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

gtaaagtgttactaagattctttacaggagagaatgagtcagtttagaaaactctcttgagatatggatttgtgtatgtgcagATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTGCAAAAGCTGCGGGAATGACTTGTATAGTTACAAAGAGTGG

Basic information

species Arabidopsis thaliana
transcript AT3G48420.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G48420.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G18320.1 (Glycine max), 3'ss of exon 7
---------------------gtaaagtgttactaagatt-ctttacaggagagaatgagtcagtttagaaaactctcttgagatatggatttgtgtatg-tgcagATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTGCAAAAGCTGCGGGAATGACTTGTATAGTTACAAAGAGTGG
                      | ||||| |  ||   |  ||||  |       |   ||||  || |||        ||| || |   | | ||| |  | ||||||||| ||||| || ||||| || || || ||||||||||| ||||| || |||||||| |||||||| |||||||| ||
agtaggtgtattttggcttagctcaagtgcttttacattcactttttattcattgacatgtcacatttgaatg------tgaaatgtcattatttgttttctacagATGTGTTGTGGTGGAGGACAGTGCCATAGGCCTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG
















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|124883211|gb|EH962113.1|EH962113
EST:     GCCATCTACAACTTAGCAGCTGAAACCCTTTGGAGTTGATCCCTCAAA                         ATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTGCAAAAG
genomic: GCCATCTACAACTTAGCAGCTGAAACCC-TTGGAGTTGATCCCTCAAAgtaaagtgtt ... gtatgtgcagATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTGCAAAAG
EST: gi|86078346|gb|DR374103.1|DR374103
EST:     GCCATCTACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAA                         ATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTGCAAAAGCTGC
genomic: GCCATCTACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAAgtaaagtgtt ... gtatgtgcagATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTGCAAAAGCTGC
EST: gi|19798937|gb|AU230227.1|AU230227
EST:     GCCATCTACAAGCTTACCAGCTGAAACCCTTGGAGTTGATCCCTCAAA                         ATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTCCAAAAGCTCC
genomic: GCCATCTACAA-CTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAAgtaaagtgtt ... gtatgtgcagATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTGCAAAAGCTGC
EST: gi|86086839|gb|DR382598.1|DR382598
EST:     AAACCCTTGGAGTTGATCCCTCAAA                         ATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTGCAAAAGCTGC
genomic: AAACCCTTGGAGTTGATCCCTCAAAgtaaagtgtt ... gtatgtgcagATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTGCAAAAGCTGC
EST: gi|125141975|gb|EL179476.1|EL179476
EST:     GAGTTGATCCCTCAAA                         ATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTGCAAAAGCTGC
genomic: GAGTTGATCCCTCAAAgtaaagtgtt ... gtatgtgcagATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTGCAAAAGCTGC
EST: gi|124973012|gb|EL046671.1|EL046671
EST:     GCCATCTACAACTTAGCAGCTGAAACCCTTGGAGTTGNTCCCTCAAA                         ATGTGTAGTGGTTGAAGACAGC
genomic: GCCATCTACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAAgtaaagtgtt ... gtatgtgcagATGTGTAGTGGTTGAAGACAGC
EST: gi|47832151|gb|CK121835.1|CK121835
EST:     GCCATCTACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAA                         ATGTGTAGTGGTTGAAGACAGCGCGAT
genomic: GCCATCTACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAAgtaaagtgtt ... gtatgtgcagATGTGTAGTGGTTGAAGACAGCGCGAT
EST: gi|125298382|gb|EL312467.1|EL312467
EST:     GCCATCTTACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAA                         ATGTGTAGTGGTTGAAGACAGCGCGATCGGG
genomic: GCCATC-TACAACTTAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAAgtaaagtgtt ... gtatgtgcagATGTGTAGTGGTTGAAGACAGCGCGATCGGG
EST: gi|125145682|gb|EL180879.1|EL180879
EST:     TAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAA                         ATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTGCAAAAGCTGC
genomic: TAGCAGCTGAAACCCTTGGAGTTGATCCCTCAAAgtaaagtgtt ... gtatgtgcagATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTGCAAAAGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagaatgagtcagtttagaaaactctcttgagatatggatttgtgtatgtgcagATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTGCAAAAGCTGCGGGAATGACTTGTATAGTTACAAAGAGTGG
              tttagaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtgttactaagattctttacaggagagaatgagtcagtttagaaaactctcttgagatatggatttgtgtatgtgcagATGTGTAGTGGTTGAAGACAGCGCGATCGGGCTAGCAGCTGCAAAAGCTGCGGGAATGACTTGTATAGTTACAAAGAGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC