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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttcaatttctcccaagaaaaatctttaccttcttttgatattgcctctggttcaagtgttctttcctgcatttgatatccttaaattttatttagGTCGAGACACCTATGATGAACATGATTGCTGGTGGAGCAGCTGCTAGACCTTTTGTGACACATCACAATGATCTAGATATGAGGCTGTACATGCGAATCG

Basic information

species Arabidopsis thaliana
transcript AT3G11710.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os03g38980.1 (Oryza sativa), 3'ss of exon 9
gtgttcaatttctcccaagaaaaatctttaccttcttttgatattgcctctggttcaagtgttctttcctgcatttgatatccttaaattttatttagGTCGAGACACCTATGATGAACATGATTGCTGGTGGAGCAGCTGCTAGACCTTTTGTGACACATCACAATGATCTAGATATGAGGCTGTACATGCGAATCG
          |   ||     ||    ||   || || |  | |||  | |  ||| |||   | |||    || |||      ||  | || | ||||| ||||| || ||||||||||||||||| |||||||||||||| || |||||||| |||||||| |||||  || | |||||||| || ||||| || |
---------gtgggcctgtgcaatctattctgttattcttcttttgtatattcttccagt---ccttc--aaatctgaatattctatgtcttttctagGTGGAGACTCCAATGATGAACATGATTGCAGGTGGAGCAGCTGCAAGGCCTTTTGTCACACATCATAATGAGTTAAACATGAGGCTTTATATGCGTATTG

upper sequence: AT3G11710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G146589_T02 (Zea mays), 3'ss of exon 9
gtgttcaatttctcccaagaaaaatctttaccttcttttgatattgcctctggttcaagtgttctttcctgcatttgatatccttaaattttatttagGTCGAGACACCTATGATGAACATGATTGCTGGTGGAGCAGCTGCTAGACCTTTTGTGACACATCACAATGATCTAGATATGAGGCTGTACATGCGAATCG
                          |   |      ||  |   |  |||  ||| |||   |  | |   || |||   |||||  |||| | ||||| ||||| || |||||||||||||||||||||||||||||||| || |||||||| ||||||||||||||  || | ||| |||| |  ||||| || |
-------------------------gtaagcacaagatttgtgcagtttct--ttccagttgacacttcaatatctga---ccttatgtttt-tctagGTGGAGACTCCGATGATGAACATGATTGCTGGTGGAGCAGCTGCAAGGCCTTTTGTTACACATCACAATGAATTAAACATGCGGCTTTTTATGCGCATTG

upper sequence: AT3G11710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G316679_T01 (Zea mays), 3'ss of exon 3
gtgttcaatttctcccaagaaaaatctttaccttcttttgatattgcctctggttcaagtgttctttcctgcatttgatatccttaaattttatttagGTCGAGACACCTATGATGAACATGATTGCTGGTGGAGCAGCTGCTAGACCTTTTGTGACACATCACAATGATCTAGATATGAGGCTGTACATGCGAATCG
                           | | |   || ||   || | |    | ||  || |  |||    || |||   ||||   | || | ||||| ||||| || |||||||||||||||||||||||||||||||| || |||||| | ||||||||||||||  || |||||||||| |  ||||| || |
--------------------------gtaagcaatttctgcagtttctt----tccagttgatacttca-atatctga---ccttttgtgttttctagGTGGAGACTCCGATGATGAACATGATTGCTGGTGGAGCAGCTGCAAGGCCTTTTATTACACATCACAATGAATTAAATATGAGGCTTTTTATGCGCATTG

upper sequence: AT3G11710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G386714_T01 (Zea mays), 3'ss of exon 9
gtgttcaatttctcccaagaaaaatctttaccttcttttgatattgcctctggttcaagtgttctttcctgcatttgatatccttaaattttatttagGTCGAGACACCTATGATGAACATGATTGCTGGTGGAGCAGCTGCTAGACCTTTTGTGACACATCACAATGATCTAGATATGAGGCTGTACATGCGAATCG
                ||||||  |||  |  ||||||  |    |    |  |||||  |||      |  |  |||   ||||   | || | ||||| ||||| || |||||||||||||||||||||||||||||||| || |||||| | ||||| ||||||||  || | |||||||| |  ||||| || |
--------------gtaagaaatttctgcagtttctttcca----gttgatacttcaatagtt------tagacatga---ccttttgtgttttctagGTGGAGACTCCGATGATGAACATGATTGCTGGTGGAGCAGCTGCAAGGCCTTTTATTACACACCACAATGAATTAAACATGAGGCTTTTTATGCGCATTG

upper sequence: AT3G11710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G21870.1 (Glycine max), 3'ss of exon 9
gtgttcaatttctcccaagaaaaatctttaccttcttttgatattgcctctggttcaagtgttctttcctgcatttgatatccttaaattttatttagGTCGAGACACCTATGATGAACATGATTGCTGGTGGAGCAGCTGCTAGACCTTTTGTGACACATCACAATGATCTAGATATGAGGCTGTACATGCGAATCG
        | | | | | |     ||      ||||  || |    ||| ||||| |  ||||||| | | ||| |  | |  ||  ||    || |||| || ||||| |||||||||||||||||||||||||| || ||  | || ||||| |||||||||||||||||  | |||||| | | |||| | || |
-------gtctgttctatg-----tccgagtattctgatgctggatcctgtggttta--tgttcttccattcatctacttt--ttgcatcactttcagGTTGAAACACCAATGATGAACATGATTGCTGGTGGAGCTGCAGCCCGTCCATTTGTAACACATCACAATGATCTTAACATGAGGTTATTCATGAGGATTG

