGACTGTACATTCATAAGAGTTTCAGGGTCCGAGCTAGTCCAGAAATACATCGGAGAAGGGTCGAGGATGGTGCGAGAGCTTTTCGTCATGGCAAGgtatcgtaatgtccatattctatcctagtatagttacgtttttctgtgttttcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT