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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatttccccccttctctacttttctagggttttagttcctcttcgttgggtttgtatttgagttttgttttcgtttcaatcggaacaaagaataatcctaatcgattgttctatttgggtaatttagagaaagctgttaaatttgggatctgttgtaaattactcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATAATGTCTACGTCTGCCGCTCTGGATCG

Basic information

species Arabidopsis thaliana
transcript AT4G31300.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G31300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g04800.1 (Oryza sativa), 3'ss of exon 1
gtgagatttccccccttctctacttttctagggttttagttcctcttcgttgggtttgtatttgagttttgttttcgtttcaatcggaacaaagaataatcctaatcgattgttctatttgggtaattta----gagaaagctgttaaatttgggatctgttgtaaattactcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATAATGTCTACGTCTGCCGCTCTGGATCG
                                                                          | | | |||||| ||  || | |||        | |   |||  |||  || |||        ||     ||   ||||  || || ||| ||||  |     ||| ||||| || ||||| || || ||||| || ||||| |||||||| || ||||| |||||||||||||||||||| 
--------------------------------------------------------------------------ttgatccaatcgaaatcaatattaagttggtgtgctctgtctgcttgtctattttttccctttaatttaattgcctttgttatgtggtgttaattctt-----agGAATGTATGTGGCGAACCGTGCATCTGACAAAATTACTCAACTGACTGACAATGTGTACGTCTGCCGCTCTGGATCT

upper sequence: AT4G31300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G152775_T03 (Zea mays), 3'ss of exon 1
gtgagatttccccccttctctacttttctagggttttagttcctcttcgttgggtttgtatttgagttttgttttcgtttcaatcggaacaaagaataatcctaatcgattgttctatttgggtaatttagagaaagctgttaaatttgggatctgttgtaaattactcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATAATGTCTACGTCTGCCGCTCTGGATCG-----------------------
                                                                        |   ||||| | |  || | |      |  ||| |   |||  | |||   |  | |   |  |  || |||  ||    | |||||     | |   | |||| ||||| ||||| || || ||||| || |||||||| ||||||||||| ||||| || ||||| |||||||||||                        
-----------------------------------------------------------------------ctcctgtttccacca-aatagaattcgttattaagctgatgtagtctttattttctatttggccaagtgctaatatttt--tgtgttgcctgct-ccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTGTAAGTGCCATTGTCTTCTAATG

upper sequence: AT4G31300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G152775_T04 (Zea mays), 3'ss of exon 1
gtgagatttccccccttctctacttttctagggttttagttcctcttcgttgggtttgtatttgagttttgttttcgtttcaatcggaacaaagaataatcctaatcgattgttctatttgggtaatttagagaaagctgttaaatttgggatctgttgtaaattactcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATAATGTCTACGTCTGCCGCTCTGGATCG
                                                                        |   ||||| | |  || | |      |  ||| |   |||  | |||   |  | |   |  |  || |||  ||    | |||||     | |   | |||| ||||| ||||| || || ||||| || |||||||| ||||||||||| ||||| || ||||| ||||||||||| 
-----------------------------------------------------------------------ctcctgtttccacca-aatagaattcgttattaagctgatgtagtctttattttctatttggccaagtgctaatatttt--tgtgttgcctgct-ccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCT

upper sequence: AT4G31300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G374881_T01 (Zea mays), 3'ss of exon 1
gtgagatttccccccttctctacttttctagggttttagttcctcttcgttgggtttgtatttgagttttgttttcgtttcaatcggaacaaagaataatcctaatcgattgttctatttgggt-aatttagagaaagctgttaaatttgggatctgttgtaaattactcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATAATGTCTACGTCTGCCGCTCTGGATCG-----------------------
                                                                  ||||| |   |||||   |  || |||    | |  ||| |   |||  | |||   | || || |   |||   | | ||||     ||| |  || |        |||| ||||| ||||| || || ||||| || |||||||| ||| ||||||| ||||| ||||| || |||||||||||                        
---------------------------------------------------------------tgcttttgctcctgtttctgcca-aataaatttcattattaagctgatgtattctttattttaaatttggccaagtgctaacattt----cctgctccaact--------cagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCTGTAAGTGTTGTTGTCTTCTAATG

upper sequence: AT4G31300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G374881_T02 (Zea mays), 3'ss of exon 1
gtgagatttccccccttctctacttttctagggttttagttcctcttcgttgggtttgtatttgagttttgttttcgtttcaatcggaacaaagaataatcctaatcgattgttctatttgggt-aatttagagaaagctgttaaatttgggatctgttgtaaattactcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATAATGTCTACGTCTGCCGCTCTGGATCG
                                                                  ||||| |   |||||   |  || |||    | |  ||| |   |||  | |||   | || || |   |||   | | ||||     ||| |  || |        |||| ||||| ||||| || || ||||| || |||||||| ||| ||||||| ||||| ||||| || ||||||||||| 
---------------------------------------------------------------tgcttttgctcctgtttctgcca-aataaatttcattattaagctgatgtattctttattttaaatttggccaagtgctaacattt----cctgctccaact--------cagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT

upper sequence: AT4G31300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0008g02850.t01 (Vitis vinifera), 3'ss of exon 1
gtgagatttccccccttctctacttttctagggttttagttcctcttcgttgggtttgtatttgagttttgttttcgtttcaatcggaacaaagaataatcctaatcgattgttctatttgggtaatttagagaaagctgttaaatttgggatctgttgtaaattactcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATAATGTCTACGTCTGCCGCTCTGGATCG
                                                                         |      ||||      || | |  || ||  |  | | |   | ||   |  | ||| |   | ||||  ||     || | || |       | ||  ||| ||||| || || ||  |||| || || || || ||||| |||||||||||||||||| | || ||||||||||||
--------------------------------------------------------------------caacctagaacccaattttg--aatgcaagattctgttaaagtttggaactt---ttctgtagcgtttgatgtttgatgcaatatat-ttatgttggggttgc-tagGAATGTATGTCGCTAACAGAGCATCGGACAAAATCACACAGCTGACAGATAATGTCTACATTTGTCGCTCTGGATCG

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|116424148|gb|EG466740.1|EG466740
EST:     CACTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCG                         GTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATA
genomic: CACTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCGgtgagatttc ... actcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATA
EST: gi|116475826|gb|EG518418.1|EG518418
EST:     CACTTACAATGGAGGTGTCGTCCCCGGAGCCGACTCACGTACCAGCACCG                         GTATGTACGTAGCGAATCGAGC
genomic: CACTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCGgtgagatttc ... actcgcgcagGTATGTACGTAGCGAATCGAGC
EST: gi|124904356|gb|EH978436.1|EH978436
EST:     CACTTACAATGGAGGTGTCGTCCCCGGAGCCGACTCACGTACCAGCACCG                         GTATGTACGTAGCGAATCGAGCTTCTGATAAGATT
genomic: CACTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCGgtgagatttc ... actcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAAGATT
EST: gi|116444628|gb|EG487220.1|EG487220
EST:     CACTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCG                         GTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATA
genomic: CACTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCGgtgagatttc ... actcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATA
EST: gi|47831542|gb|CK121226.1|CK121226
EST:     CACTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCG                         GTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATA
genomic: CACTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCGgtgagatttc ... actcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATA
EST: gi|86078013|gb|DR373770.1|DR373770
EST:     CACTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCG                         GTATGTACGTAGC
genomic: CACTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCGgtgagatttc ... actcgcgcagGTATGTACGTAGC
EST: gi|116475847|gb|EG518439.1|EG518439
EST:     CACTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCG                         GTATGTACGTAGCGAATCGAGC
genomic: CACTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCGgtgagatttc ... actcgcgcagGTATGTACGTAGCGAATCGAGC
EST: gi|125066719|gb|EL133487.1|EL133487
EST:     CACTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCG                         GTATGTACGTAGCGAATCGAGCTTCTGATAA
genomic: CACTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCGgtgagatttc ... actcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAA
EST: gi|116444625|gb|EG487217.1|EG487217
EST:     CTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCG                         GTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATA
genomic: CTTACAATGGAGGTGTCGTCCTCGGAGCCGACTCACGTACCAGCACCGgtgagatttc ... actcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtaatttagagaaagctgttaaatttgggatctgttgtaaattactcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATAATGTCTACGTCTGCCGCTCTGGATCG
                  tgttaaattt  TA-rich tract