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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatctcgaatgcaactgtgtgtgaccttaatgtggccaactatttaagtgctgaaggaatttggttgtgtttcctgatgcagGGGTCCCGATTACAAAGGGATGTATGCTATAAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC

Basic information

species Arabidopsis thaliana
transcript AT4G24740.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
-----------------------------------------gtatatctcgaatgcaactgtgtgtgaccttaatgtggc-caactatttaag--tgctgaaggaatttggttgtgtttcctgatgcagGG-GTCCCGATTACAAAGGGATGTATGCTAT---AAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC
                                           |  |||    |  | | | || |  | | | | ||   |||| |||| |   |        |||     |    |  ||| |        ||||| |  | || ||| |  | ||||   ||     |||| || || ||||| || ||||||||||||||||| |||||||| ||||| |  |      
gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccg-gtttagc-tgattatgattcaacaattttatgttatctttctaatccttctacaatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC------

upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G179308_T04 (Zea mays), 3'ss of exon 3
-----------gtatatctcgaatgcaactgtgtgtgaccttaatgtggccaactatttaagtgctgaa---ggaatt--tggttgtgtttcctgatgcagGG----GTCCCGATTACAAAGGGATGTATGCTAT---AAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC
            | || || |       || |||       |  |||       || | || |  ||||   || | |  |  |  | ||| |   |||  ||     |||||||  | || ||| | || ||||   ||  | ||||| || || ||||| || ||||||||||||||||||||||| || ||||| |  |      
acctacccaagatttaccttgccctgtgct-tgttgatttctgttgtaataggttagtgaa-tattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC------

upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 6
-------------------------------------gtatatctcgaatgcaactgtgtgtgaccttaatgtggccaactatttaagtgctgaa---ggaatt--tggttgtgtttcctgatgcagGG----GTCCCGATTACAAAGGGATGTATGCTAT---AAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC
                                      | || || |       || |||       |  |||       || | || |  ||||   || | |  |  |  | ||| |   |||  ||     |||||||  | || ||| | || ||||   ||  | ||||| || || ||||| || ||||||||||||||||||||||| || ||||| |  |      
gtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgct-tgttgatttctgttgtaataggttagtgaa-tattgaatatggtactgatcctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC------

upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 7
-------------------------------------gtatatctcgaatgcaactgtgtgtgaccttaatgtggccaactatttaagtgctgaaggaat----ttggttgtgtttcctgat--gcagGG----GTCCCGATTACAAAGGGATGTATGCTAT---AAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC
                                       || |  |   ||| | ||  |||    ||| ||||      ||     |     ||   ||     || |  | |||  | ||  ||  ||     |||| ||  | || ||| |  | ||||   ||     |||| || || ||||| || |||||||||||||| |||||||| |||||||| |  |      
gtatatcttgttcttttatatttaattcacctacccaagatttaccttgtgcta-tgcttgttcttttattgtgtattggtagcgggggtagaaaaatatggtactgatcctcttttttcatttgccagGTCTCATCCCAATCCCCAAAGGAGGGGTCCTATTACAAGCAGTTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTCGGTAGCACTACTTATGATCAAC------

upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G063792_T05 (Zea mays), 3'ss of exon 4
---------gtatatctcgaatgcaactgtgtgtgaccttaatgtggccaactatttaagtgctgaaggaat----ttggttgtgtttcctgat--gcagGG----GTCCCGATTACAAAGGGATGTATGCTAT---AAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC
           || |  |   ||| | ||  |||    ||| ||||      ||     |     ||   ||     || |  | |||  | ||  ||  ||     |||| ||  | || ||| |  | ||||   ||     |||| || || ||||| || |||||||||||||| |||||||| |||||||| |  |      
acctacccaagatttaccttgtgcta-tgcttgttcttttattgtgtattggtagcgggggtagaaaaatatggtactgatcctcttttttcatttgccagGTCTCATCCCAATCCCCAAAGGAGGGGTCCTATTACAAGCAGTTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTCGGTAGCACTACTTATGATCAAC------

upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 6
---------gtatatctcgaa-tgcaactgtgtgtg-----accttaatgtggccaactatttaagtgctgaaggaatttggttgtgtttcctgatgcagGGGTCCCGATTACAAAGGGATGTATGCTATAAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC
         | ||   |  || || ||||| || ||     ||| |  | |  |       || | || | ||  | |    |    |||  |  | ||| | ||      |  |     |   |  |  || ||||| || ||||||||||| |||||||| ||||||||||| ||||| |||||||||||  | || |
gtcgtacctggatgaataaaaatgaaactgagtatggaagtacccttttctatctttagcattgattgatcaatcattgacatccattttatttttacagAGTTCATCTAGATCATCATGTTCCTATTTCAAGAGAGTTCCCAAATCAAGTGCTATAAAGGTTATTGATTTTGGCAGCACCACTTATGAGCGAGAAGATC

upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 6
----------gtatatctcgaatgcaactgtgtgtg-----accttaatgtggccaactatttaagtgctgaaggaatttggttgtgtttcctgatgcagGGGTCCCGATTACAAAGGGATGTATGCTATAAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC
          |   ||    |||| |||   || ||     ||| |  | | ||       |  | || | ||  | |    ||   |||  |  | ||| | ||      |  |     |   |  |  || ||||| || ||||||||||| |||||||| ||||||||||| ||||| |||||||||||  | || |
gttggacctggaggataaaaaatgaaaccaagtatggaactacccttttctagctttagcatcgattgatcaatcattgacattcattttatttttacagAGTTCATCTAGATCACCAAGTTCCTATTTCAAGAGAGTTCCCAAATCAAGTGCTATAAAGGTTATTGATTTTGGCAGCACCACTTATGAGCGAGAAGATC

upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 7
--------------------gtatatctcgaatgcaactgtgtgtgaccttaatgtg--------gccaactatttaagtgctgaaggaatttggttgtgtttcctgatgcagGG---GTCCCGATTACAAAGGGATG---TATGCTATAAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC
                     | | | |  | ||  |    || |  | ||| | |           | || ||     || |   | ||  |   | |||| | |  | ||||     ||||| | ||  | |||||     | || ||| ||||| || ||||||||||| || || |||||||||||||| |||||||| |||||||| |      
gtactccagatgttaacttgatgtgtattaagtggcatatggttttgctttattattctttctgcatctacaatgcccttgttattgtaacatatatttgttgcatt-ttcagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAATCAAGTGCTATTAAAGTGATTGATTTTGGAAGCACAACATATGAGCGAC------

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|125084975|gb|EL144996.1|EL144996
EST:     AAAATATTCTGTTAGTCTCCTCAGACTATGTGAAGATTCCCGAGTACAAG                         GGGTCCCGATTACAAAGGGATGTATGCTATAAAAGAGTGCCTAAA
genomic: AAAATATTCTGTTAGTCTCCTCAGACTATGTGAAGATTCCCGAGTACAAGgtatatctcg ... cctgatgcagGGGTCCCGATTACAAAGGGATGTATGCTATAAAAGAGTGCCTAAA
EST: gi|124753928|gb|EH844058.1|EH844058
EST:     TCTGTTAGTCTCCTCAGACTATGTGAAGATTCCCGAGTACAAG                         GGGTCCCGATTACAAAGGGATGTATGCTATAAAAGAGTGCCTAAATCAAGT
genomic: TCTGTTAGTCTCCTCAGACTATGTGAAGATTCCCGAGTACAAGgtatatctcg ... cctgatgcagGGGTCCCGATTACAAAGGGATGTATGCTATAAAAGAGTGCCTAAATCAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgtggccaactatttaagtgctgaaggaatttggttgtgtttcctgatgcagGGGTCCCGATTACAAAGGGATGTATGCTATAAAAGAGTGCCTAAATCAAGTGCAATAAAGGTGATTGATTTTGGTAGCACAACTTATGAGCGCCAGGACC
                                            tcctgat  putative branch site (score: 3)
                                        tgtttcct  CT-rich tract
          aactatttaa  TA-rich tract