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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgaaatctattcaacggtgttagttttttaagtctttttgatttttgtgccttcaagttgtgtgtggattctcatggtttgctgtttttgtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAA

Basic information

species Arabidopsis thaliana
transcript AT5G53120.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G53120.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G13210.1 (Glycine max), 3'ss of exon 1
ctgaaatctattcaacggtgttagttttttaagtctttttgatttttgtgccttcaagttgtgtgtggattctcatggtttg-ctgtttttgtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAA
           | |  | ||  | ||||||   | ||||| |||| ||  | |  |  | ||| |   ||| || |    || |   |  |||   | |||||||||||| |||||||  | |||||||||||   | ||||||||  | ||  |||| |||||||| ||||| ||| |||||||||||||||||||||||
----------gtaagtgctgcgatttttttt--tttttttaatttatgaacttaaagatggtgggataattttcttttcgtgacaactcatgtgcttatagTATACAGAGACTGGAGCCTGAGAAGAAAAGGAGAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCCGAAGACTATGGATGGGAAGGCGAGTAA

upper sequence: AT5G53120.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G13210.3 (Glycine max), 3'ss of exon 1
ctgaaatctattcaacggtgttagttttttaagtctttttgatttttgtgccttcaagttgtgtgtggattctcatggtttg-ctgtttttgtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAA-------
      ||| |  |  | ||  | ||||||   | ||||| |||| ||  | |  |  | ||| |   ||| || |    || |   |  |||   | |||||||||||| |||||||  | |||||||||||   | ||||||||  | ||  |||| |||||||| ||||| ||| |||||||||||||||||||||||       
-----ctctgta-agtgctgcgatttttttt--tttttttaatttatgaacttaaagatggtgggataattttcttttcgtgacaactcatgtgcttatagtatacagAGACTGGAGCCTGAGAAGAAAAGGAGAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCCGAAGACTATGGATGGGAAGGCGAGTAACGGGAAT

upper sequence: AT5G53120.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G13210.2 (Glycine max), 3'ss of exon 1
--ctgaaatctattcaacggtgttagttttttaagtctttttgatttttgtgccttcaagttgtgtgtggattctcatggtttg-ctgtttttgtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAA
  ||  | ||| |  |  | ||  | ||||||   | ||||| |||| ||  | |  |  | ||| |   ||| || |    || |   |  |||   | |||||||||||| |||||||  | |||||||||||   | ||||||||  | ||  |||| |||||||| ||||| ||| |||||||||||||||||||||||
cactttactctgta-agtgctgcgatttttttt--tttttttaatttatgaacttaaagatggtgggataattttcttttcgtgacaactcatgtgcttatagTATACAGAGACTGGAGCCTGAGAAGAAAAGGAGAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCCGAAGACTATGGATGGGAAGGCGAGTAA

upper sequence: AT5G53120.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 1
ctgaaatctattcaacggtgttagt-tttttaagtctttttgatttttgtgccttcaagttgtgtgtggattctcatggtttgctgtt-tttgtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAA-------
          |       ||| |||  |  ||  | || ||  | |||||    | || |   ||| |     |  | |||||       |  | ||  || | ||||||| |||||||  | ||||||||| ||  | ||||||||  | ||  |||| |||||||| ||||||||| |||||||||||||||| ||||||       
---------gtctggttttgtaagtgctgctattttttatttttatttgttttatgaaatatggtgggatagttttttgtttgtgaccactcatgtgcttattttacagAGACTGGAGCCTGCGAAGAAAAGAATAATTTATGGAGGACGGCGCAGGAAGAGGTTTGGAATGCCAGAAGACTATGGATGGGAAGGTGAGTAACAGTAAT

upper sequence: AT5G53120.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 1
ctgaaatctattcaacggtgttagttttttaagtctttttgatttttgtgccttcaagttgtgtgtggattctcatggtttgctgtttttgtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAA-----
   | || |         | | |  |     | ||  | ||||   |    | |    |  | || | |    |||  | | || | |   | ||| |  | |  |||| ||||||| || |||||||| |||  ||||||||||| | ||  |||| |||||||| ||||| ||| | |||||||||||||||||||||     
--catattttgatgggattttgaagtgaaacattcaatatgatggctactgccttttctactatgagaaactccat--tcttct-tataactatgtttgatttctAGAGACTGGAGCCGGAGAAGAAAAAGATAATCTATGGAGGGCGGCGCAGGAAAAGGTTTGGAATGCCCGAAGATTATGGATGGGAAGGCGAGTAACGGGA

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|86043712|gb|DR339467.1|DR339467
EST:     TTTCTTCCCATACGTCTCTCCGTTTACGACCAG                         TATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
genomic: TTTCTTCCCATACGTCTCTCCGTTTACGACCAGgtaggtctct ... gtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
EST: gi|86043709|gb|DR339464.1|DR339464
EST:     ATCAATCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAG                         TATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
genomic: ATCAATCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAGgtaggtctct ... gtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
EST: gi|86043707|gb|DR339462.1|DR339462
EST:     ATCAATCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAG                         TATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
genomic: ATCAATCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAGgtaggtctct ... gtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
EST: gi|86043711|gb|DR339466.1|DR339466
EST:     ATCAATCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAG                         TATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
genomic: ATCAATCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAGgtaggtctct ... gtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
EST: gi|86043708|gb|DR339463.1|DR339463
EST:     ATCAATCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAG                         TATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
genomic: ATCAATCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAGgtaggtctct ... gtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
EST: gi|86073008|gb|DR368765.1|DR368765
EST:     TCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAG                         TATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
genomic: TCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAGgtaggtctct ... gtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
EST: gi|86043705|gb|DR339460.1|DR339460
EST:     ATCAATCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAG                         TATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
genomic: ATCAATCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAGgtaggtctct ... gtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
EST: gi|86043706|gb|DR339461.1|DR339461
EST:     ATCAATCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAG                         TATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
genomic: ATCAATCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAGgtaggtctct ... gtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACG
EST: gi|86043710|gb|DR339465.1|DR339465
EST:     ATCAATCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAG                         TATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGAC
genomic: ATCAATCACCGTTTAGCTTTCTTCCCATACGTCTCTCCGTTTACGACCAGgtaggtctct ... gtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgccttcaagttgtgtgtggattctcatggtttgctgtttttgtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAA
                                        tttttgttt  CT-rich tract
                                        tttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgaaatctattcaacggtgttagttttttaagtctttttgatttttgtgccttcaagttgtgtgtggattctcatggtttgctgtttttgtttgtgtagTATACAGAGGCTGGAGCTGGGGAAGAAAAGGATTGTCTATGGAGGGAGACGTCGGAATAGGTTTGGTATGCCAGAATACTATGGATGGGAAGGCGAGTAA

ctgaaat
- - - - -attcaac
- - - - - - - - - - - - - - - - - - - - - - - - - ccttcaa