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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttcctttctgatatgaagttcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA

Basic information

species Arabidopsis thaliana
transcript AT3G23940.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os08g44530.1 (Oryza sativa), 3'ss of exon 10
-------------------------gtaatttcctttctgatatgaagttcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
                         | |||    |   | |   | |   |    ||    || ||| |  ||   |   ||| ||  ||| |        ||||| |  || || || ||  ||||||| || || ||||| || ||||| |||||||| ||| |||| || || ||||||||||||||||| |||||||| |
tatttccttttacgctcttgacaagggaatgcattagttcactgggacaaccatgcatagtcttgttctgaattact---ctgctggcatgcaat-cacaacagGGGAAGGTAGTAGTGATACGAGGAGAAGGACCGAAAGGTGGACCAGGGATGCCTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGA

upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: AC234528.1_FGT005 (Zea mays), 3'ss of exon 10
-----------------------------------------------------------------------------------------gtaatttcctttctgata-tgaagt---tcatctcaggagctggttatatatctt---ttatctgatgaaatgtatcgtgttt-cagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
                                                                                          |  | | || ||||  | || |     |  | ||||    ||  |   |||      | || | ||       || || |   |||||||  || || || ||| ||||||| || || |||||||| ||||| |||||||| |||||||| || |||||||||||||||||||| ||||| ||||
gtaatatgtgcgatgcaagtattttctgcatgtgccactgtcgctattgcttgccatttcttcctttttatttggagagcacgattgcctttttcttctctctgcgagtggaacatattgtttcagagcatgcattcgtatgacaaatcattttattgctctgatggtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATGCCTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAA

upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G014069_T01 (Zea mays), 3'ss of exon 10
--------------------------------------------------------------------------------gtaatttcctttctgata-tgaagttcatc--tcaggagctggttatatatcttttatctgatgaaatgtatcgt-------gtttc---agGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
                                                                                 |  | | || ||||||| || | |  ||   |   ||||  ||| |  ||  ||      |   | | ||| |        |||||   ||||||  || || || ||| ||||||| || || ||||| || ||||| ||||| || |||||||| || ||||| |||||||||||||| ||||||||||
gtaatatgtgcagtgcaagtattttctgcatttgctactgccgctattgaatgccatttcttcctttttttgtagattgccttttcttctctctgatagtggaatatattgtttcagagcaagttttgcattcttatgacaaatcattttattgctctgatggtttcaacagGGAAAGGTAGTAGTGATCCGAGGAGAAGGACCAAAAGGCGGGCCAGGGATGCCCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAA

upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 10
-------------gtaatt-tcctttctgatatgaagttcatctcaggagctggt--------tatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
             ||| || |    | ||| |   |  | | | ||| || || |        |  | || |  | |||  || | | |    | |||||||| |  |||||||| ||||| |||||||| || || || ||||| || |||||||||||||| ||||| |||||||||||||||||||| ||||||||||
caattttgctgtagtatttgtttggtttgacacagatataaccacagtaggtgatggctaaaatggaaatatgatttcttttgtattttcattt-tttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA

upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 10
----------------gtaatttcctttctgatatga--------agttcatct-caggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
                 ||  |  ||  |||||| ||        | || ||       |   || ||| ||  ||||  ||  |    | ||     |||||||| |  || ||| |||| ||||||||||| || || || || ||||| |||||||| |||||||| || ||||| ||||||||||| || |||||||| |
tcatattttttctattttatgtgtctcactgataggatggtgtataattgattcatcaaaatgggatatctaattttttgcttttctgttatac----tttcagGGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGGCCAGGAATGCCTGAAATGTTGACTCCAACAAGCGCAATAATGGGAGCAGGTCTTGGGA

upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ36479 (Selaginella moellendorffii), 3'ss of exon 9
gtaatttcctttctgatatgaagttcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
                   |   |   | ||   |||  |  ||||     | | ||| |||   ||    |  | |||||  | ||| |||||||||| ||||| || || ||||| ||||| || |||||||||||| | || || |||||||| || |||||||| ||  | || |
-------------------gttctctctgtccaaagcaag--atatgataatca-ctggtgattggtgaaatact-cagGGCTCCGTGATTGTTATCAGGGGAGAAGGTCCCAAAGGTGGTCCGGGAATGCCTGAGATGCTAACTCCTACAAGTGCGATCATGGGTGCTGGCTTGGGGA

upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ18570 (Selaginella moellendorffii), 3'ss of exon 10
gtaatttcctttctgatatgaagttcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA--
    | | |||| |  | | | || ||   || ||  || | ||  |    | ||| | |||||||         ||||||  | ||| |||||||||| ||||| || || ||||| ||||| || |||||||||||| | || || |||||||| || |||||||| ||  | || |  
---gtatacttttttctct-atgtccaaaacaagatatgataat-cactggtgatc-ggtgaaatgc--------tcagggctccgtgattgttatcagGGGAGAAGGTCCCAAAGGTGGTCCGGGAATGCCTGAGATGCTAACTCCTACAAGTGCGATCATGGGTGCTGGCTTGGGGAAG

upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ18571 (Selaginella moellendorffii), 3'ss of exon 11
gtaatttcctttctgatatgaagttcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
    ||| |||| |  | |   || ||   || ||  || | ||  |    | ||| | ||||||          ||||||  | ||| |||||||||| ||||| || || ||||| ||||| || |||||||||||| | || || |||||||| || |||||||| ||  | || |
---gtttacttttttctctct-gtccaaagcaagatatgataat-cactggtgatc-ggtgaaatac--------tcagGGCTCCGTGATTGTTATCAGGGGAGAAGGTCCCAAAGGTGGTCCGGGAATGCCTGAGATGCTAACTCCTACAAGTGCGATCATGGGTGCTGGCTTGGGGA

upper sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ36478 (Selaginella moellendorffii), 3'ss of exon 10
gtaatttcctttctgatatgaagttcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
    | | |||| |  | |   || ||   || ||  || | ||  |    | ||| | ||||||          ||||||  | ||| |||||||||| ||||| || || ||||| ||||| || |||||||||||| | || || |||||||| || |||||||| ||  | || |
---gtatacttttttctctct-gtccaaagcaagatatgataat-cactggtgatc-ggtgaaatac--------tcagGGCGCCGTGATTGTTATCAGGGGAGAAGGTCCCAAAGGTGGTCCGGGAATGCCTGAGATGCTAACTCCTACAAGTGCGATCATGGGTGCTGGCTTGGGGA

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|125159717|gb|EL187667.1|EL187667
EST:     GAGAGGAATCTATGTTGGCTGCTATATCAGCAGACCCAATGAGTTTTAAG                         GGAACTGTGGTTGTTA
genomic: GAGAGGAATCTATGTTGGCTGCTATATCAGCAGACCCAATGAGTTTTAAGgtaatttcct ... cgtgtttcagGGAACTGTGGTTGTTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA
                             atctgat  putative branch site (score: 4)
                ttatatatcttttatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttcctttctgatatgaagttcatctcaggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG