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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttactaaaagttcttcttatgtatttttttttgtttcctcgttggacgttttcttacaagctttttctaagctatctgtatgtttcgtagGATATCTTCAAAGAGTTCTATTTAAGCAAGTACAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G46210.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 11
gttttactaaaagttcttctta-tgtatttttttttgtttcctcgttggac-gttttcttacaagctttttctaagctatctgtatgtttcgtagGATATCTTCAAAGAGTTCTATTTAAGCAAGTACAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAG
   | |    | |||||    | | | ||| ||     |   |  ||  |     | | |  ||  |  ||   || | ||| | | | |  |||||||| || ||||| |||||||| |||||||| ||||| ||| | || ||||||||||| ||||| || |||||||| ||||| ||||| ||| | ||||
--gtcaggccatgttctcaaaactatgtttgttggcagtaaatatttatattaactgcctggaaattaattt--agttttctatttttctgatagGATATATTTAAAGAATTCTATTTGAGCAAGTATAGTGGAAGGCGTTTGATGTGGCAAAACTCATTGGGTCACTGTGTATTAAAAGCAGAGTTCCCAAAAG

upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 11
----------------------------------------------------------gttttactaaaagttcttcttatgtatttttttttgtttcctcgttggacgttttct--------tacaagctttttctaagctatctgtatgtttcgtagGATATCTTCAAAGAGTTCTATTTAAGCAAGTACAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAG
                                                          || | | ||   |||   | | |    | ||| |   | | | |||  | ||| ||         |  |  |||| | ||| |          | |   ||||||| || ||||||||||||||||||||||||||||| ||| | ||||||||||| ||||| || || |||||||| || || ||||| ||  ||||||
gttagtatatggccttggtggtggtagtaaatattttaacgtcagtctgagtattttagtctgaatatttgtttaacctctcccctctttctgaatactttgtttaatgttctcccctctttctgaatactttgtttaatcctctccctcttctgacagGATATATTTAAAGAGTTCTATTTAAGCAAGTACAGTGGAAGGCGTTTAATGTGGCAGAATTCTTTGGGACACTGTGTCTTGAAAGCAGACTTTCCCAAAG

upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 12
gttttactaaaagttc---ttcttatgtatttttttttgtttcctcgttggacgttttcttacaag--ctttttctaagctatctgtatgtttcgtagGATATCTTCAAAGAGTTCTATTTAAGCAAGTACAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAG
|||   |  |||       | ||| ||||  |      | | | | |   ||| ||  || ||| |  |  ||||    | || | |   |     ||||||| ||||||||||||||| |||| || || ||||| ||| |  | |||||||||||||||||||| |||||||| ||||||||||| ||  | ||||
gttcagcacaaaccatgaatgcttttgtaactgcaagggatactttgagtgac-ttccctgacatggtccctttcctttccat-tattcttccttcagGATATTTTCAAAGAGTTCTATCTAAGTAAATATAGTGGAAGGCGTCTGATGTGGCAAAATTCATTAGGTCACTGTGTCTTAAAGGCAGAGTTTCCTAAAG

upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G10030.2 (Glycine max), 3'ss of exon 11
gttttac--------taaaagttcttctta-tgtatttttttttgtttcctcgttggacgttttcttacaagctttttctaagctatctgtatgtttcgtagGATATCTTCAAAGAGTTCTATTTAAGCAAGTACAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAG
|||   |        | || | |||| | | || |  | |  ||| | | |   ||    ||  || ||| | |  ||          | | | |     ||||||| ||||||||||||||| ||||||| || ||||| ||| |  | |||||||||||||||||||| ||||||||  |||||||||| ||  | ||||
gttcagcacaaaccatgaatgctcttgtaactgcaggtgtccttgatacttgagtgac--ttccctgacatggtcctttcctttccattatttttccttcagGATATTTTCAAAGAGTTCTATCTAAGCAAATATAGTGGGAGGCGTCTGATGTGGCAAAATTCATTAGGTCACTGTGTCCTAAAGGCAGAGTTTCCTAAAG

upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 11
---------gttttactaa--aagttcttcttatgtatttttttttgtttcctcgttggacgttttcttacaagctttttctaagctatctgtatgtttcgtagGATATCTTCAAAGAGTTCTATTTAAGCAAGTACAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAG
         ||  || | |   | ||||  ||    ||| |  | |   |  | ||| |   |    | ||| | |  ||     |  ||| |  |      ||||||| ||||||||||||||| ||||||| |||||||| ||     | ||||||||||||||| |||| |||||||| || |||||||| ||  ||||||
gttctgcacgtgctattgactgaattctcttttaacattgtggtct---tggtagtttgtgatcccttgacatggtcctttctttcc-tctatcgggccttcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACATCTGATGTGGCAAAATTCACTAGGTCACTGTGTCTTGAAGGCAGAGTTTCCCAAAG

upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 11
---------gttttactaaa-agttcttcttatgtatttttttttgtttcctcgttggacgttttcttacaagctttttctaagctatctgtatgtttcgtagGATATCTTCAAAGAGTTCTATTTAAGCAAGTACAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAG
         ||  || | |    ||  |||| |   | |  | ||| |   | |   ||  |    | ||| | |  ||     |  ||| |  |      ||||||| ||||||||||||||| ||||||| |||||||| ||  |  | ||||||||||||||| |||| || ||||| || |||||||| ||  ||||||
gttctgcacgtgctagtgactgatttctcttttaactgtggtcttggtattttgagtgat-tcccttgacatggtcctttctttcc-tctatcgggcattcagGATATTTTCAAAGAGTTCTATCTAAGCAAATACAGTGGAAGACGTCTGATGTGGCAAAATTCACTAGGTCATTGTGTCTTGAAGGCAGAGTTTCCCAAAG

upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------gttttactaaaagt--tcttcttatgtatttttttttgtttcctcgttggacgttttcttacaagctttttctaagctatctgtatgtttcgtagGATATCTTCAAAGAGTTCTATTTAAGCAAGTACAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAG
                               |||||       |   | | ||| | |||  || | || ||  | |      |||||  |      ||||| |   |      |  ||  |  |||| || ||||| |||||||| || ||||| |||||||| ||| | |||||||||||||| |||||||| ||||||||||| || ||||| ||  | ||||
gtttggcagcctaagtgatggtttctttcaagttttggcgctgggcatatacttttatataattatctgattttttgggttttgtttttgtgtttttttttttttttcccctgttgggtgccacagGACATTTTCAAGGAGTTCTACTTGAGCAAATACAGTGGGAGGCGATTAATGTGGCAAAACTCATTAGGACACTGTGTTTTGAAAGCAGAGTTTCCAAAAG

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|164116687|gb|ES001014.1|ES001014
EST:     GCCTATGGATGTTAAGCTTCCTCATGAACTAAATGTCTATCAG                         GATATCTTCAAAGAGTTCTATTTAAGCAAGTACAGTG
genomic: GCCTATGGATGTTAAGCTTCCTCATGAACTAAATGTCTATCAGgttttactaa ... tgtttcgtagGATATCTTCAAAGAGTTCTATTTAAGCAAGTACAGTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctcgttggacgttttcttacaagctttttctaagctatctgtatgtttcgtagGATATCTTCAAAGAGTTCTATTTAAGCAAGTACAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAG
               ttcttac  putative branch site (score: 2)
                          tttttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttactaaaagttcttcttatgtatttttttttgtttcctcgttggacgttttcttacaagctttttctaagctatctgtatgtttcgtagGATATCTTCAAAGAGTTCTATTTAAGCAAGTACAGTGGTAGGAGGTTAATGTGGCAAAATTCATTAGGCCACTGTGTTTTAAAGGCAGATTTCTCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT