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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcttttcttatatctacggccgatctctggcttcatttccccctgttgtttcgttcgttattcaattgaatagtttgtattgtggtcttgtgtctcagAGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAG

Basic information

species Arabidopsis thaliana
transcript AT3G06700.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g19840.1 (Oryza sativa), 3'ss of exon 1
-----------gttagcttttcttatatctacggccgatctct---ggcttcatt--tccccctgttgtttcgttcgttattcaattgaatagtttgtattgtggtctt---gtgtctca---gAGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAG
            |   |  ||   ||  |  |   |||| |||    | || ||   ||  | | || || |  |  ||  | | ||   | |||||| | || |||||     |  ||    |||||||||||||||||||| ||||||||||| |||||||||   || || ||||||||||| ||||||||||| | | | ||||| || |          
gtaaccgacgattcctccatttccatcgcctcattcgatgtctctttgatttatcgatcttcgttttcttcccctgattcctgatttttttcgtttgt-tcgtcgtctttgaagGATTCGGGGGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGGATCAAGAAGCCCAAGCGCCACCGCCAGA----------

upper sequence: AT3G06700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
--------------gttagcttttcttatatctacggccgatctctggcttcatttccccctgttgtttcgttcgttattcaattgaatagtttgtattgtggtcttgtgtctcagAGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAG
               |  |||     | |  ||||    ||| | | | ||| | | | ||     |     ||    ||    ||| | |  | |  | ||      |     ||||||||||||||||||||| ||||||||||| |||||||||   || || ||||||||||| ||||||||||| | | | ||||| ||            
gtaactctccggcactccgctcgatctgttcctacta--gatgtgttg-ttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG-----------

upper sequence: AT3G06700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G147791_T01 (Zea mays), 3'ss of exon 1
------gttagcttttcttat--atctacggccgatc--tctggcttcatttccccctgttgtttcgttcgtt-attcaattgaatagtttgtattgtggtcttgtgtctc--agAGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAG
       | ||     |   |  ||||    |  |||  | ||  ||   |   | | ||     |   | |  | | | |   ||        |||| | |  |  ||    ||| ||||||||||||||||| ||||||||||| |||||||||   || || ||||||||||| || ||||| || | | | ||||| ||            
gtaattctcaggcaccccgctcgatctcatcctaatcggtgtgattttcgtcttcaccgtcaacccacccctccacttactctgatt-cgcactttgttggcagGCATCCGGAAGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG-----------

upper sequence: AT3G06700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G147791_T02 (Zea mays), 3'ss of exon 1
gttagcttttcttatatctacggccgatctctggcttcatt-tccccctgttgtttcgttcgttattcaattgaatagtttgtattgtggtcttgtgtctcagAGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAG
                     |   ||| |  | |||||   ||  ||      | |  |   || ||   |    | ||||| | |  | | |  |    ||| ||||||||||||||||| ||||||||||| |||||||||   || || ||||||||||| || ||||| || | | | ||||| ||            
---------------------gtgtgattttcgtcttcaccgtcaacccacccctccact---tactctgattcgcactttgt-tggcagGCATCCGGA--AGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG-----------

upper sequence: AT3G06700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G147791_T03 (Zea mays), 3'ss of exon 1
-------gttagcttttcttatatctacggccgatctctggcttcatt-tccccctgttgtttcgttcgttattcaattgaatagtttgtattgtggtcttgtgtctcagAGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAG
       | | | | |  |  ||      |  ||| |  | |||||   ||  ||      | |  |   || ||   |    | ||||| | |  | | |  |    ||| ||||||||||||||||| ||||||||||| |||||||||   || || ||||||||||| || ||||| || | | | ||||| ||            
gcaccccgctcgatctcatcctaatcggtgt-gattttcgtcttcaccgtcaacccacccctccact---tactctgattcgcactttgt-tggcagGCATCCGGA--AGAAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG-----------

upper sequence: AT3G06700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0005g01340.t01 (Vitis vinifera), 3'ss of exon 1
gttagcttttcttatatctacggccgatctctggcttcatttccccctgttgtttcgttcgttattcaattgaatagtttgtattgtggtcttgtgtctcagAGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAG
                  ||| |||  |   |   ||  |    |   |  ||||        ||   | |||||  ||    ||    |  |||      || ||||| ||||||||||| ||||| || || ||||||||    |||||||||||||| ||||||||||| ||  | |  ||||| |||||| | |||  
-----------------gtacagcctctgcatcttttggtaaaacgacgccgtttttgctcccatctcactgaattcttccactttcaatgctgtag-

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|125228244|gb|EL242329.1|EL242329
EST:     ATCTACCTCTCTCTCTCAGTACTCAG                         AGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCC
genomic: ATCTACCTCTCTCTCTCAGTACTCAGgttagctttt ... tgtgtctcagAGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCC
EST: gi|124909856|gb|EH983936.1|EH983936
EST:     CGGAAAGTAAACCTAGCCGAGCAGATCTACCTCTCTCTCTCAGTACTCAG                         AGATGGCCAAGT
genomic: CGGAAAGTAAACCTAGCCGAGCAGATCTACCTCTCTCTCTCAGTACTCAGgttagctttt ... tgtgtctcagAGATGGCCAAGT
EST: gi|125317018|gb|EL331103.1|EL331103
EST:     AGATCTACCTCTCTCTCTCAGTACTCAG                         AGATGGCCAAGTCGAAGAATCACACGGCGCATAA
genomic: AGATCTACCTCTCTCTCTCAGTACTCAGgttagctttt ... tgtgtctcagAGATGGCCAAGTCGAAGAATCACACGGCGCATAA
EST: gi|164085038|gb|EL988409.1|EL988409
EST:     CTCTCT-AGTACTCAG                         AGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCC
genomic: CTCTCTCAGTACTCAGgttagctttt ... tgtgtctcagAGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCC
EST: gi|116412941|gb|EG455533.1|EG455533
EST:     CGGAAAGTAAACCTAGCCGAGCAGATCTACCTCTCTCTTTCAGTACTCAG                         AGATGGCCAAGTCGAAGAATCACACGGGGCATAACCAGTCGGGGAAAGCCC
genomic: CGGAAAGTAAACCTAGCCGAGCAGATCTACCTCTCTCTCTCAGTACTCAGgttagctttt ... tgtgtctcagAGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCC
EST: gi|125202534|gb|EL217488.1|EL217488
EST:     CGGAAAGTAAACCTAGCCGAGCAGATCTACCTCTCTCTCTCAGTACTCAG                         AGATGGCCAAGTCGAAGAATCACACGGCG
genomic: CGGAAAGTAAACCTAGCCGAGCAGATCTACCTCTCTCTCTCAGTACTCAGgttagctttt ... tgtgtctcagAGATGGCCAAGTCGAAGAATCACACGGCG
EST: gi|125231042|gb|EL245127.1|EL245127
EST:     CTCTCTCTCAGTACTCAG                         AGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCC
genomic: CTCTCTCTCAGTACTCAGgttagctttt ... tgtgtctcagAGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgtttcgttcgttattcaattgaatagtttgtattgtggtcttgtgtctcagAGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAG
              ttattcaattgaata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcttttcttatatctacggccgatctctggcttcatttccccctgttgtttcgttcgttattcaattgaatagtttgtattgtggtcttgtgtctcagAGATGGCCAAGTCGAAGAATCACACGGCGCATAACCAGTCGGCGAAAGCCCACAAGAACGGAATCAAGAAGCCAAGGAGACACCGTCACACCCCAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA