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

...tacctctgtatgattatattattgatctatgcatgtctgttgctctgtactcagacttaatatctttctattgtccatttggatttttgtgtgattgcagTGTGAAGAAGATAGAGCGACCAGCGCCACACTCGCAACTCGATGCAGATTTAGCTGGTGGAATGGGAATGCCAGACAATGGTCCAAAGCTGATGTCTGCC

Basic information

species Arabidopsis thaliana
transcript AT2G36930.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G36930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G20550.1 (Glycine max), 3'ss of exon 2
---tacctc-tgtatgattatattattgatctatgcatgtc-tgttgctctgtactcagacttaatatctttctattgtccatttggatttttgtgtgattgcagTGTGAAGAAGATAGAGCGACCAGCGCCACACTCGCAACTCGATGCAGATTTAGCTGGTGGAATGGGAATGCCAGACAATGGTCCAAAGCTGATGTCTGCC
    |||     ||| ||   |  || | ||    |||| | | || || | || |       |||   |||   |     |||    ||| | ||||    |||| | ||  | ||   | | || || |||||  | ||||| ||||| ||| |||||| ||| ||||| |||||||||||||| |||||||| ||||||   
gaagaccaaacctataatgccaacatcgctc-gcacatggcatctttctatatattggagtggaatgattttgattctgatattacagtttctttgtg----cagTATAAAACAAATGATGGGTCCTGCACCACATACTCAACTTGATGCCGATGTAGCTGCTGGGATGGGTATGCCAGACAATGGACCAAAGCTAATGTCTATG

upper sequence: AT2G36930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G06240.1 (Glycine max), 3'ss of exon 2
tacctctgtatgattatatt---attgatctatgcatgtctgttgctctgtactcagacttaatatctttctattgtccatttggatttttgtgtgattgcagTGTGAAGAAGATAGAGCGACCAGCGCCACACTCGCAACTCGATGCAGATTTAGCTGGTGGAATGGGAATGCCAGACAATGGTCCAAAGCTGATGTCTGCC
||        ||| |  |||   ||||| |||        ||  ||    | |||| | |  ||||     |    |  |||| | ||  | | |   |||||| | ||  | ||   | | || || |||||  | ||||| ||||| |||||||||  ||| ||||| |||||||||||||| |||||||| ||||||   
taaacggacttgaatccattccaattgaactacttcaacttg--gcatctttctcacattatatattggagtggaatg-attttggttagtttctttgtgcagTATAAAACAAATGATGGGTCCTGCACCACATACTCAACTTGATGCCGATTTAGCTTCTGGGATGGGTATGCCAGACAATGGACCAAAGCTAATGTCTATG

upper sequence: AT2G36930.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0007g05070.t01 (Vitis vinifera), 3'ss of exon 3
tacctctgtatgattatattattgatctatgcatgtctgttgctctgtactcagacttaatatctttctattgtccatttggattt-------ttgtgtgattgcagTGTGAAGAAGATAGAGCGACCAGCGCCACACTCGCAACTCGATGCAGATTTAGCTGGTGGAATGGGAATGCCAGACAATGGTCCAAAGCTGATGTCTGCC
          |  | || |||   | | |    ||  | |||| ||   ||  |  |||  |||| |  |  |  |||||   |||       |  | |   |||||| | ||| | ||   | | || || || ||  | ||||| ||||| || || |||| |||||||||  ||||||| |||||||||||||| |||||    
-----tcacttagtaattttaacaagcaacaactgattcttgccct--tctatgtgttagcatctgtggagagaacatttaattttaatccactctttttgatgcagTTTAAAGCAAATGATGGGGCCTGCACCCCATACCCAACTTGATGCTGACTTGGCTGCTGGAATGGGTCTGCCAGATAATGGTCCAAAGCTTATGTCAATT

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|164059145|gb|ES093412.1|ES093412
EST:     AATGCATCAGTGATGGATTATCATTTCAAGACTAAGAAACACAAAAAGCG                         TGTGAAGAAGATAG
genomic: AATGCATCAGTGATGGATTATCATTTCAAGACTAAGAAACACAAAAAGCGgtatgtggat ... gtgattgcagTGTGAAGAAGATAG
EST: gi|164074228|gb|ES141966.1|ES141966
EST:     ATTTCAAGACTAAGAAACACAAAAAGCG                         TGTGAAGAAGATAGAGGGACCAGCGCCACACTCGCAACTCGATGCAGATTT
genomic: ATTTCAAGACTAAGAAACACAAAAAGCGgtatgtggat ... gtgattgcagTGTGAAGAAGATAGAGCGACCAGCGCCACACTCGCAACTCGATGCAGATTT
EST: gi|164089988|gb|ES048140.1|ES048140
EST:     TGGATTATCATTTCAAGACTAAGAAACACAAAAAGCG                         TGTGAAGAAGATAGAGGGACCAGCGCCACACTCGCAACTCGATGCAGATTT
genomic: TGGATTATCATTTCAAGACTAAGAAACACAAAAAGCGgtatgtggat ... gtgattgcagTGTGAAGAAGATAGAGCGACCAGCGCCACACTCGCAACTCGATGCAGATTT
EST: gi|125238841|gb|EL252926.1|EL252926
EST:     AATGCATCAGTGATGGATTATCATTTCAAGACTAAGAAACACAAAAAGCG                         TGTGAAGAAGATAGAGCGACCAGCGCCACACTCGCAA
genomic: AATGCATCAGTGATGGATTATCATTTCAAGACTAAGAAACACAAAAAGCGgtatgtggat ... gtgattgcagTGTGAAGAAGATAGAGCGACCAGCGCCACACTCGCAA
EST: gi|164172662|gb|ES104769.1|ES104769
EST:     TGGATTATCATTTCAAGACTAAGAAACACAAAAAGCG                         TGTGAAGAAGATAGAGGGACCAGCGCCACACTCGCAACTCGATGCAGATTT
genomic: TGGATTATCATTTCAAGACTAAGAAACACAAAAAGCGgtatgtggat ... gtgattgcagTGTGAAGAAGATAGAGCGACCAGCGCCACACTCGCAACTCGATGCAGATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtactcagacttaatatctttctattgtccatttggatttttgtgtgattgcagTGTGAAGAAGATAGAGCGACCAGCGCCACACTCGCAACTCGATGCAGATTTAGCTGGTGGAATGGGAATGCCAGACAATGGTCCAAAGCTGATGTCTGCC
         acttaat  putative branch site (score: 4)
           ttaatatctttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacctctgtatgattatattattgatctatgcatgtctgttgctctgtactcagacttaatatctttctattgtccatttggatttttgtgtgattgcagTGTGAAGAAGATAGAGCGACCAGCGCCACACTCGCAACTCGATGCAGATTTAGCTGGTGGAATGGGAATGCCAGACAATGGTCCAAAGCTGATGTCTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- cctctgt
- - - - - - - - - - - - - ctatgca
- - - - - - - - - - - - - - - - - - ctgttgc
- - - - - - - - - - - - - - - - - - - - - - - - -ctcagac