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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAATTCGTGGgtaaggttcttgatgtcaataagatttcttttatttaacttacacagcacttgactcatgtcggaatggttgctctcag

Basic information

species Arabidopsis thaliana
transcript AT3G53390.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G53390.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA19G36480.2 (Glycine max), 5'ss of exon 4
TGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAATTCGTGGgtaaggt---tcttgatgtcaataagatttcttttatttaacttacacagcacttgactcatgtcgg-------aatggttgctctcag
|||||| || |||||||| ||||| |||||||||||||||||||| ||||| ||||| ||||| || |||||||| ||||||||||||||||| || |||||||| |   | || || |         | ||| ||   |||||    | |||  |||| |||| |        ||  | ||   ||||
TGGAAAATATATTTTGACGGGAGGGGAAGATGATTTAGTTCAAGTTTGGAGCATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGACATAACTCATGGgtaagttgtgtgttaattttttgtcatgtgcttgtagcaaactttgctaccacaggactgatgtagtttgtgtcaaatgctgtgatcag

upper sequence: AT3G53390.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA10G05890.1 (Glycine max), 5'ss of exon 10
TGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAATTCGTGGgtaaggt---------tcttgatgtcaataagatttcttttatttaacttacacagcacttgactcatgtc-ggaatggttgctctcag------------
|||||| || |||||||| ||||| || ||||||||||||||||| ||||||||||| ||||| || |||||||| |||||||||||||| || || |||||||| |         ||||||    |  || ||||   || ||||    | | || | |  | |  | |  ||   | ||   | ||             
TGGAAAATATATTTTGACGGGAGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGACACAACTCATGGgtaagttgcatggtaatcttgactagacaaaaattttaattttttataccata-agtaataaattagtatgaggtgagatttggcacaacagtaaggtttt

upper sequence: AT3G53390.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA03G33740.2 (Glycine max), 5'ss of exon 9
TGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAATTCGTGGgtaaggttcttgatgtcaataagat---ttcttttatttaacttacacagcacttgactcatgtcggaatggttgctctcag---------------------
|||||| || |||||||| ||||| |||||||||||||||||||| ||||| ||||| ||||| || |||||||| ||||| ||||||||||| || |||||||| | | |||      | || |   | ||| ||   |||||    | |    |  | ||||   | || |||     |                      
TGGAAAATATATTTTGACGGGAGGGGAAGATGATTTAGTTCAAGTTTGGAGCATGGAAGATCGCAAGGTTGTGGCATGGGGCGAGGGACATAACTCATGGgtaagttgcctgacaatttttagttgtgtgcttgtagcaaactttgctaccgtagggttaatgt---agtgtttgtatcaaatgccatgatcaggtcagtgga

upper sequence: AT3G53390.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA03G33740.1 (Glycine max), 5'ss of exon 9
TGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAATTCGTGGgtaaggttcttgatgtcaataagat---ttcttttatttaacttacacagcacttgactcatgtcggaatggttgctctcag------------
|||||| || |||||||| ||||| |||||||||||||||||||| ||||| ||||| ||||| || |||||||| ||||| ||||||||||| || |||||||| | | |||      | || |   | ||| ||   |||||    | |    |  | ||||   | || |||     |             
TGGAAAATATATTTTGACGGGAGGGGAAGATGATTTAGTTCAAGTTTGGAGCATGGAAGATCGCAAGGTTGTGGCATGGGGCGAGGGACATAACTCATGGgtaagttgcctgacaatttttagttgtgtgcttgtagcaaactttgctaccgtagggttaatgt---agtgtttgtatcaaatgccatgatcag

upper sequence: AT3G53390.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA13G20240.1 (Glycine max), 5'ss of exon 10
TGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAATTCGTGGgtaaggttcttgatg---tcaataagatttcttttatttaacttacacagcac-ttgactcatgtcggaatggttgctctcag-----------------
||||||||| |||||||| || || || ||||||||||||||||| ||||||||||| ||||| || |||||||| ||||||||||| || || || |||||||| | | ||||    |  |   ||      || | || | |    |  |  ||   |   |  |  ||  |      |||                 
TGGAAAGTATATTTTGACGGGGGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGGCACAACTCATGGgtaagttgcatgataatcttgactggacaaaaattttataccatgagtaataaattagtttgaggtgagattttgcacaacagtaaggttttgctatctt

upper sequence: AT3G53390.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv08s0040g01960.t01 (Vitis vinifera), 5'ss of exon 9
TGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAATTCGTGGgtaag-gttctt---gatgtcaataagatttcttttatttaactta--cacagcacttg-actcatgtcggaatggttg-ctctcag
|||||| || ||||||||||||||||| |||||| |||||||||| ||||||||||| |||||||| |||||||| |||||||||||||| || || |||||||| |||||     |||||     |   |  |||  |  || |    | | |  |     | || |   ||||| || ||  |||
TGGAAAATATATTTTGACTGGAGGTGAGGATGATCTAGTTCAAGTTTGGAGTATGGAAGATCGGAAGGTTGTGGCATGGGGTGAGGGACACAACTCTTGGgtaagtgttctatcaaatgtctgcttgtcataatttcatagacatgattataaccttcatgattatcttttaatggatgtctgccag

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|116472333|gb|EG514925.1|EG514925
EST:     GGAAAGTTGTGGCGTGGGGTGAGGGACATAATTCGTGG                         GTAAGTGGAGTAGCGTTTGATTTCAATTGGTCGTCACCAAACTCGGATGGG
genomic: GGAAAGTTGTGGCGTGGGGTGAGGGACATAATTCGTGGgtaaggttct ... ttgctctcagGTAAGTGGAGTAGCGTTTGATTCCAATTGGTCGTCACCAAACTCGGATGGG
EST: gi|116472334|gb|EG514926.1|EG514926
EST:     GGAAAGTTGTGGCGTGGGGTGAGGGACATAATTCGTGG                         GTAAGTGGAGTAGCGTTTGATTTCAATTGGTCGTCACCAAACTCGGATGGG
genomic: GGAAAGTTGTGGCGTGGGGTGAGGGACATAATTCGTGGgtaaggttct ... ttgctctcagGTAAGTGGAGTAGCGTTTGATTCCAATTGGTCGTCACCAAACTCGGATGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAATTCGTGGgtaaggttcttgatgtcaataagatttcttttatttaacttacacagcacttgactcatgtcggaatggttgctctcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT