Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttatatagacttgaatgctagatgtttacttttgaacaagtcttgttttaactctctagggttttactcaattgtaacacttactctactgaatgtatttaggaaaattcgttgatgatttgcaaattgttttatgtgcttgagtcttggtttgatgatggaaaagtgttcaaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTGAAGAGCTTTTTCGAAGAACATTTGCACACTGATGAAGAGATCCGTTACT

Basic information

species Arabidopsis thaliana
transcript AT4G14710.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G28860.2 (Glycine max), 3'ss of exon 3
gtttgtttatatagacttgaatgctagatgtttacttttgaacaagtcttgttttaactctctagggttttactcaattgtaacact-tactctactgaatgtatttaggaaaattcgttgatgatttgcaaattgttttatgtgcttgagtcttggtttgatgatggaaaagtgttcaaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTGAAGAGCTTTTTCGAAGAACATTTGCACACTGATGAAGAGATCCGTTACT
                                                                   ||||| | |  | ||||| | | | ||||| | || || |  || | |  |   ||| ||       | ||||   |  || |  |   ||            |  | |||    |||||||  |||||||||| ||||| |||||| | ||||| ||||||  |||| | || ||||| || ||||| ||| | ||||||||||| |||||||| |  |
-----------------------------------------------------------------aattttaattatgtctaacattgtgcactactta-tgcatctttgacattctggctatgctta------tatttttaataattcaacccgagtc-----------accttttc----tgcagGATGTTTGTGAGGTCTGCCCAGAAAAGTTGCCAAATTATGAACAGAAAATCAAAAGCTTCTTTGAAGAGCATCTTCACACTGATGAGGAGATCCGCTTTT

upper sequence: AT4G14710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G38940.2 (Glycine max), 3'ss of exon 3
gtttgtttatatagacttgaatgctagatgtttacttttgaacaagtcttgttttaactctctagggttttactcaattgtaacacttactctactgaatg-tatttaggaaaattcgttgatgatttgcaaattgttttatgtgcttgagtcttggtttgatgatggaaaagtgttcaaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTGAAGAGCTTTTTCGAAGAACATTTGCACACTGATGAAGAGATCCGTTACT
||||||     ||   ||  ||  ||   |||||   || |       ||   | ||   |   |  | |   |  | | |||   | | | |  ||  |   |||  | |  |||  |  ||   |||  | |     |||||   ||  | ||  |    | |    |      |     | |||||  |||||||||| ||||| |||||| | ||||| |||||   |||| | || ||||| || ||||||||| | ||||||||||| |||||||| |  |
gtttgtaatactaatgtttcattataatggtttagaattaactttccttttgctcaatattaatgaatatatgtagactataattttaattattatgtctaacattgtgcactatttatgcat--cttggcattctggctatgtttatgttttttaataatttaacctgagtcacctttttcttcagGATGTTTGTGAGGTCTGCCCAGAAAAGTTGCCAAATTATGAGCAGAAAATCAAAAGCTTCTTTGAAGAACATCTTCACACTGATGAGGAGATCCGCTTTT

upper sequence: AT4G14710.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0020g04080.t01 (Vitis vinifera), 3'ss of exon 3
gtttgtttatatagacttgaatgctagatgtttacttttgaacaagtcttgttttaactctctagggttttactcaattgtaacacttactctactgaatgtatttaggaaaattcgttgatgatttgcaaattgttttatgtgcttgagtcttggtttgatgatggaaaagtgttcaaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTGAAGAGCTTTTTCGAAGAACATTTGCACACTGATGAAGAGATCCGTTACT
                                   || | | | |   |  ||||  |  ||         |   ||||||  | |  | |||  | | | | |      || ||     ||    |  |  |   | | | |  |  |   | |   ||  |||| |||  | |||    | ||||| ||||||||||| ||||| ||||| || ||||| ||||||| |||  | |||| |||||| ||||| ||| | ||||||||||| ||||| || ||||
---------------------------------gtttgtcacctaacttacttttttcattcagaaaa---aggaaattgtt-ctccaattct-ttcagtttgtgccttgaatttataccatagcctatagttaagtctgtataatataag-tggaaatg--gatgtaaacattttc----tccagGATTTTTGTGAGGTTTGCCCAGAAAAACTGCCAAATTATGAAGAGAAGATCAAGAACTTTTTTGAAGAGCATCTTCACACTGATGAGGAGATTCGCTACT

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|86080820|gb|DR376577.1|DR376577
EST:     TGAAAAAGATCCGCGAATCTCGTGGTTACTCTTACATG                         GACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
genomic: TGAAAAAGATCCGCGAATCTCGTGGTTACTCTTACATGgtttgtttat ... caaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
EST: gi|86074670|gb|DR370427.1|DR370427
EST:     CCGATGAGGATTTGAAAAAGATCCGCGAATCTCGTGGTTACTCTTACATG                         GACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
genomic: CCGATGAGGATTTGAAAAAGATCCGCGAATCTCGTGGTTACTCTTACATGgtttgtttat ... caaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
EST: gi|86082287|gb|DR378046.1|DR378046
EST:     CCGATGAGGATTTGAAAAAGATCCGCGAATCTCGTGGTTACTCTTACATG                         GACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
genomic: CCGATGAGGATTTGAAAAAGATCCGCGAATCTCGTGGTTACTCTTACATGgtttgtttat ... caaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTG
EST: gi|124743297|gb|EH834459.1|EH834459
EST:     CCGATGAAGATTTGAAAAAGATCCGCGAATCTCGTGGTTACTCTTACATG                         GACTTTTGTGAGGCATGCCCGGAAAAGCTTCCAAACTATGAAGT
genomic: CCGATGAGGATTTGAAAAAGATCCGCGAATCTCGTGGTTACTCTTACATGgtttgtttat ... caaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttttatgtgcttgagtcttggtttgatgatggaaaagtgttcaaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTGAAGAGCTTTTTCGAAGAACATTTGCACACTGATGAAGAGATCCGTTACT
                        gtttgat  putative branch site (score: 5)
                                           ttcaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttatatagacttgaatgctagatgtttacttttgaacaagtcttgttttaactctctagggttttactcaattgtaacacttactctactgaatgtatttaggaaaattcgttgatgatttgcaaattgttttatgtgcttgagtcttggtttgatgatggaaaagtgttcaaaatgcagGACTTTTGTGAGGTATGCCCGGAAAAGCTTCCAAACTATGAAGTGAAAGTGAAGAGCTTTTTCGAAGAACATTTGCACACTGATGAAGAGATCCGTTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC