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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTTCTTCTTCTGTTGGACCTGAGTACTACGTTGGGATTTTGTCCTTCGTTGATAAAGATCAGCTTGAACCTGGATGTTCGATTTTGATGCATAATAAGgtatgtgaaattagggtttaagaatcttgtttttgttgtgattacgattgtgtgttgttgtggatttagggttgctgatttgttttatgttag

Basic information

species Arabidopsis thaliana
transcript AT4G29040.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 1
TGTTTCTTCTTCTGTTGGACCTGAGTACTACGTTGGGATTTTGTCCTTCGTTGATAAAGATCAGCTTGAACCTGGATGTTCGATTTTGATGCATAATAAGgtatgtgaaattagggtttaagaatcttgtttttgttgtga-----ttacgattgtgtgttgttgtggatttagggttgctgatttgttttatgttag---
 || || || || || || || ||||||||||| |||||  | |||||||||||||| || ||||| || ||||||||| | ||| ||||||| || ||||||| |   | | |   | | | ||   | |   |   |||     || |  |||| |    ||   |||| ||||| |       |   |  ||| |   
CGTCTCCTCGTCCGTCGGTCCCGAGTACTACGTCGGGATACTTTCCTTCGTTGATAAGGACCAGCTCGAGCCTGGATGTGCCATTCTGATGCACAACAAGgtatatctgaattgatctcatggattaagatacggaattgaaagtgttgcacttgttt-caattagtgattcagggtggtattcaggagatcagttcggga

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA03G32800.1 (Glycine max), 5'ss of exon 1
TGTTTCTTCTTCTGTTGGACCTGAGTACTACGTTGGGATTTTGTCCTTCGTTGATAAAGATCAGCTTGAACCTGGATGTTCGATTTTGATGCATAATAAGgtatgtgaaattagggtttaagaatcttgtttttgttgtgattacgattgtgtgttg-ttgtggatttagggttgctgatttgttttatgttag------------
 ||||| || || || || || |||||||| ||||| |||||||| ||||||||||| |||||||| |||||||||||  | |||||||||||||| |||||| |     |||||||||     |  || ||  ||||  |||    ||| || ||| |||          |||  ||||   ||||  |||||            
CGTTTCGTCCTCGGTGGGGCCCGAGTACTATGTTGGTATTTTGTCTTTCGTTGATAAGGATCAGCTCGAACCTGGATGCGCTATTTTGATGCATAACAAGgtagg----gttagggttttgttttgctgattg-gttg-aattgtttttgcgttttgattgaatgcactaagtttgtgatggattttgggttagggtttagtgatt

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA19G35510.1 (Glycine max), 5'ss of exon 1
TGTTTCTTCTTCTGTTGGACCTGAGTACTACGTTGGGATTTTGTCCTTCGTTGATAAAGATCAGCTTGAACCTGGATGTTCGATTTTGATGCATAATAAGgtatg-tgaaatta-------gggtttaagaatcttgtttttgttgtgatta--cgattg---tgtgttgttgtggatttagggttgctgatttgttttatgttag
 ||||| || || || || || |||||||| ||||| || ||||| ||||| ||||| |||||||| || ||||||||  | |||||||||||||| |||||| | | |   ||       |  ||   ||||  | ||   ||| |||||    || ||   | | ||||  ||||||| |||  |  |    |           
AGTTTCGTCCTCGGTGGGGCCCGAGTACTATGTTGGTATCTTGTCTTTCGTCGATAAGGATCAGCTCGAGCCTGGATGCGCTATTTTGATGCATAACAAGgtagggttagggtatgctgctgatttgttgaattgttttagcgttttgattgattgactgccctattttgtgatggattttggggggggggggggggggg------

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA13G19280.1 (Glycine max), 5'ss of exon 1
TGTTTCTTCTTCTGTTGGACCTGAGTACTACGTTGGGATTTTGTCCTTCGTTGATAAAGATCAGCTTGAACCTGGATGTTCGATTTTGATGCATAATAAGgtatgtgaaattagggtttaagaatcttgtttttgttgtgattac--gattgtgtgttgttgtggatttagggttgctgatttgttttatgttag---------
||| || || || ||||| ||||||||||| || || ||  |||| ||||||||||| |||||| | || ||||| ||| | |||||||||||||||||||| |     | | |  ||    | |||| | || || |||||||    | ||     | |   |   ||||   | |  | |||  |   ||| |         
TGTCTCCTCCTCCGTTGGGCCTGAGTACTATGTCGGAATCCTGTCTTTCGTTGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAGgttttacttactcgcttt----actcttttattggtggtgattattgaaatgaaaagtatccagttattagaaatacctaattgcctagggtttgactttgagg

upper sequence: AT4G29040.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA10G04920.1 (Glycine max), 5'ss of exon 1
TGTTTCTTCTTCTGTTGGACCTGAGTACTACGTTGGGATTTTGTCCTTCGTTGATAAAGATCAGCTTGAACCTGGATGTTCGATTTTGATGCATAATAAGgtatgtgaaattagggtttaagaatcttgtttttgttgtgattacgat----tgtgtgttgttgtggattta---gggttgctgatttgttttatgttag-
|||||| || || || || |||||||| ||||| || || ||||| ||||| ||||| |||||| | || ||||| ||| | |||||||||||||||||||| |     | | |  |||| |  | |  |  | || || |||   ||    |  ||    || || | |||   |   | |    |||  |   ||| | 
TGTTTCCTCCTCCGTCGGGCCTGAGTATTACGTCGGAATCTTGTCTTTCGTCGATAAGGATCAGTTGGAGCCTGGTTGTGCTATTTTGATGCATAATAAGgttttgctcactcgc-tttacgcttttattggtggtggttattgaaatgaaatacgtcaaattatgaaattattggaaatacctcattgcctagggtttga

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|164116649|gb|ES095266.1|ES095266
EST:     GCTTGAATCTGGATGTTCGATTTTGATGCATAATAAG                         GTTCTCTCTGTTGTTGGGATTCTACAAGATGAAGTGGATCCAATGGTGTCT
genomic: GCTTGAACCTGGATGTTCGATTTTGATGCATAATAAGgtatgtgaaa ... tttatgttagGTTCTCTCTGTTGTTGGGATTCTACAAGATGAAGTGGATCCAATGGTGTCT
EST: gi|124978040|gb|EL051290.1|EL051290
EST:     TTGATAAAGATCAGCTTGAACCTGGATGTTCGATTTTGATGCATAATAAG                         GTTCTCTTCTGTTGTTGGGAT
genomic: TTGATAAAGATCAGCTTGAACCTGGATGTTCGATTTTGATGCATAATAAGgtatgtgaaa ... tttatgttagGTTCTCT-CTGTTGTTGGGAT
EST: gi|124816600|gb|EH901466.1|EH901466
EST:     ATTTTGATGCATAATAAG                         GTTCTCTCTGTTGTTGGGATTCTACAAGATGAAGTGGATCCAATGGTGTCT
genomic: ATTTTGATGCATAATAAGgtatgtgaaa ... tttatgttagGTTCTCTCTGTTGTTGGGATTCTACAAGATGAAGTGGATCCAATGGTGTCT
EST: gi|47831321|gb|CK121005.1|CK121005
EST:     TTGATAAAGATCAGCTTGAACCTGGATGTTCGATTTTGATGCATAATAAG                         GTTCTCTCTGTTGTTGGGATTCTACAAGATGAAGTGGATCCAATGGTGTCT
genomic: TTGATAAAGATCAGCTTGAACCTGGATGTTCGATTTTGATGCATAATAAGgtatgtgaaa ... tttatgttagGTTCTCTCTGTTGTTGGGATTCTACAAGATGAAGTGGATCCAATGGTGTCT
EST: gi|164200345|gb|ES067334.1|ES067334
EST:     TTGATAAAGATCAGCTTGAACCTGGATGTTCGATTTTGATGCATAATAAG                         GTTCTCTCTGTTGTTGGGATTCTACAAGA
genomic: TTGATAAAGATCAGCTTGAACCTGGATGTTCGATTTTGATGCATAATAAGgtatgtgaaa ... tttatgttagGTTCTCTCTGTTGTTGGGATTCTACAAGA
EST: gi|163975805|gb|ES138229.1|ES138229
EST:     TGNTAAAGATCAGCTTGAACCTGGATGTTCGATTTTGTATGCATAATAAG                         GTTCTCTCTGTTGTTGGGATTCTACAAGATGAAGTGGAT
genomic: TGATAAAGATCAGCTTGAACCTGGATGTTCGATTTTG-ATGCATAATAAGgtatgtgaaa ... tttatgttagGTTCTCTCTGTTGTTGGGATTCTACAAGATGAAGTGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTTCTTCTTCTGTTGGACCTGAGTACTACGTTGGGATTTTGTCCTTCGTTGATAAAGATCAGCTTGAACCTGGATGTTCGATTTTGATGCATAATAAGgtatgtgaaattagggtttaagaatcttgtttttgttgtgattacgattgtgtgttgttgtggatttagggttgctgatttgttttatgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT