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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtttaaatactgattttcattatttttgcacttttagcataagatgttagatttgtttatatgttatgtctctgaagcgtttgatgatggttgtcagATATCACCAACTGAAATCCGTGGAGCACTCGGATCTGTGAACCAGTTGTTCATCTGTATAGGAATACTTGCAGCCTTGATAGCTGGATTACCCCTTGCAG

Basic information

species Arabidopsis thaliana
transcript AT5G16150.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G16150.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 6
gttgtttaaat--actgattttcattatttttgcactt--ttagc-ataagatgttagatttgtttatatgttatgtctctgaagcgtttgatgatg-gttgtcagATATCACCAACTGAAATCCGTGGAGCACTCGGATCTGTGAACCAGTTGTTCATCTGTATAGGAATACTTGCAGCCTTGATAGCTGGATTACCCCTTGCAG
|||||   ||   |   |||   ||| ||       ||  | ||| |  |   | ||| ||  |  | |||        ||||    |||     || |    ||||| ||||| |||||||| ||||||||||| || ||||| || ||| | || ||||| || ||||| ||||| ||  || ||||||||||||| || ||||
gttgtgataactgataaattcaaattgttgaaatgattgttcagctactactggctaggttcttgaacatgcccaacaactgagctatttacgcttgcgcctgcagATTTCACCCACTGAAATACGTGGAGCACTTGGTTCTGTTAATCAGCTTTTTATCTGCATTGGAATTCTTGCTGCTCTGGTAGCTGGATTACCTCTGGCAG

upper sequence: AT5G16150.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G098011_T02 (Zea mays), 3'ss of exon 6
--------------------------------------------gttgtttaaatactgattttcattatttttgcacttttagcataagatgttagatttgtttatatgttatgtctctgaagcgtttgatgatggttgtcagATATCACCAACTGAAATCCGTGGAGCACTCGGATCTGTGAACCAGTTGTTCATCTGTATAGGAATACTTGCAGCCTTGATAGCTGGATTACCCCTTGCAG
                                            | ||||   | |     |    ||| || ||  ||||   ||  || |  |  ||   || |      |  ||||  |    |    |  |  ||  |||||||||||||||||||| |||||| |||| || || || || ||  | || ||||| || ||||| |||||||| ||| |||||||||| ||  | ||||
gttgtgatacgatgaaacgacagttgctttgttcaaaacctgatgctgttgtgaaat--gctacagttacttctgt-ctttgttcaatagctactgcatgcattgacga---acatctccaacaaatgaacttgtactttgcagATATCACCAACTGAAATTCGTGGAACACTTGGTTCCGTTAATCAACTTTTTATCTGCATTGGAATTCTTGCAGCTTTGTTAGCTGGATTGCCTTTGGCAG
















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|124729138|gb|EH820540.1|EH820540
EST:     TTGGAATTGGAATCTCATCAGCGATTGTACCACTTTACATATCTGAG                         ATATCACCAACTGAAATCCGTGGAGCACTCGGATCTGTGAACCAG
genomic: TTGGAATTGGAATCTCATCAGCGATTGTACCACTTTACATATCTGAGgttgtttaaa ... tggttgtcagATATCACCAACTGAAATCCGTGGAGCACTCGGATCTGTGAACCAG
EST: gi|164028401|gb|ES205992.1|ES205992
EST:     GGAATTGGAATCTCATCAGCGATTGTACCACTTTACATATCTGAG                         ATATCACCAACTGAAATCCGTGGAGCACTCGGATCTGTGAACCAGTTGTTC
genomic: GGAATTGGAATCTCATCAGCGATTGTACCACTTTACATATCTGAGgttgtttaaa ... tggttgtcagATATCACCAACTGAAATCCGTGGAGCACTCGGATCTGTGAACCAGTTGTTC
EST: gi|163999189|gb|ES179449.1|ES179449
EST:     GGAATTGGAATCTCATCAGCGATTGTACCACTTTAACATATCTGAG                         ATATCACCAACTGAAATCCGTGGAGCACTCGGATCTGTGAACCAGTTGTTC
genomic: GGAATTGGAATCTCATCAGCGATTGTACCACTTT-ACATATCTGAGgttgtttaaa ... tggttgtcagATATCACCAACTGAAATCCGTGGAGCACTCGGATCTGTGAACCAGTTGTTC
EST: gi|164237903|gb|ES032559.1|ES032559
EST:     GAATTGGAATTGGAATCTCATCATCGATTGTACCACTTTACATATCTGAG                         ATATCACCAACTGAAATCC
genomic: GAATTGGAATTGGAATCTCATCAGCGATTGTACCACTTTACATATCTGAGgttgtttaaa ... tggttgtcagATATCACCAACTGAAATCC
EST: gi|124767061|gb|EH857191.1|EH857191
EST:     ATCTCATCAGCGATTGTACCACTTTACATATCTGAG                         ATATCACCAACTGAAATCCGTGGAGCACTCGGATCTGTGAACCAGTTGTTC
genomic: ATCTCATCAGCGATTGTACCACTTTACATATCTGAGgttgtttaaa ... tggttgtcagATATCACCAACTGAAATCCGTGGAGCACTCGGATCTGTGAACCAGTTGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgttagatttgtttatatgttatgtctctgaagcgtttgatgatggttgtcagATATCACCAACTGAAATCCGTGGAGCACTCGGATCTGTGAACCAGTTGTTCATCTGTATAGGAATACTTGCAGCCTTGATAGCTGGATTACCCCTTGCAG
                                    gtttgat  putative branch site (score: 5)
        atttgtttatatgtta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtttaaatactgattttcattatttttgcacttttagcataagatgttagatttgtttatatgttatgtctctgaagcgtttgatgatggttgtcagATATCACCAACTGAAATCCGTGGAGCACTCGGATCTGTGAACCAGTTGTTCATCTGTATAGGAATACTTGCAGCCTTGATAGCTGGATTACCCCTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA