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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACATAGAGCTGCTGGGCCACAACTCAGAGCTGCATGCTATGAGGTTCCTGAAGTTCGTCCTGGAGTCCGTTGTCCAACTGGAGAAGCAAGAATTACTCCgtgagattaccctttttttaactcgtgtataaatgtagattgaggtagtttgaaattggtattgttgagtgatggaaaccagttggattgaaaaattggaacag

Basic information

species Arabidopsis thaliana
transcript AT2G40600.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G40600.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G062425_T03 (Zea mays), 5'ss of exon 3
TACATAGAGCTGCTGGGCCACAACTCAGAGCTGCATGCTATGAGGTTCCTGAAGTTCGTCCTGGAGTCCGTTGTCCAACTGGAGAAGCAAGAATTACTCCgtgagat-----taccctttttttaactcgtgtataaatgtagattgaggtagtttgaaattggtattgttgagtgat--ggaaaccagttggattgaaa---aattggaacag
|||||  ||||||||| ||| | ||       ||||||    | ||||| || ||    || |||||||||||||| ||||||||||| || |||||||||| ||       ||||  | | || |||    |       ||  | |   | |||  ||  |   |||  ||  |  |    | | |  || |    | |    ||  || |||
TACATCAAGCTGCTGGACCAGAGCTAGTGCAAGCATGCCGGAAAGTTCCAGAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtacttcgtacctatctattcactttgattgtttcataagtcggaat-gttcaaacctaaaatttatgtatcctttacacatccctttgcccaatattcgatgtgagcag

upper sequence: AT2G40600.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G062425_T02 (Zea mays), 5'ss of exon 3
TACATAGAGCTGCTGGGCCACAACTCAGAGCTGCATGCTATGAGGTTCCTGAAGTTCGTCCTGGAGTCCGTTGTCCAACTGGAGAAGCAAGAATTACTCCgtgaga-----ttaccctttttttaactcgtgtataaatgtagattgaggtagtttgaaattggtattgttgagtgat--ggaaaccagttggattgaaa---aattggaacag
         ||||||| ||| | ||       ||||||    | ||||| || ||    || |||||||||||||| ||||||||||| || |||||||||| ||       ||||  | | || |||    |       ||  | |   | |||  ||  |   |||  ||  |  |    | | |  || |    | |    ||  || |||
---------CTGCTGGACCAGAGCTAGTGCAAGCATGCCGGAAAGTTCCAGAGGTCAAACCAGGAGTCCGTTGTCCTACTGGAGAAGCTAGGATTACTCCgttagtacttcgtacctatctattcactttgattgtttcataagtcggaat-gttcaaacctaaaatttatgtatcctttacacatccctttgcccaatattcgatgtgagcag

upper sequence: AT2G40600.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv13s0067g02950.t01 (Vitis vinifera), 5'ss of exon 3
TACATAGAGCTGCTGGGCCACAACTCAGAGCTGCATGCTATGAGGTTCCTGAAGTTCGTCCTGGAGTCCGTTGTCCAACTGGAGAAGCAAGAATTACTCCgtgagattaccctttttttaactcgtgtataaatgtagattgaggtagtttgaaattggtattgttgagtgatggaaaccagttggattgaaaaattggaacag
|||||||||||||||| ||| | ||   ||| || |||||| |||| || |||||||| || ||| | || || || |||||||||||||||||||| | ||  |       || || ||  | |  |    || ||||||    |  |   ||  |  |  ||||   | ||      |||                      
TACATAGAGCTGCTGGTCCAGAGCTTGTAGCAGCTTGCTATAAGGTCCCAGAAGTTCGACCCGGAATTCGCTGCCCTACTGGAGAAGCAAGAATTACCCAgtagg-------ttcttatacgttggttcattatatagattattttcctcacaatgtactgatgtt--ctaataatttgcag----------------------

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|116425484|gb|EG468076.1|EG468076
EST:     GAAGTTCGTCCTGGAGTCCGTTGTCCAACTGGAGAAGCAAGAATTACTCC                         GGGTTTTAACTTGCCTGCATCGCGTGTGATTCACACTGTTGGACCTATCTA
genomic: GAAGTTCGTCCTGGAGTCCGTTGTCCAACTGGAGAAGCAAGAATTACTCCgtgagattac ... attggaacagGGGTTTTAACTTGCCTGCATCGCGTGTGATTCACACTGTTGGACCTATCTA
EST: gi|124728727|gb|EH820129.1|EH820129
EST:     GGAGTCCGTTGTCCAACTGGAGAAGCAAGAATTACTCC                         GGGTTTTAACTTGCCTGCATCGCGTGTGATTCACACTGTTGGACCTATCTA
genomic: GGAGTCCGTTGTCCAACTGGAGAAGCAAGAATTACTCCgtgagattac ... attggaacagGGGTTTTAACTTGCCTGCATCGCGTGTGATTCACACTGTTGGACCTATCTA
EST: gi|124741014|gb|EH832176.1|EH832176
EST:     TCCGTTGTCCAACTGGAGAAGCAAGAATTACTCC                         GGGTTTTAACTTGCCTGCATCGCGTGTGATTCACACTGTTGGACCTATCTA
genomic: TCCGTTGTCCAACTGGAGAAGCAAGAATTACTCCgtgagattac ... attggaacagGGGTTTTAACTTGCCTGCATCGCGTGTGATTCACACTGTTGGACCTATCTA
EST: gi|124817025|gb|EH901891.1|EH901891
EST:     CCTGGAGTCCGTTGTCCAACTGGAGAAGCAAGAATTACTCC                         GGGTTTTAACTTGCCTGCATCGCGTGTGATTCACACTGTTGGACCTATCTA
genomic: CCTGGAGTCCGTTGTCCAACTGGAGAAGCAAGAATTACTCCgtgagattac ... attggaacagGGGTTTTAACTTGCCTGCATCGCGTGTGATTCACACTGTTGGACCTATCTA

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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACATAGAGCTGCTGGGCCACAACTCAGAGCTGCATGCTATGAGGTTCCTGAAGTTCGTCCTGGAGTCCGTTGTCCAACTGGAGAAGCAAGAATTACTCCgtgagattaccctttttttaactcgtgtataaatgtagattgaggtagtttgaaattggtattgttgagtgatggaaaccagttggattgaaaaattggaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA