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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgtggttttctccttacatatatgggatgataaacaagatatttttagggatgttatgaatctcaactcatccgtggagtgagagacttgggagagtgaggatgtggatgggatttggctaatgtaatatccgtcaatgatgtttgttgctgacatagcttattctcttcaattcacagGCTCCGGAGGGTTATGGTACTCAGCATGATCCAAATCATCG

Basic information

species Arabidopsis thaliana
transcript AT3G54230.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G54230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G18030.1 (Glycine max), 3'ss of exon 1
gtaattgtggttttctccttacatatatgggatgataaacaagatatttttagggatgttatgaatctcaactcatccgtggagtgagagacttgggagagtgaggatgtggatgggatttggctaatgtaatatccgtcaatga--tgtttgttgctgacatagcttattctcttcaattcacagGCTCCGGAGGGTTATGGTACTCAGCATGATCCAAATCATCG
                                                                                        ||   |||| |      ||| ||||    ||||| ||||         |  || |    | |||||| |||||||||||||||||||| ||| |||||||||  ||||| ||  | ||    ||||| || ||    ||
--------------------------------------------------------------------------------------ctagctgtgggggcagtcagatatggactccatttgcctaaccctcgtctcaccatttgattatttgttcctgacatagcttattctcttgaatccacagGCTCTTGAGGGATACAGCACCGTCCATGACCCCAACTTCCG

upper sequence: AT3G54230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G35510.1 (Glycine max), 3'ss of exon 1
gtaattgtggttttctccttacatatatgggatgataaacaagatatttttagggatgttatgaatctcaactcatccgtggagtgagagacttgggagagtgaggatgtggatgggatttggctaatgtaatatccgtcaatgat-gtttgttgctgacatagcttattctcttcaattcacagGCTCCGGAGGGTTATGGTACTCAGCATGATCCAAATCATCG
                                                                                     |  ||   |||| |      ||| ||||    ||||| ||||         |  || ||||  |||||| |||||||||||||||||||| ||| |||||||||  ||||| || ||  |    || || || ||    ||
-------------------------------------------------------------------------------------gctagctgtgggggcagtcagatatggactccatttgcctaaccctcgtctcaccattgattatttgttcctgacatagcttattctcttgaatccacagGCTCTTGAGGGATACGGCGCCGTCCACGACCCCAACTTCCG

upper sequence: AT3G54230.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0012g00870.t01 (Vitis vinifera), 3'ss of exon 1
gtaattgtggttttctcctta----catatatgggatgataa-acaagatatt-----tttagggat-----gttatgaatctcaactcatccgtg--------gagtgagagacttgggagagtgaggatgtggatgggatttggctaatgtaatatccgtcaatgat-gtttgttgctgacatagcttattctcttcaattcacagGCTCCGGAGGGTTATGGTACTCAGCATGATCCAAATCATCG
         |||| |||||||    | ||||||||||||||| |||||| |||     | |   |||      || |  ||  || ||||||| |         ||| || || | ||||  | ||||||| ||||  ||||||| |||   |  || |     |||||  ||||||||||||||||||||||||||| ||| ||||||||  |||||| |||||  ||   |||||  ||||    ||
---------gtttcctccttaatcacctatatgggatgataatacaagaaattagggctcttctgattgtccattttttatggcatctcatccttaagaacaatgagagaaagccgtggggcattgaggatatggaatggatttgcctacc-tcgtacc-----atgattatttgttgctgacatagcttattctcttgaatccacagGCTTTGGAGGGGTATGGAGCTGTTCATGACGCAAACTTCCG

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|125299566|gb|EL313651.1|EL313651
EST:     TGGTCGTCAGCAAGAATGGGATAATAACAGT                         GCTCCGGAGGGTTATGGTACTCAGCATGATCCAAATCATCG
genomic: TGGTCGTCAGCAAGAATGGGATAATAACAGTgtaattgtgg ... caattcacagGCTCCGGAGGGTTATGGTACTCAGCATGATCCAAATCATCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatatccgtcaatgatgtttgttgctgacatagcttattctcttcaattcacagGCTCCGGAGGGTTATGGTACTCAGCATGATCCAAATCATCG
                       tgctgac  putative branch site (score: 2)
                                  cttattctcttc  putative PPT
                                   ttattct  TA-rich tract