upper sequence: AT3G11710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G03140.1 (Glycine max), 3'ss of exon 7
gtgttcaatttctcccaagaaaaatctttaccttcttttgatatt--gcctctggttca--agtgttctttcctgcatttga-tatccttaaattttatttagGTCGAGACACCTATGATGAACATGATTGCTGGTGGAGCAGCTGCTAGACCTTTTGTGACACATCACAATGATCTAGATATGAGGCTGTACATGCGAATCG
                        | | | |  | | |   ||||  |   |||| ||   ||| |  || | | ||||    ||   ||  ||    || |||| || |||||||||||||| ||||||||||||||||| || ||  | || ||||| |||||||||||||||||  | |||||| | | |||| | || |
-----------------------gtttgttctgtgtctgagtatttggatgctggatccttagtttctttactttcattcacctacttttgcatcactttcagGTTGAAACACCTATGATGAATATGATTGCTGGTGGAGCTGCAGCCCGTCCATTTGTAACACATCACAATGATCTTAACATGAGGTTATTCATGAGGATTG

upper sequence: AT3G11710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G08040.1 (Glycine max), 3'ss of exon 9
gtgttcaatttctcccaagaaaaatctttaccttcttttgatattgcctctggttcaagtgttctttcctgcatttgatatccttaaattttatttagGTCGAGACACCTATGATGAACATGATTGCTGGTGGAGCAGCTGCTAGACCTTTTGTGACACATCACAATGATCTAGATATGAGGCTGTACATGCGAATCG
        ||| | | | |     ||      ||||  || |     || ||||| |  ||| ||| | | ||  | || |  ||  ||    || |||| || ||||| |||||||||||||||||||||||||| || ||  | || ||||| || ||||||||||||||  | |||||| | | |||| | || |
-------gtttgttctatg-----tccgagtattctgatgctggattctgtggttta--tgtacttccattcacctaattt--ttgcatcactttcagGTTGAAACACCAATGATGAACATGATTGCTGGTGGAGCTGCAGCCCGTCCATTTGTAACTCATCACAATGATCTTAACATGAGGTTATTCATGAGGATTG

upper sequence: AT3G11710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv14s0060g02350.t01 (Vitis vinifera), 3'ss of exon 25
-----------------gtgttcaatttctcccaagaaaaatctttaccttcttttgata-ttgcctctggttcaagtgttctttcctgcatttgata--tccttaaatttta----tttagGTCGAGACACCTATGATGAACATGATTGCTGGTGGAGCAGCTGCTAGACCTTTTGTGACACATCACAATGATCTAGATATGAGGCTGTACATGCGAATCG
                 ||||| |  |||    |  |  ||| ||    |  | ||  ||   | ||   |  ||||  || | || |    | | |   || || | | |      || |||| || || || ||||||||||||||| |||| || ||||| ||| | || |||||||| ||||||||||||||| | |||| | | || ||||| ||||
gttagtcatttgttcaggtgttaatcttcctttattatcaatatt-gtttaatattattagccgtctaatgcccaagctttatctctttttctcgttcattcattgagtctccacacttcagGTTGAAACTCCAATGATGAACATGATTCCTGGGGGTGCAGCGGCTCGTCCATTTGTGACTCATCACAATGATCTAAACATGAAGTTATATATGCGTATCG

upper sequence: AT3G11710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv15s0024g00700.t01 (Vitis vinifera), 3'ss of exon 10
-----------------gtgttcaatttctcccaagaaaaatctttaccttcttttgata-ttgcctctggttcaagtgttctttcctgcatttgatatccttaaatttta---tttagGTCGAGACACCTATGATGAACATGATTGCTGGTGGAGCAGCTGCTAGACCTTTTGTGACACATCACAATGATCTAGATATGAGGCTGTACATGCGAATCG
                 ||||| ||| |     |  |  ||| ||    |  | ||  ||  || ||   |  |||| ||| | || |    |   |      |   |  |   || |||| || || || |||||||||||||||||||| |||||||| ||| | || |||||||| ||||||||||| ||| | |||| | | || ||||| ||||
gttagtcatctgttcaggtgtt-aatcttctttattatcaatatt-gtttaatattattagctgtctaatgcccaagcgttatctctttttctcattcattcgagtctccacacttcagGTTGAAACTCCAATGATGAACATGATTGCTGGAGGAGCAGCGGCTCGTCCATTTGTGACTCATCACAATGACCTAAACATGAAGTTATATATGCGTATCG

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|125066340|gb|EL133249.1|EL133249
EST:     GATTCCTCGACAACAAAAATTTCTTGGAG                         GTCGAGACACCTATGATGAACATGATTGCTGGTGGAGCAGCTGCTAG
genomic: GATTCCTCGACAACAAAAATTTCTTGGAGgtgttcaatt ... ttttatttagGTCGAGACACCTATGATGAACATGATTGCTGGTGGAGCAGCTGCTAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcctctggttcaagtgttctttcctgcatttgatatccttaaattttatttagGTCGAGACACCTATGATGAACATGATTGCTGGTGGAGCAGCTGCTAGACCTTTTGTGACACATCACAATGATCTAGATATGAGGCTGTACATGCGAATCG
                             atttgat  putative branch site (score: 5)
                                             ttttattt  putative PPT
                             atttgatatccttaaa  TA-rich tract