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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtgatctcttctctgtttaattgctttcgatctgatcgtaattgatgaatgtagtaactttagtggatagattgaatctgttttgatattcatctgatggctgcttgaagtagattcactgaaaaggtgtttggatttgtttattagGAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG

Basic information

species Arabidopsis thaliana
transcript AT3G60750.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 1
gtctgtgatctcttctctgtttaattgctttcgatctgatcgtaattgatgaatgtagtaactttagtggatagattgaatctgttttgatattcatctgatggctgcttgaagtagattcactgaaaaggtgtttggatttgtttattagGAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG
                                           || |  || | ||  |   |  ||||  ||   ||    ||  || |  |||| |||||   || |   |      |  ||| ||   ||   | || |   |   ||||||| || |||||||| ||| | ||||||||||||||||| ||||| ||||| ||||| |||||||| || ||| ||||||| || ||||
-------------------------------------------aaattctgga-gtgatcggtgaagtgtttaatatgg--ttgacttcagtttcaactgat--ttgttc--atcgagcttgctgtaactatggccgcatattgctgc-agGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 1
gtctgtgatctcttctctgtttaattgctttcgatctgatcgtaattgatgaatgtagta-actttagtggatagattgaatctgttttgatattcatctgatggctgcttgaagtagattcactgaaaaggtgtttggatttgtttattagGAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG
                                           || |  |||  ||| |  || | ||  ||  | |   || ||||| ||||  |||||  |   |  |   | | ||||   |  ||  ||| |||| | |||     ||||||| || |||||||||||| | |||||||||||||  ||||| || || |||||||| || |||||||| ||| ||||||| || || |
-------------------------------------------aactattgagcgtaattcacctcagcaga--gctgccatgtgttt-gataagcatctcttatgttatgtgactggatttgttctaactgtggttgg-tatgt-----agGAGGAGGACTTGAAGCAGTTCAGGCAATGGGGAAGCAGAACACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 1
gtctgtgatctcttctctgtttaattgctttcgatctgatcgtaattgatgaatgtagtaactttagtggatagat--tgaatctgttttgatattcatctgatggctgcttgaagtagattcactgaaaaggtgtttggatttgtttattagGAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG
                                             || ||  ||| |  | ||||  |||||| ||  |      | ||| | | |  |  |||  || | | |  |  |||   ||        ||| |  ||   |  ||||| |||||  ||||| | ||||| |||||||| |||| ||| || |||||||||||||| || |||||   |||||||||||| ||||| |
------------------------------------------aggttcat--atggatgacctttgatggatatataattgtgaagcttttaaagttgtgggat--cttcattagctgaatttgttgt-------tttcgggttacatgatagGAAGAAGACCTGAAGGAATTCCGACAATGGGGGAGCAGGACTCCTGGACATCCTGAGAACTTTGAGACAGTTGGAATTGAAGTGACTACAG

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 1
gtctgtgatctcttctctgtttaattgctttcgatctgatcgtaattgatgaatgtagtaactttagtggatagattgaatctgttttgatattcatctgatggctgcttgaagtagattcactgaaaaggtgtttggatttgtttattagGAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG
                                    || |  | ||  ||| | || |||| | |  ||  |   |||    | | |||||      |||| |      |||||| | |    |     |||       |   | | |||||| || ||||||| | | || || |||||||| ||||  || || ||||| ||||||||||| |||||||| ||||||||||| || || |
---------------------------------tgttgtttttgat--atgtacgtggtaagtgtgatgagt---ttgtgcatatcttgatcaaagactgaag------tgaagttgttgtgtttggggggt-------tgactcttttagGAAGAGGATTTGAGGGAATTTCGCCAATGGGGGAGCAGAACTCCGGGACACCCTGAGAATTTTGAGACTCCGGGAATTGAAGTTACAACAG

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 1
gtctgtgatctcttctctgtttaattgctttcgatctgatcgtaattgatgaatgtagtaactttagtggatagattgaatctgttttgatattcatctgatggctgcttgaagtagattcactgaaaag--gtgtttggatttgtttattagGAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG
                                             || ||  || || | | |||  ||     | |     || | ||| || ||| ||| |  |  | |        |  ||||||    |||||| |  |   ||| ||||| ||||| |||||    |||||||||||||||||||  ||||| || || || || ||||| ||||| |||||  |||||||||||||||
---------------------------------------------tttatttatttatttatttttctgagcttagttttgttgctatgagatccatttgaggtgtcttcg--------ttcctgaaattttgtgttttggatgaattaatagGAAGAAGACTTGAAAAGTTTCCGTCAATGGGGAAGCACAACACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ07676 (Selaginella moellendorffii), 3'ss of exon 1
gtctgtgatctcttctctgtttaattgctttcgatctgatcgtaattgatgaatgtagtaactttagtggatagattgaatctgttttgatattcatctgatggctgct--tgaagtagattcactgaaaaggtgtttggatttgtttattagGAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG
                                                                           | |  |||   ||||| |   |  ||    | ||    ||||   | |  | || | |  |||     |  ||   |||| || ||||||||||| |||||||||||||| ||||  || || || ||||| ||||| ||||||||||| ||  | |||||||| ||||
--------------------------------------------------------------------------gtaggctctccattgatctagtttcgagcttttctatcaaagttcttcctttcaacatggatttcttgcttgtttccagGAAGAGGATTTGAAGCAATTCCGTCAATGGGGCAGCAGAACTCCTGGCCATCCAGAGAACTTCGAGACTCCCGGCGTGGAAGTCACGACTG

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ07729 (Selaginella moellendorffii), 3'ss of exon 1
gtctgtgatctcttctctgtttaattgctttcgatctgatcgtaattgatgaatgtagtaactttagtggatagattgaatctgttttgatattcatctgatggctgct--tgaagtagattcactgaaaaggtgtttggatttgtttattagGAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG
                                                                           | |  |||   ||||| |   |  ||    | ||    ||||   | |  | || | |  |||    ||  ||   |||| || ||||||||||| |||||||||||| | ||||  || || || ||||| ||||| ||||||||||| ||  | |||||||| ||||
--------------------------------------------------------------------------gtaggctctccattgatctagtttcgagcttttctatcaaagttcttcctttcaacatggatttcttgtttgtttccagGAAGAGGATTTGAAGCAATTCCGTCAATGGAGCAGCAGAACTCCTGGTCATCCAGAGAACTTCGAGACTCCCGGCGTGGAAGTCACGACTG

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|124951090|gb|EL026493.1|EL026493
EST:     GTATGTTGCTCTACGCGTTGCTCCATCTTGCCGGCTACGACAGCGTCCAG                         GAGGAAGATTTGAAGCAGTTCCG
genomic: GTATGTTGCTCTACGCGTTGCTTCATCTTGCCGGCTACGACAGCGTCCAGgtctgtgatc ... tgtttattagGAGGAAGATTTGAAGCAGTTCCG
EST: gi|124709204|gb|EH800606.1|EH800606
EST:     GTATGTTGCTCTACGCGTTGCTTCATCTTGCCGGCTACGACAGCGTCCAG                         GAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAA
genomic: GTATGTTGCTCTACGCGTTGCTTCATCTTGCCGGCTACGACAGCGTCCAGgtctgtgatc ... tgtttattagGAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAA
EST: gi|124747581|gb|EH837711.1|EH837711
EST:     GTATGTTGCTCTACGCGTTGCTTCATCTTGCCGGCTACGACAGCGTCCAG                         GAGGAAGATTTGAAGCAGTT
genomic: GTATGTTGCTCTACGCGTTGCTTCATCTTGCCGGCTACGACAGCGTCCAGgtctgtgatc ... tgtttattagGAGGAAGATTTGAAGCAGTT
EST: gi|124723519|gb|EH814921.1|EH814921
EST:     TATGTTGCTCTACGCGTTGCTTCATCTTGCCGGCTAACGACAGCGTCCAG                         GAGGAAGATTTG
genomic: TATGTTGCTCTACGCGTTGCTTCATCTTGCCGGCTA-CGACAGCGTCCAGgtctgtgatc ... tgtttattagGAGGAAGATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgatggctgcttgaagtagattcactgaaaaggtgtttggatttgtttattagGAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG
 atctgat  putative branch site (score: 4)
                                           tttgttt  putative PPT
                                          atttgtttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtgatctcttctctgtttaattgctttcgatctgatcgtaattgatgaatgtagtaactttagtggatagattgaatctgttttgatattcatctgatggctgcttgaagtagattcactgaaaaggtgtttggatttgtttattagGAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG