Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgattgagaaacaataatatggaatgcgttttatgtgagtgggtgtcattgtgaatgttaatgtatgaatgatgaaactgttttgcaactattttcagTTTAGAACACACAAGGTGATATACAGGCGTTATGCTGGATTGTTTTTCTCTGTGTGCGTGGATATAACCGACAATGAGTTGGCTTACTTGGAGAGTATCC

Basic information

species Arabidopsis thaliana
transcript AT1G47830.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 3
tgtgattgagaaacaataatatggaatgcgttttatgtgagtgggtgtcattgtgaatgttaatgtatgaatgatgaaactgttttgcaactattttca----gTTTAGAACACACAAGGTGATATACAGGCGTTATGCTGGATTGTTTTTCTCTGTGTGCGTGGATATAACCGACAATGAGTTGGCTTACTTGGAGAGTATCC
|||    ||| | ||  ||  |  ||   |||   | |||   |  ||| ||| | || |     |  | || ||  |  |  ||||  |  |||||||    |||  | || || || || ||||||||||| ||||| ||| ||||||||||  |||| |||||||| || |||||||||||||| ||||||||  | ||||
tgttgg-gagtatcatcaagtttcaaaatgttacttctga-cagcagtctttg-gtatatgggaatcagtat-attcactttctttgtgataattttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCAATGTGTGTGGATATCACTGACAATGAGTTGGCATACTTGGAATGCATCC

upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G40430.2 (Glycine max), 3'ss of exon 3
--------------------------------------------------tgtgattgaga-------aacaataatatggaatgcg-ttttatgtgagtgggtgtca--ttgtgaatgttaatgtatgaatgat-gaaactgttttgcaact--attttcagTTTAGAACACACAAGGTGATATACAGGCGTTATGCTGGATTGTTTTTCTCTGTGTGCGTGGATATAACCGACAATGAGTTGGCTTACTTGGAGAGTATCC
                                                  ||| ||||           |||  ||| |   ||| | || |   |  || | | | |  ||||     ||  | ||  | |||| |    |   | | ||||    || |||||| | || |||||| | ||||||||||| |||||||| |||||||||||  | || || ||||| || || ||||||||||| || || ||| | ||||
gtcagtactctctccacgattttcaatttcttcctttgctttcgctgagttgtaattgcattatttctgacatgaatgttctatgaggttcttcttttgttgctcttaggttgtctcatttgctatacaattgattgccgtttgatagtaacttgtcttgcagTTTCGTACGCACAAGATAATATACAGGCGATATGCTGGGTTGTTTTTCTCAATCTGTGTTGATATCACTGATAATGAGTTGGCGTATTTAGAGTGCATCC

upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0023g03340.t01 (Vitis vinifera), 3'ss of exon 3
tgtgattgagaaacaataatatggaatgcgttttatgtgagtgggtgtcattgtgaatgttaatgtatgaatgatgaaactgt---tttgcaactattttcagTTTAGAACACACAAGGTGATATACAGGCGTTATGCTGGATTGTTTTTCTCTGTGTGCGTGGATATAACCGACAATGAGTTGGCTTACTTGGAGAGTATCC
   |||| |||        |      ||  | || | | |     |    | |    |||  || |  | ||||| ||   |    |||     |  ||||||||  | ||||||||||| || |||||||| |||||||||||||| |||||  |||| || ||||| || || |||||||| || || |||||| | ||||
--agatttagagcagggggtcctttgtgactattttattaaatcattgtgtagcagctgtccat-tgagcatgattaagtaggagatttaattttcctttcagTTCCGTACACACAAGGTCATCTACAGGCGATATGCTGGATTGTTCTTCTCATTGTGTGTTGATATCACTGATAATGAGTTAGCATATTTGGAGTGCATCC

upper sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 4
tgtgattgagaaacaataatatggaatgcgtttta----tgtgagtgggtgtcattgtgaatgttaatgtatgaatgatgaaactgttttgcaactatttt---cagTTTAGAACACACAAGGTGATATACAGGCGTTATGCTGGATTGTTTTTCTCTGTGTGCGTGGATATAACCGACAATGAGTTGGCTTACTTGGAGAGTATCC
        || |  | || |||  | |   || ||    |     |   ||   || |  || |  ||  | |  |||| | ||    ||  || | |||    |||||  | ||||||||||| || |||||||| ||||||||||| ||||||||  |||| || ||||| || || ||||||||||| || || ||| | ||||
------ccagcacaattattatcaattattttataacattacctttacatgctgttctctat-tggattaagggctgattatacctgattataaatttttcttgcagTTCCGTACACACAAGGTAATCTACAGGCGATATGCTGGATTATTTTTCTCACTGTGTGTTGATATGACAGATAATGAGTTGGCATATTTAGAGTGCATCC

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|116464176|gb|EG506768.1|EG506768
EST:     TTCATAGGTTAGTGGTGAATCGCGACGCCAAATTCACCAACTTCGTTGAG                         TTTAGAACACACAAGGTGATATACAGGCGTTATGCTGGATTGTTTTTCTCT
genomic: TTCATAGATTAGTGGTGAATCGCGACGCCAAATTCACCAACTTCGTTGAGgtttgctgtt ... ctattttcagTTTAGAACACACAAGGTGATATACAGGCGTTATGCTGGATTGTTTTTCTCT
EST: gi|116464171|gb|EG506763.1|EG506763
EST:     TTCATAGATTAGTGGTGAATCGCGACGCCAAATTCACCAACTTCGTTGAG                         TTTAGAACACACAAGGTGATATACAGGCGTTATGCTGGATTGTTTTTCTCT
genomic: TTCATAGATTAGTGGTGAATCGCGACGCCAAATTCACCAACTTCGTTGAGgtttgctgtt ... ctattttcagTTTAGAACACACAAGGTGATATACAGGCGTTATGCTGGATTGTTTTTCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcattgtgaatgttaatgtatgaatgatgaaactgttttgcaactattttcagTTTAGAACACACAAGGTGATATACAGGCGTTATGCTGGATTGTTTTTCTCTGTGTGCGTGGATATAACCGACAATGAGTTGGCTTACTTGGAGAGTATCC
            tgttaat  putative branch site (score: 3)
                                             ctattttc  putative PPT
          aatgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgattgagaaacaataatatggaatgcgttttatgtgagtgggtgtcattgtgaatgttaatgtatgaatgatgaaactgttttgcaactattttcagTTTAGAACACACAAGGTGATATACAGGCGTTATGCTGGATTGTTTTTCTCTGTGTGCGTGGATATAACCGACAATGAGTTGGCTTACTTGGAGAGTATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - -gaaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgaaa