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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaattatgtatttgcagatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA

Basic information

species Arabidopsis thaliana
transcript AT3G15980.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaattatgta-tttgcagatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
    | || |  ||    | |   | |  ||| |   | |  ||       | || | |    |||| || |  |  ||||       ||||| ||||| || ||||| || || ||||| ||||| || || || || ||||||||  ||||||| || ||||||||||| |||||||| ||||| || |
----gttttttttttctatccacttttgagtgttccaagtatccacgattctgtgcagtcctaagatggtgtggtcatggtgaac---cagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA

upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 8
gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaattatgtatttgcagatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
                      |  |  ||| | ||    |   |||| ||| || |  |   ||  |   | | ||     |   | |||| ||||| |||||||| || || ||||| || || || || || ||  |||| ||||| ||||| |||||||||||||| ||||||||||||||||| |
--------------------gtatgacatgttcatttgcacatatgagcattttggacattatgactg---attggttaacttgaattagGTTTGGGATTATCAAACAAAGAGCTGTGTTCAAACACTTGAAGGACATGCACATAATGTCTCTGCTGTATGTTTCCATCCTGAGCTTCCAATAATAATGA

upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 7
gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaat-tatgtatttgcagatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
           |||   | |   ||        ||  | |||  ||   ||  ||| | |    |||     | || ||||      |||||| |||||||| ||||| || || || || || || || || || ||  |||| ||||||||||| ||||||||||| |||||||| || |||||||| |
-----------gtttgtcatatgatgcactgaattgtactcctgtggtcatgcatgcactctgtgatgac--attattggt--caaatcagGTTTGGGACTACCAAACAAAGAGCTGCGTTCAAACACTTGAAGGACATGCACATAATGTTTCTGCTGTATGTTTCCACCCAGAGCTACCTATAATAATTA

upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 7
-------gtatgcttctggttaagcttccaatatctgtgctttgattc---ccctgagaattatgtatttgcag--atcgtt-tactagtggtactttt---tcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
        | |  ||   |||       |   ||||   || | |||      |  | | || | |||    ||  ||  || | |   |   || |||   |||||||||||| |||||||||||||||||||||||||| ||||| || |||||||||||||| ||||| ||||| || ||||| || || || ||||| || |
gtttgttttctattttctgttttttcctcttcatcttccctctaatttggtttcctatatttgtatatggataggaattattatgccgataaaacctttgaatcagGTATGGGATTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTA

upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 7
---------gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaat-tatgtatttgca----gatcgtt-tactagtggtactttt---tcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
          |||  ||||| ||       |   ||||   |||| |||    ||   || | ||||| || |     ||  || | | | |   || |||    |||||||||||||||||||||||||||||||||||||| ||||| || |||||||||||||| ||||| || || || ||||| || || || ||||| || |
gtttgttttctat-tttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattatgccaataaaacctttgaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA

upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 7
gtatgcttctggttaagcttccaatatctgtgctt----tgattcccctgagaattatgtatttgcagatcgtttactag--tggtactttt---tcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
|| |  || |  ||        ||| | | |||||     |    | |  | |   |  | | || | |    | ||  |  ||  ||||     |||||||||||| ||||| |||||||||||||||||||| ||||| || |||||||||||||| ||||| ||||| || ||||| || ||||| ||||| || |
gttttgttttcatttgttgcttaatctatctgcttgtcgcgcacacgcacacacacacatgtatgaaaaggaataacatggatgaaacttacgaatcagGTATGGGATTATCAGACCAAAAGTTGTGTCCAGACCCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTTCCTATAATCATTA

upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 7
-----------gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaat-tatgtatttgcagatcgtt--tactagtggtactttt---tcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
            | || | || | |     | |  | |  |   ||  ||   | |    || ||| ||| || | |    |   |    ||  |||| |   |||||||||||| ||||| |||||||||||||||||||| ||||| || |||||||||||||| ||||| ||||| || ||||| || ||||| ||||| || |
gttttgttttcatttgttgcttgatctatctgct-tgtacgcatttacatatacatacatatatatatatatgaaaaggaataacatggatgaaacttatgaatcagGTATGGGATTATCAGACCAAAAGTTGTGTCCAGACCCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTTCCTATAATCATTA

upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 7
gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaattatgtatttgca-gatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
|| |||   || | |   ||   | | ||||| || |  |       |  | ||  |     | | || |  || | |  | |   | ||||| |||||||||||||||||||||||||||||||| || || || |||||||||||||||||||| || || |||||||| || ||||| |||||||| |
gtctgccgttgataattattttca-agctgtgtttagtatttatgcggtttgatagaaggaaatgttcatggacaaatcctccaaatgcagGTGTGGGACTATCAAACCAAAAGTTGTGTCCAGACACTGGAAGGCCACACACACAATGTTTCTGCAGTCTGCTTCCATCCTGAACTTCCCATAATAATAA

upper sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 7
gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaattatgtatttgcagatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
|| |   |||| |      |  | ||  |  ||||  |||    ||      || |  || |     ||     | |  |  |    ||||| |||||||| ||||||||||||||||| ||||| ||||| || |||||||||||||||||| | || |||||||||||||||||||| || ||  | |
gtgtttatctgat-gcttattgactaaata-gcttccatttatgtgcattccatttgattactttctgtgattaaattttggtggaacagGTGTGGGACTACCAAACCAAAAGTTGTGTTCAGACACTAGAAGGCCACACACACAATGTTTCTTCAGTCTGTTTCCATCCAGAGCTTCCTATTATTTTTA

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|116382436|gb|EG425028.1|EG425028
EST:     GGGGTGATAAACCCTATCTAATTACCGGCTCTGATGATCATACTGCTAAG                         GTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACA
genomic: GGGGTGATAAACCCTATCTAATTACCGGCTCTGATGATCATACTGCTAAGgtatgcttct ... actttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACA
EST: gi|116382434|gb|EG425026.1|EG425026
EST:     GGGGTGATAAACCCTATCTAATTACCGGCTCTGATGATCATACTGCTAAG                         GTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACA
genomic: GGGGTGATAAACCCTATCTAATTACCGGCTCTGATGATCATACTGCTAAGgtatgcttct ... actttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattcccctgagaattatgtatttgcagatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA
 ctttgat  putative branch site (score: 5)
                                            tactttttc  putative PPT
           agaattatgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaattatgtatttgcagatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT