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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctgcaacaatttctcccctcttgtttgtaaactatttgagtattgacacttaaagatttttgctttcatcatcattgcttcagTTTTCTGAAGATTTCCAAATATTGTTATTCCATTATGATGGCCGAACAACTGAGTGGGACCAGTTTGAGTGGTCTAAAAATGCAATACATATCAGTGCAA

Basic information

species Arabidopsis thaliana
transcript AT1G08040.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g19510.3 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------------gttctgcaacaatttctcccctcttgt----ttgtaaac----tatttgagtattgacacttaaagatttttgctttcatcatcattgcttc------agTTTTCTGAAGATTTCCAAATATTGTTATTCCATTATGATGGCCGAACAACTGAGTGGGACCAGTTTGAGTGGTCTAAAAATGCAATACATATCAGTGCAA
                                                                | |   ||   | |  | |  ||  ||    | |||  |    | | | | | |  | |   ||  |||  | ||    ||||    ||||       ||||||| ||  | |||   ||  || ||||||||||||||||||| || ||||| |||||  | ||||||||||||||||  || || ||| | ||||  |
gtaactgagacggacatcttgcattgcttaaatttggtgcatcaatcaactataccctgtaacagataaacagttaatcttgcattccggtgaactggtagtcactttttcttaatgtaaatatgcaattattgcttctgaattcatagaagcttttcatatagTTTTCAGATAAATTCACTATCATGCTATTCCATTATGATGGCCGGACTACTGAATGGGATGAATTTGAGTGGTCTAAAAGAGCTATCCATGTGAGTGTCA

upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G801369_T01 (Zea mays), 3'ss of exon 6
gttctgcaacaatttctcccctcttgtttgtaaactatttgagtattgacac-ttaaagatttttgctttcat---catcattgcttcagTTTTCTGAAGATTTCCAAATATTGTTATTCCATTATGATGGCCGAACAACTGAGTGGGACCAGTTTGAGTGGTCTAAAAATGCAATACATATCAGTGCAA
            |    |  |     |   |||| |||  ||| | ||| |  ||  || ||||    ||||      || |  || |||||||| ||  | |||  |||  |||| |||||||||||||| || ||||||||||||||  | ||||||||||| ||||  ||  | ||| | ||||  |
-----------gtaagacatcctaaatgcttaaaatatgcgaggaatgatatattgtagtttttcagattcacatatgtcttctctacagTTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGTCGGACAACTGAGTGGGATGAATTTGAGTGGTCAAAAAGGGCCGTCCATGTGAGTGTCA

upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G006507_T02 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------gttctgcaacaatttctcccc----tcttgtttgtaa--actatttgagtattgacacttaaagatttttgctttcatcatcattgcttc---agTTTTCTGAAGATTTCCAAATATTGTTATTCCATTATGATGGCCGAACAACTGAGTGGGACCAGTTTGAGTGGTCTAAAAATGCAATACATATCAGTGCAA
                                                                 | | | ||  |  |   |  |    |     |||||   ||| | |  | | |||   |  |    |     ||||||     || |||    ||||||| ||  | |||   ||  || | |||||||||||||| || || |||||||||||  | ||||||||||||||||  ||||| ||| | ||||  |
gtaactggcagactgccatcttacctgcttaaccttggtgcaccaaacttctgagctttgggactgatgtacactagatctgcatcgtgattaaacttgtagtcactttatttgaaatgagcatgcagtcctaccaatttcatgtatgtttcttttatagTTTTCAGACAAATTCACTATTATGCTGTTCCATTATGATGGTCGGACTACTGAGTGGGATGAATTTGAGTGGTCTAAAAGAGCAATCCATGTGAGTGTCA

upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G119725_T02 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------gttctgcaacaatttctcccc----tcttgtttgtaaac----tatttgagtattgacacttaaagatttttgc---tttcatcatcattgcttc---agTTTTCTGAAGATTTCCAAATATTGTTATTCCATTATGATGGCCGAACAACTGAGTGGGACCAGTTTGAGTGGTCTAAAAATGCAATACATATCAGTGCAA
                                                                 | | | ||  |  | | |  |    |     |||||  |    |||||||  ||   ||  ||    ||| | |   |||||      || |||    ||||||| ||  | |||   ||  |||| |||||||||||||| || || || ||||||||  | ||||||||||||||||  ||||| ||| | ||||| |
gtaactgacagactggcaccttacctacttaagctcagtgtatcaaacttctgaactctgggactgatgtacagtagatccacatcgtgattaaacttgtagtcactttatttgaa-atgagcatgtagtcctttcttccaatttcacgtaagtttcttttatagTTTTCAGACAAATTCACCATTATGTTGTTCCATTATGATGGTCGGACTACAGAGTGGGATGAATTTGAGTGGTCTAAAAGAGCAATCCATGTGAGTGCCA

upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 6
--gttctgcaacaatttctcccctcttgtttgtaaactattt-gagtattgacacttaaagatttttgctttcatcatcattgcttcagTTTTCTGAAGATTTCCAAATATTGTTATTCCATTATGATGGCCGAACAACTGAGTGGGACCAGTTTGAGTGGTCTAAAAATGCAATACATATCAGTGCAA
    ||  ||  |     |||    || |   | |  ||||| || | ||      ||  || |||    | | |     |||   ||||||||||| ||||||||||| ||| | || || |||||||| ||||||| ||| ||||| || ||||||||||| |||| |||||| ||| | |||||||
gtcatccacatgagccgttccataattttcatttatttattttgattgtttctggatattgagtttcagatgcttatgttttgtggcagTTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGTGAATGGGATCAATTTGAGTGGTCAAAAACTGCAATTCATGTTAGTGCAA

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|164222412|gb|ES001763.1|ES001763
EST:     TTACAGTTGGATTTGAGCAGAGAAACAACATTAATGCAGCTGTTAAGAAG                         TTTTCTGAAGATTTCCAAATATTGTTATTCCATTATGATGGCCGAACAA
genomic: TTACAGTTGGATTTGAGCAGAGAAACAACATTAATGCAGCTGTTAAGAAGgttctgcaac ... attgcttcagTTTTCTGAAGATTTCCAAATATTGTTATTCCATTATGATGGCCGAACAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactatttgagtattgacacttaaagatttttgctttcatcatcattgcttcagTTTTCTGAAGATTTCCAAATATTGTTATTCCATTATGATGGCCGAACAACTGAGTGGGACCAGTTTGAGTGGTCTAAAAATGCAATACATATCAGTGCAA
            tattgac  putative branch site (score: 2)
                                              ttgcttc  putative PPT
                   acttaaagattttt  TA-rich tract