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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttctattgctagatcttcacatgttttaaaaccgtaacaaccctacacaactcacaaagaagcttttcgacagGTTCGGATCATATCCGTGAGAAAGATGGGATCTGGGCAGTTCTTGCTTGGCTATCAATACTGGCTCACAAGAACAAGGAAACCCTTGATGGGAATGCAAA

Basic information

species Arabidopsis thaliana
transcript AT1G70730.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 13
-----gtgagcttctattgctagatcttcacatgttt--taaaaccgtaacaaccctaca--caactcacaaagaagctt------------ttcgacagGTTCGGATCATATCCGTGAGAAAGATGGGATCTGGGCAGTTCTTGCTTGGCTATCAATACTGGCTCACAAGAACAAGGAAACCCTTGATGGGAATGCAAA
      |||   || | ||    |  || | ||  |   | | || | |   |   ||     | ||||| | || ||||            ||    |||||| ||||| || |||||||||||||| || ||||| ||||| || ||| |||| || || |||  |||||||||||| | |||||  ||  ||     
catcaatgaaaatcaagtggatcacatttaaataatgagtcacactgcagtcaggatatgactagctcaccaggatgcttatacctactatgttgtttagGTTCTGATCACATTCGTGAGAAAGATGGTATTTGGGCTGTTCTAGCATGGTTATCTATTCTTGCTTTCAAGAACAAGGACAACCTTGGAGGCGATAAGCT

upper sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 13
---------------------gtgagcttctattgctagatcttcacatgttttaaaaccgtaacaaccctacacaactcacaaagaagcttttcgacagGTTCGGATCATATCCGTGAGAAAGATGGGATCTGGGCAGTTCTTGCTTGGCTATCAATACTGGCTCACAAGAACAAGGAAACCCTTGATGGGAATGCAAA
                       |||   | |  |    |  ||||  | | ||||||||                | |         | || | || |||||| || ||||| |||||||||||||| |||||||||||| | || |||||||| ||||| ||  | || || || || |  ||||| |  ||      
gtatgtgtttgctattgcattaagaggagcaaa-gtacaactttcaactttattaaaacctagtttttatcttgtgattattccttgtgtttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAGACAAGCTTGT

upper sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 13
---------------------gtgagcttctattgctagatcttcacatgttttaaaacc--gtaacaaccctacacaactcacaaagaa-------gcttttcgacagGTTCGGATCATATCCGTGAGAAAGATGGGATCTGGGCAGTTCTTGCTTGGCTATCAATACTGGCTCACAAGAACAAGGAAACCCTTGATGGGAATGCAAA
                       |||   | |  |    |  ||||  | | ||||||||  ||   || | |    | ||    |  |        |||| | || |||||| || ||||| |||||||||||||| |||||||||||| | || |||||||| ||||| ||  | || || || || |  ||||| |  ||      
gtatgtgtttgctattgcattaagaggagcaaa-gtacaactttcaactttattaaaacctagttttaaactttt-tatcttgtgattattccttgtgcttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAGACAAGCTTGT

upper sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 14
gtgagcttctattgctagatcttcacatgttttaaaaccgtaacaaccctacacaactcacaaag----aagcttttc--------gacagGTTCGGATCATATCCGTGAGAAAGATGGGATCTGGGCAGTTCTTGCTTGGCTATCAATACTGGCTCACAAGAACAAGGAAACCCTTGATGGGAATGCAAA---
||  | ||| ||   | |    | | || | |   ||   | |||  |  | |       |||       | || ||         |||||||||||| || || |||||||||||||| |||||||| ||| | |||||||| || || || ||| |  | || ||||||| ||||| |||    |||||   
gtaggtttc-atattttgtgtatgaaatttctgttaattatgacatacacatatgtaaagcaatattttgatctgttgtatctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGCTTTCTATTCTCGCTTATGAAAATAAGGAAAACCTTGGTGGA---GCAAAGCT

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|125081719|gb|EL142834.1|EL142834
EST:     GTGCTCTGTATGCGGAGAAGAAAGTTTTGGAACCG                         GTTCGGATCATATCCGTGAGAAAGATGGGATCTGGGCAG
genomic: GTGCTCTGTATGCGGAGAAGAAAGTTTTGGAACCGgtgagcttct ... ttttcgacagGTTCGGATCATATCCGTGAGAAAGATGGGATCTGGGCAG
EST: gi|125320229|gb|EL334314.1|EL334314
EST:     AATGGATGCTGGGATGTGCTCTGTATGCGGAGAAGAAAGTTTTGGAACCG                         GTTCGGATCATATCCGTGAGAAAGATGGGATCTGGGCAGTTCTTGCTT
genomic: AATGGATGCTGGGATGTGCTCTGTATGCGGAGAAGAAAGTTTTGGAACCGgtgagcttct ... ttttcgacagGTTCGGATCATATCCGTGAGAAAGATGGGATCTGGGCAGTTCTTGCTT
EST: gi|125056916|gb|EL126432.1|EL126432
EST:     CGGAGAAGAAAGTTTTGGAACCG                         GTTCGGATCATATCCGTGAGAAAGATGGGATCTGGGCAGTTCTTGCTTGGC
genomic: CGGAGAAGAAAGTTTTGGAACCGgtgagcttct ... ttttcgacagGTTCGGATCATATCCGTGAGAAAGATGGGATCTGGGCAGTTCTTGCTTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgttttaaaaccgtaacaaccctacacaactcacaaagaagcttttcgacagGTTCGGATCATATCCGTGAGAAAGATGGGATCTGGGCAGTTCTTGCTTGGCTATCAATACTGGCTCACAAGAACAAGGAAACCCTTGATGGGAATGCAAA
                              aactcac  putative branch site (score: 2)
                                            cttttc  putative PPT
     ttttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcttctattgctagatcttcacatgttttaaaaccgtaacaaccctacacaactcacaaagaagcttttcgacagGTTCGGATCATATCCGTGAGAAAGATGGGATCTGGGCAGTTCTTGCTTGGCTATCAATACTGGCTCACAAGAACAAGGAAACCCTTGATGGGAATGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA