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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacttttgtctatttctctcggtaagaccatcaagaggcattatgataagtcaagccaccgagttttatgtgttctctttgctttggtcatggtgaaaaaactgatgtgagtgagggtgtttgtttggtgacagGTATTCCCCAAACCTGAGGGAGATTAAGGTGGTGGACAAGAAGAAAGTAAGAAGAGCCAAGCTCTATTACCTCAGGGACAAGGTGAATGCTCTCAAGAAG

Basic information

species Arabidopsis thaliana
transcript AT5G11750.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G11750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv17s0000g09390.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtacttttgtctatttctctcggtaagaccatcaagaggcattatgataagtcaagccaccgagttttatgtgttctctttgctttggtcatggtgaaaaaactgatgtgagtga-gggtgtttgtttggtgacagGTATTCCCCAAACCTGAGGGAGATTAAGGTGGTGGACAAGAAGAAAGTAAGAAGAGCCAAGCTCTATTACCTCAGGGACAAGGTGAATGCTCTCAAGAAG
                                   |     |   || ||    |||     |||   ||| ||   || | |||| || |   ||| |   |         | |  |     ||  ||  || ||||||||| || || | | | | |||||| |||||  |||||||||||||||| ||||| |||||||| ||||| |||||||||||  ||||||| || | ||| 
-----------------------------------ttttctgattttgtgg---gtctt-ttacctgctttcatcatttgtttttgatt-gacaatgctcttagtctctgcataatggccaaatgagtgcgtgatgacagGTACTCACCCAGCATAAAGGAGATCAAGGTTCTGGACAAGAAGAAAGTGAGAAGGGCCAAGCTTTATTATCTCAGGGACAAAATGAATGCACTTAGGAAA
















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|124790375|gb|EH880054.1|EH880054
EST:     AGAATTAGAAGGCTTGTTGCTGGAGTGGGCGTTGAATCCATGTTCCCCTT                         GTATTCCCCAAACCTGAGGGAGATTAAGGTGGTGGACAAGAAGAAAGTAAG
genomic: AGAATTAGAAGGCTTGTCGCTGGAGTGGGCGTTGAATCCATGTTCCCCTTgtaagtactt ... ttggtgacagGTATTCCCCAAACCTGAGGGAGATTAAGGTGGTGGACAAGAAGAAAGTAAG
EST: gi|164134607|gb|ES128327.1|ES128327
EST:     AGAATTAGAAGGCTTGTCGCTGGAGTGGGCGTTGAATCCATGTTCCCCTT                         GTATTCCC-AA-CCTGAGGGAGATTAAGGTGGTGGACAAGAAGAAAGTAAG
genomic: AGAATTAGAAGGCTTGTCGCTGGAGTGGGCGTTGAATCCATGTTCCCCTTgtaagtactt ... ttggtgacagGTATTCCCCAAACCTGAGGGAGATTAAGGTGGTGGACAAGAAGAAAGTAAG
EST: gi|164227810|gb|ES106851.1|ES106851
EST:     GTCGCTGGAGTGGGCGTTGAATCCATGTTCCCCTT                         GTATTCCCCAAACCTGAGGGAGATTAAGGTGGTGGACAAGAAGAAAGTAAG
genomic: GTCGCTGGAGTGGGCGTTGAATCCATGTTCCCCTTgtaagtactt ... ttggtgacagGTATTCCCCAAACCTGAGGGAGATTAAGGTGGTGGACAAGAAGAAAGTAAG
EST: gi|164228645|gb|ES009276.1|ES009276
EST:     AATTAGAAGGCTTGTTCGTCTGGAGTGGGCGTTGAATCCATGTTCCCCTT                         GTATTCCCCAAACCTGAGGGAGATTAAGGTGGTGGACAAGAAGAAAGTAAG
genomic: AATTAGAAGGCTTG-TCG-CTGGAGTGGGCGTTGAATCCATGTTCCCCTTgtaagtactt ... ttggtgacagGTATTCCCCAAACCTGAGGGAGATTAAGGTGGTGGACAAGAAGAAAGTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctttggtcatggtgaaaaaactgatgtgagtgagggtgtttgtttggtgacagGTATTCCCCAAACCTGAGGGAGATTAAGGTGGTGGACAAGAAGAAAGTAAGAAGAGCCAAGCTCTATTACCTCAGGGACAAGGTGAATGCTCTCAAGAAG
                    aactgat  putative branch site (score: 3)
                                        tttgttt  putative PPT
              tgaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtacttttgtctatttctctcggtaagaccatcaagaggcattatgataagtcaagccaccgagttttatgtgttctctttgctttggtcatggtgaaaaaactgatgtgagtgagggtgtttgtttggtgacagGTATTCCCCAAACCTGAGGGAGATTAAGGTGGTGGACAAGAAGAAAGTAAGAAGAGCCAAGCTCTATTACCTCAGGGACAAGGTGAATGCTCTCAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG