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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATTGGATCTGCCCAAGTTGTGGCAATGTCAACTTTTCATTCAGGACAACTTGCAATATGCGTAATTGCACTCAGCCTAGACCTGCAGATCATAATGGAgtaagttattttgtgttgcaatatcgaatatatgtctttctgctttgaaacagttttgtgtgcaaaacagtcattgacttcttggcgggtttagtagata...

Basic information

species Arabidopsis thaliana
transcript AT1G67325.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G67325.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA11G36990.3 (Glycine max), 5'ss of exon 3
TGATTGGATCTGCCCAAGTTGTGGCAATGTCAACTTTTCATTCAGGACAACTTGCAATATGCGTAATTGCACTCAGCCTAGACCTGCAGATCATAATGGAgtaagttattttgtgttgcaatatcgaatatatgtctttctgctttgaaacagttttgtgtgcaaaacagtcattgacttcttggcgggttta-gtagata
||||||||  ||||| || |||||||||||||| || || |||||||||||||| || ||||||||||||||||| || || || || |||||||||   ||| | |||| | |||      ||    | | |    |     ||| |    |||     |  |       |||| | ||  ||     |||   |  || 
TGATTGGACATGCCCCAGCTGTGGCAATGTCAATTTCTCTTTCAGGACAACTTGTAACATGCGTAATTGCACTCAACCAAGGCCGGCTGATCATAATTCGgtatgatattatatgtaatgtcattttttttttaaaatgtgattttcatttcgttaatgatttatggttaacatttatttgatgatttctttttatcaat-

upper sequence: AT1G67325.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA18G00920.1 (Glycine max), 5'ss of exon 3
TGATTGGATCTGCCCAAGTTGTGGCAATGTCAACTTTTCATTCAGGACAACTTGCAATATGCGTAATTGCACTCAGCCTAGACCTGCAGATCATAATGGAgtaagttattttgtgttgcaatatcgaatatatgtctttctgctttgaaacagttttgtgtgcaaaacagtcattgacttcttggcgggtttagtagata------
||||||||  ||||| || ||||| ||||| || || || |||||||||||||| || ||||||||||||||||| || || || || |||||||||   ||||| |||| |||||   |||  | | | | |   ||| |    || |    |||  | |||  ||   |    |     ||     | | |  | ||       
TGATTGGACATGCCCCAGCTGTGGTAATGTTAATTTCTCTTTCAGGACAACTTGTAACATGCGTAATTGCACTCAACCAAGGCCGGCTGATCATAATTCTgtaagatattatgtgt---aatgcc-actgtgttattttttaaaatgtagt--tttcatctgcttaatgatttaaggtacatttatttgatgaaaaaatgttatca

upper sequence: AT1G67325.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv01s0010g03700.t01 (Vitis vinifera), 5'ss of exon 3
TGATTGGATCTGCCCAAGTTGTGGCAATGTCAACTTTTCATTCAGGACAACTTGCAATATGCGTAATTGCACTCAGCCTAGACCTGCAGATCATAATGGAgtaagttattttgtgttgcaatatcgaatatatgtctttctgctttgaaacagttttgtgtgcaaaacagtcattgacttcttggcgggtttagtagata---------
|||||||| ||| || || ||||||||||| || ||||| || ||||| |||||||||||||| ||||| || || || ||||| || ||||||||   |||||| | |    |  || | ||||         | ||| ||    | |||||       |      ||||  || || |  |||      || |  |           
TGATTGGACCTGTCCTAGCTGTGGCAATGTTAATTTTTCTTTTAGGACGACTTGCAATATGCGCAATTGTACCCAACCCAGACCAGCTGATCATAACTCAgtaagatgtggacttctgtagtatc---------tttttatgtggaggaacagaaccacatttgtttcagtatttcacatgctggaatacataatctactaatagatta

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|116475626|gb|EG518218.1|EG518218
EST:     CTTGCAATATGCGTAATTGCACTCAGCCTAGACCTGCAGATCATAATGGA                         AAGTCTGCTCCCAAACCTATGCAACATCAACAAGGTTTCTCATCACCCGGG
genomic: CTTGCAATATGCGTAATTGCACTCAGCCTAGACCTGCAGATCATAATGGAgtaagttatt ... tctgtaacagAAGTCTGCTCCCAAACCTATGCAACATCAACAAGGTTTCTCATCACCCGGG
EST: gi|164114272|gb|ES052848.1|ES052848
EST:     GACCTGCAGATCATAATGGA                         AAGTCTGCTCCCAAACCTATGCAACATCAACAAGGTTTCTCATCACCCGGG
genomic: GACCTGCAGATCATAATGGAgtaagttatt ... tctgtaacagAAGTCTGCTCCCAAACCTATGCAACATCAACAAGGTTTCTCATCACCCGGG
EST: gi|125081616|gb|EL142772.1|EL142772
EST:     TATGCGTAATTGCACTCAGCCTAGACCTGCAGATCATAATGGA                         AAGTCTGCTCCCAAACCTATGCAACATCAACAAGGTTTCTCATCACCC
genomic: TATGCGTAATTGCACTCAGCCTAGACCTGCAGATCATAATGGAgtaagttatt ... tctgtaacagAAGTCTGCTCCCAAACCTATGCAACATCAACAAGGTTTCTCATCACCC
EST: gi|116475625|gb|EG518217.1|EG518217
EST:     CTTGCAATATGCGTAATTGCACTCAGCCTAGACCTGCAGATCATAATGGA                         AAGTCTGCTCCCAAACCTATGCAACATCAACAAGGTTTCTCATCACCCGGG
genomic: CTTGCAATATGCGTAATTGCACTCAGCCTAGACCTGCAGATCATAATGGAgtaagttatt ... tctgtaacagAAGTCTGCTCCCAAACCTATGCAACATCAACAAGGTTTCTCATCACCCGGG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATTGGATCTGCCCAAGTTGTGGCAATGTCAACTTTTCATTCAGGACAACTTGCAATATGCGTAATTGCACTCAGCCTAGACCTGCAGATCATAATGGAgtaagttattttgtgttgcaatatcgaatatatgtctttctgctttgaaacagttttgtgtgcaaaacagtcattgacttcttggcgggtttagtagata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA