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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtctcctctccgtgaatttcaagttaaaacagccatgagaggtttaaaattaattatgtgttgtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA

Basic information

species Arabidopsis thaliana
transcript AT3G06400.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 12
----gttggtctcctctccgtgaatttcaagttaaaacagccatga--gaggtttaaaattaattatgtgttgtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
    ||   |||  |||    |||| | | || | ||        |  ||  | ||| ||    |         ||  || |||| | | || ||||||||||||||||| || || ||||||||| | ||| | |||||| |||| |||||||||||  || ||||||| ||||| |
gtttgtcaatcttttcttta-gaatattacgtaacaatcttttgtattgatatctaagataggatgacgaaaacttaatttcagTATACCATCGAGGAGAAAGTGATTGAGAGGGCATACAAGAAGCTTGCATTGGATGCTTTGGTCATTCAACAAGGCCGACTGGCAGAGCAGAAGA

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 12
---------gttggtctcctctccg----tgaatttcaagttaaaacagccatgagaggtttaaaattaat-----tatgt----gttgtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
         ||| | |||   |  |    | | ||| ||||             ||   ||||  |||  |     ||| |     | ||   |  ||||| | | |||||||| ||||| |||||||| |||||||||||| | ||||||||||||||||| ||||| |||||| |||| || |||||||| |
tcaagatgtgtttgactctggtttggcagtcattttgaagtgttggtgctttctagttatttactatttgtgtcaatatctcatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 12
--------gttggtctcctctccgtga---atttcaagttaaaacagccatgagaggtttaaaattaat----------tatgtgttgtttgtt-tacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
        ||| | | |   |  |  |   ||||  |  |            ||   ||||  |||  |           || |  || |  ||  ||||| | | |||||||| ||||| |||||||| |||||||| ||| | || |||||||||||||| ||||| |||||| |||| || |||||||| |
caagatgtgtttgacactggtttggaagtcattttgaagtgttgtgcttcctagttatttactatttgtgtcaatgtctcatatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAAAAGCTTGCTCTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 12
-------------gttggtctcctctccgtgaatttcaagttaaaacagc-catgagaggtttaaa-attaattatgtgttgtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
                  | |  |     | ||||    ||| |  | |    | ||  | | |   | | ||| |   ||||     |||||| | | || || |||||||| |||||||| || ||||| ||| | ||||||||||||||||| ||||| |||||| ||||||| || ||||| |
gtttgcaattttaaactttattttacttttcaattcattgttcactctgtgtgttagtagctcatctaatcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 12
------gttggtctcctctccgtgaatttcaagttaa--aacagccatgagaggtttaaaat-taattatgt----gttgtttgtt----tacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
        |  |   || |   | |||||| | || |       |  || | |  |||  || | ||   ||    ||  |||||     |||||| | | || || |||||||| |||||||| || ||||| ||| | ||||||||||||||||| ||||| |||||| ||||||| || ||||| |
gtttgcaattttaaactttattttaatttccaattcattgttcactctgtgtgtgttagtatctcatctcgtcattgtaatttgtaatggtacagTATACAATAGAAGAGAAAGTCATTGAAAGGGCCTACAAAAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTGGCTGAGCAGAAGA

upper sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 12
gttggtctcctctccgtgaatt---tcaagttaaa-acagccatgagaggtttaaaattaattatgtgtt----gtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
|||  | |  |    |||  ||   | ||| ||   | ||  || | |  |  |   ||| || |   ||    |||  ||  |||| | | || ||||| || |||||||| |||||||| || || || ||||| |||||| |||| |||||||||||  | || ||||| |||||||
gttcattttgttcttgtgttttgcattaagctatctaaagatatcatatataaatgcttatttcttctttctgggttaattatcagTATACCATCGAGGAAAAGGTGATTGAGAGAGCTTATAAAAAATTGGCACTCGATGCTTTGGTGATTCAACAAGGACGGTTAGCAGAGCAGAAAA

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|116473628|gb|EG516220.1|EG516220
EST:     ATAGGATTGGTCNNNNNNNNGAAGTTCAAGTGTTTCGATTCTGCACTGAG                         TCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTT
genomic: ATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAGgttggtctcc ... ttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagttaaaacagccatgagaggtttaaaattaattatgtgttgtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
                            aattaat  putative branch site (score: 3)
                                            tttgttt  putative PPT
                       tttaaaattaattatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtctcctctccgtgaatttcaagttaaaacagccatgagaggtttaaaattaattatgtgttgtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT