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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaattttattagccgtttgattatataagtagcagtgctagttgtgttattgtcttgttatagaggtacttacatttcgtagtggttcttaaccgtcacttctatattcaattcttttcttttctttctatcttcgttccgtcttttgtctaactggtggttgctgtgggatggtggatgtacagCCGAACCGTATTCTCTTAGTCACAATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGC

Basic information

species Arabidopsis thaliana
transcript AT1G43190.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G43190.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g64770.2 (Oryza sativa), 3'ss of exon 5
gtttgtaattttattagccgtttgattatataagtagcagtgctagttgtgttattgtcttgttatagaggtacttacatttcgtagtggttcttaaccgtcacttctatattcaattcttttcttttctttctatcttcgttccgtcttttgtctaactggtggt-tgctgtgggatggtggatgtacagCCGAACCGTATTCTCTTAGTCACAATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGC
                                                                               ||||      ||||  |   |      ||||  |    |||||  |  |  ||||||||   | |  | || | |||   |  | || |||||  ||      |  | | | || ||||| ||||| ||||| || || ||||| ||||| || || || ||  |||| || || |||||||| |||||||||||||||||||| |      
-------------------------------------------------------------------------------tttctcttctgttccaactagatgtgcctattct----tctttattcattcttctatctctctcctcttttctttctcggtactcgtctgctgctgggcctcag-

upper sequence: AT1G43190.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G30820.1 (Glycine max), 3'ss of exon 5
gtttgtaattttattagccgtttgattatataagtagcagtgctagttgtgttattgtcttgttatagaggtacttacatttcgtagtggttcttaaccgtcacttctatattcaattcttttcttttctttctatcttcgttccgtcttttgtctaactggtggttgctgtgggatggtggatgtacagCCGAACCGTATTCTCTTAGTCACAATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGC
                                                                                  | |  |  |  ||| |    |||||| |||| |    || || ||||| |||||||     |  ||| |   ||  |  |  || |    || |   |||||| |||||| ||||| ||||||||||||||| | ||||||||||||||||| || || || || || ||| ||||||| ||||||||| |||||| ||| || ||| 
----------------------------------------------------------------------------------cttttttctctttatcatgtacttctctattta----ttctcctttctctctatctcttcactttctctatgctgtcctgctgtcg----ggaactctggatgcacagCCAAACCGAATTCTCTTAGTCACAGTTCATCACATGCTGTATCCTATGACAGTGGATGTGCTGTATCAAGTATTTTCTCCCCATGGATCTGTGGAAAAGA

upper sequence: AT1G43190.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G36770.1 (Glycine max), 3'ss of exon 4
gtttgtaattttattagccgtttgattatataagtagcagtgctagttgtgttattgtcttgttatagaggtacttacatttcgtagtggttcttaaccgtcacttctatattcaattcttttcttttctttctatcttcgttccgtcttttgtctaactggtggttgctgtgggatggtggatgtacagCCGAACCGTATTCTCTTAGTCACAATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGC
                                                                                  | |  |  |  ||| |    |||||| |||| | ||||| ||| | || ||| |   | |||  | |   |||   |||   |   || |       |||||| |||||| ||||| ||||||||||||||| | ||||||||| ||||||| || ||||| || || ||| ||||||| ||||||||| |||||| ||| || ||| 
----------------------------------------------------------------------------------cctttttctctttatcatgtacttctctattta-ttcttctctct-ctgtctcttcgctttctctatgccgtcctgctgtctggaactctc------tggatgcacagCCAAACCGAATTCTCTTAGTCACAGTTCATCACATGTTGTATCCTATGACTGTGGATGTGCTGTATCAAGTATTTTCTCCCCATGGATCTGTGGAAAAGA

upper sequence: AT1G43190.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G08870.1 (Glycine max), 3'ss of exon 5
gtttgtaattttattagccgtttgattatataagtagcagtgctagttgtgttattgtcttgttatagaggtacttacatttcgtagtggttcttaaccgtca-cttctatattcaattcttttcttttctttctatcttcgttccgtcttttgtctaactggtggttgctgtgggatggtggatgtacagCCGAACCGTATTCTCTTAGTCACAATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGC
                                                                                    |  |   |||| | |   | ||||| |||| | |    ||  | ||| ||| |  || |||  | |  |||||  |||  ||   || |       |||||| |||||| || || ||||||||||| ||| | ||||||||||||||||| || || |  || || || |||||||| ||||||||| |||||||||| || ||| 
------------------------------------------------------------------------------------ttctttctctttatcacaaacttctctatttattctcctttctctctctctcttctctttctctatgctgtctg-ctgtcggcaactctc------tggatgcacagCCAAATCGAATTCTCTTAGTTACAGTTCATCACATGCTGTATCCTATAACAGCGGATGTGCTACATCAAGTGTTTTCTCCCCATGGATTTGTGGAAAAGA

upper sequence: AT1G43190.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv18s0072g00310.t01 (Vitis vinifera), 3'ss of exon 4
gtttgtaattttattagccgtttgattatataagtagcagtgctagttgtgttattgtcttgttatagaggtacttacatttcgtagtggttcttaaccgtcacttctatattcaattcttttcttttctttctatcttcgttccgtcttttgtctaactggtggttgctgtgggatggtggatgtacagCCGAACCGTATTCTCTTAGTCACAATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGC
                                                                                         ||||||   | |    ||||| |    |||| |  || |  |  | |||   | | |||| |   |         || |  |        ||||   |||||| || || ||||||||||| ||||| |||||| |||| || || || || || || || ||||||||||| ||||||||  |||| ||||| |||||| 
----------------------------------------------------------------------------------------agttctttctccttttctctatctgttcttctctatttattctcttctctctctcctgtctctatgccggtctaccgtcg--ggcactctctggacacacagCCTAATCGAATTCTCTTAGTTACAATTCATCACCTGCTATACCCTATAACAGTGGAGGTGCTGCATCAAGTGTTTTCTCCTCATGGTTTTGTGGAGAAGA

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|164105228|gb|ES166383.1|ES166383
EST:     GGGAAGATGAG                         CCGAACCGTATTCTCTTAGTCACAATCCATCACATGCTGTATCCAATTACT
genomic: GGGAAGATGAGgtttgtaatt ... ggatgtacagCCGAACCGTATTCTCTTAGTCACAATCCATCACATGCTGTATCCAATTACT
EST: gi|124951456|gb|EL026822.1|EL026822
EST:     ACCAAGAATTGACAACGATAGAGCAGAATATTCATGGAAGGGAAGATGAG                         CCGGACCGTATTCT
genomic: ACCAAGAATTGACAACGATAGAGCAGAATATTCATGGAAGGGAAGATGAGgtttgtaatt ... ggatgtacagCCGAACCGTATTCT
EST: gi|124733694|gb|EH825096.1|EH825096
EST:     ACGATAGAGCAGAATATTCATGGAAGGGAAGATGAG                         CCGAACCGTATTCTCTTAGTCACAATCCATCACATGCTGTATCCAATTACT
genomic: ACGATAGAGCAGAATATTCATGGAAGGGAAGATGAGgtttgtaatt ... ggatgtacagCCGAACCGTATTCTCTTAGTCACAATCCATCACATGCTGTATCCAATTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcgttccgtcttttgtctaactggtggttgctgtgggatggtggatgtacagCCGAACCGTATTCTCTTAGTCACAATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGC
                 gtctaac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtaattttattagccgtttgattatataagtagcagtgctagttgtgttattgtcttgttatagaggtacttacatttcgtagtggttcttaaccgtcacttctatattcaattcttttcttttctttctatcttcgttccgtcttttgtctaactggtggttgctgtgggatggtggatgtacagCCGAACCGTATTCTCTTAGTCACAATCCATCACATGCTGTATCCAATTACTGTTGACGTCCTGCATCAAGTTTTTTCTCCCTATGGATTTGTCGAGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC