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

gtaatgcctaagttcttgttttgattgcttagccggatcgttttgttatggataagaccattgttttataaagtggtttcttaagccttttgatgttgttgcagGAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTG

Basic information

species Arabidopsis thaliana
transcript AT5G40850.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G40850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0064g01470.t01 (Vitis vinifera), 3'ss of exon 1
gtaatgcctaagttcttgttttgattgcttagccggatcgttttgttatggataagaccattgttttataaagtggtttcttaagccttttgatgttgttgcagGAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTG
    ||| | | |||||| |||| || |  |      |  |||   | ||  |  |    || ||   | | |   |   |  |    ||   |||  |||||||| ||||| |||||| |||| || | ||||||||||||||| || || ||||| || |||||||| || ||||| |||
agtttgcttgatttcttgatttggtttcacaattttttaattt--ctgtgagtgggtgtgttcttgattgaggaaatgagt--aattattgactgtaattgcagGAGGAGATACATGAATTACTTCTGAGTTTTGCTGAAGCTGGAGCTACAGTTGTGAGACTTAAAGGAGGGGATCCACTG
















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|124720815|gb|EH812217.1|EH812217
EST:     CTAGACTTCTTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAG                         GAAGAGATTCATGAACTACTCCTAAATTTTG
genomic: CTAGACTTCTTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAGgtaatgccta ... gttgttgcagGAAGAGATTCATGAACTACTCCTAAATTTTG
EST: gi|124756298|gb|EH846428.1|EH846428
EST:     TCGGCAAAACTGCTGGTTATCATAGCAGAACTCAG                         GAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCA
genomic: TCGGCAAAACTGCTGGTTATCATAGCAGAACTCAGgtaatgccta ... gttgttgcagGAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCA
EST: gi|125059759|gb|EL128436.1|EL128436
EST:     GTTATCATAGCAGAACTCAG                         GAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTT
genomic: GTTATCATAGCAGAACTCAGgtaatgccta ... gttgttgcagGAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTT
EST: gi|116459489|gb|EG502081.1|EG502081
EST:     CTAGACTTCTTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAG                         GAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTT
genomic: CTAGACTTCTTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAGgtaatgccta ... gttgttgcagGAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTT
EST: gi|125247482|gb|EL261567.1|EL261567
EST:     CTAGACTTCTTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAG                         GAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCT
genomic: CTAGACTTCTTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAGgtaatgccta ... gttgttgcagGAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCT
EST: gi|164196037|gb|ES057016.1|ES057016
EST:     AGACTTCTTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAG                         GAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCC
genomic: AGACTTCTTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAGgtaatgccta ... gttgttgcagGAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCC
EST: gi|116459483|gb|EG502075.1|EG502075
EST:     CTAGACTTCTTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAG                         GAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTT
genomic: CTAGACTTCTTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAGgtaatgccta ... gttgttgcagGAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTT
EST: gi|116459485|gb|EG502077.1|EG502077
EST:     CTAGACTTCTTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAG                         GAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTT
genomic: CTAGACTTCTTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAGgtaatgccta ... gttgttgcagGAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTT
EST: gi|124725160|gb|EH816562.1|EH816562
EST:     TTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAG                         GAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTT
genomic: TTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAGgtaatgccta ... gttgttgcagGAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTT
EST: gi|86080219|gb|DR375976.1|DR375976
EST:     CTAGACTTCTTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAG                         GAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTT
genomic: CTAGACTTCTTTATGTCGGCAAAACTGCTGGTTATCATAGCAGAACTCAGgtaatgccta ... gttgttgcagGAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggataagaccattgttttataaagtggtttcttaagccttttgatgttgttgcagGAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTG
                                      ttttgat  putative branch site (score: 4)
          attgttttataaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgcctaagttcttgttttgattgcttagccggatcgttttgttatggataagaccattgttttataaagtggtttcttaagccttttgatgttgttgcagGAAGAGATTCATGAACTACTCCTAAATTTTGCTGAAGCTGGTGCCACTGTTGTCAGGCTTAAAGGTGGAGATCCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC