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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttttag

Basic information

species Arabidopsis thaliana
transcript AT3G06400.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 8
TCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatg-gatgcacccattccttgcattgagt--ttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttttag------
  |  ||||||| || ||||| || || || || ||||||||||||||||||||||||||||| ||||| ||||| || ||||| ||||| || || |||||  |  ||  | |         || ||  |  |||| ||  |   |  |        |   | | | ||||||||  || ||        
CTTGTTGCCTGAAATATTTAGCTCTGCTGAAACATTTGATGAATGGTTTCAAATTTCTGGTGAAAATGATCAGCAGGAGGTTGTTCAACAGCTTCATAAGgtgagtaatataactcccatgctcaatggctcattatgctaataatttgggacaacctgcatagttcattcatgtaaattcttctatgaag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 8
TCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttttag---
  | || ||||| || ||||| || || || || |||||||||||||||||||||||||| || ||||| || || || || || || || || || |||||  ||||  |   ||       | | | | || |   ||       | || ||   |||||| |||| || | |||||      
CTTGCTCCCTGAAATATTTAGCTCTGCGGAAACCTTTGATGAATGGTTTCAAATTTCTGGGGAAAATGATCAACAGGAGGTGGTCCAGCAGCTTCATAAGgttgggatataattatcatgataactaattatagtactttaaaatgaactcttaa--taattg-tttcttgcaacttttgcaaag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 5
TCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttttag---
  | || ||||| || ||||| || || ||||| |||||||||||||||||||| ||||| || ||||| || || || || ||||| || || || |||||  ||||  |    |      ||   | |||| |   ||       | || |    |||||| ||||  | | |||||      
CTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAAATGATCAACAGGAGGTGGTGCAGCAGCTTCATAAGgttgggatatagttttcgtgatcaccaattttagtaccttaaaatgaactcttta--taattg-tttctcgcaacttttgcaaag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 8
TCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatgg-atgcacccattccttg--cattgagtttattctgt-tctgtgtgagtcgtag--gttaattgc-tttcatgtatctttttag
||||||||| || ||||||||||| || || ||||||||||||||||||||||| |||||||| |||||||| || || ||||| |||||| | |||||||||    |   | || |   |||    |||    |  |   | |   | ||   | ||   || | || | |||  | | | | |  ||
TCTTCTGCCCGAAATTTTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAAATGACCAACAGGAGGTTGTTCAACAATTACACAAGgtaaattacagaaccttcttttgattgttggaagtccttaatgttaatctggcacataattgtcattttcattttctatgtatatcaag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 8
TCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatgg-atgcacccattccttg--cattgagtttattctgt-tctgtgtgagtcgtag--gttaattgc-tttcatgtatctttttag
||||||||| || ||||||||||| || || ||||||||||||||||||||||| |||||||| ||||| || || || ||||| |||||| | |||||||||    |   | || |   |||    |||    |  |   | |   | ||   | ||   || | || | |||  | | | | |  ||
TCTTCTGCCCGAAATTTTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAAATGATCAACAGGAGGTTGTTCAACAATTACACAAGgtaaattacagaaccttcttttgattgttggaagtccttgatgttaatctggcacataattgtcattttcattttctatgtatatcaag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 8
TCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatggat--gcacccattccttgcattgagtttattctgttctg-tgt-gagtcgtaggttaattgctttcatgtatctttttag-
|||| ||||||| || |||||||| || || ||||||||||||||||||||||| |||||||| |||||| | || || ||||| |||||||| ||||||||| |  |     |   ||| |||    | || |||| || |    ||| |  |  ||   |  |   |||| ||| | |  |||  
TCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAAATGACGAACATGAGGTTGTTCAACAACTACACAAGgtaagccttgaagcttcttcattgttaagggtctattgtgataaaatgttgtataataatgttttcattttc-tgtgtgtaattaag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA07G38050.2 (Glycine max), 5'ss of exon 8
TCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtaggtta-attgctttca-----tgtatctttttag-
|||| ||||||| || |||||||| || || ||||||||||||||||||||||| |||||||| |||||| | || || ||||| |||||||| ||||||||| |  |  |  | ||| ||| ||||  |    |||  | ||    | |  ||  | | | || |||||     |||   |  |||  
TCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAAATGACGAACATGAGGTTGTTCAACAACTACACAAGgtaagccttgaagc-ttctttg-attgtttagggtctactgtgataaaatgttatataataatgttttcaatttctgtgcatgattaag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 8
TCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatct---ttttag
||| ||||| ||||| |||| |||||| |||||||||||||||||||| ||||||||||| || ||||||||||| || ||||| ||||| || || ||||||         ||      |   ||   | ||   | ||   | | | |    |   ||| | ||   | | |||   ||||||
TCTACTGCCCGAGATATTTAATTCAGCTGAGACTTTTGATGAATGGTTCCAAATTTCTGGAGATAATGACCAGCAGGAGGTTGTTCAACAGCTTCATAAGgtaaacccaagacctcctaattttttagctctaccttatttcatctcatttactga--aatggtttctgtatttctgttttttag

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: EFJ32950 (Selaginella moellendorffii), 5'ss of exon 7
TCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatggatgcac-ccattccttg-cattga-gtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttttag
||| ||||| |||||||| || || || || || || || |||||||||||||| ||||| || || |||||||||||||||||||| || || ||||||||||| |||  | | || |  |  | | || | | ||  || | |                                        
TCTGCTGCCGGAGATTTTCAGCTCTGCTGAAACATTCGACGAATGGTTTCAAATATCTGGCGAAAACGACCAGCAAGAAGTTGTGCAGCAGCTTCACAAGgtatgaatgagcgctatgcgctatcgtcgatgctgataatgatttacag------------------------------------

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: EFJ15818 (Selaginella moellendorffii), 5'ss of exon 7
TCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatggatgcac-ccattccttg-cattga-gtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttttag
||| ||||| |||||||| || || || || || || || |||||||||||||| ||||| || || |||||||||||||||||||| || || ||||||||||| |||  | | || |  |  | | || | | ||  || | | |                                      
TCTGCTGCCGGAGATTTTCAGCTCTGCTGAAACATTCGACGAATGGTTTCAAATATCTGGCGAAAACGACCAGCAAGAAGTTGTGCAGCAGCTTCACAAGgtatgaatgagcgctatgcgctatcgtcgatgctgataatgattt-tacag----------------------------------

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|124885786|gb|EH964688.1|EH964688
EST:     AAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAG                         GTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAG
genomic: AAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatggatgc ... atctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAG
EST: gi|116481378|gb|EG523970.1|EG523970
EST:     AAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAG                         GTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGT
genomic: AAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatggatgc ... atctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGAATGACCAGCAAGAAGTTGTGCAACAACTGCACAAGgtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT