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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttttggagggtctgtgcaacatagtttaaaaagcttaaaacacatttacgaactatgtttttttttttttcattttcttagACTGACAAATCAAAAATCAAGAAAGTTATTGAGGAGCTTGATGAGAAGAAAAAAGAAACACTGAAAGTTACATGGGTTAAAGTTAACCA

Basic information

species Arabidopsis thaliana
transcript AT3G47460.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os01g67740.1 (Oryza sativa), 3'ss of exon 16
gttagttttggagggtctgtgcaacatagtttaaaaagcttaaaacacatttacgaactatgtttttttttttttcattttcttagACTGACAAATCAAAAATCAAGAAAGTTATTGAGGAGCTTGATGAGAAGAAAAAAGAAACACTGAAAGTTACATGGGTTAAAGTTAACCA
||  || ||      |||       |||   ||  |  ||||    | |   |  |    |     |||| ||||||| | |  ||| |||||| ||||||||||||| ||| || || ||| | ||||||||||| ||||| ||  ||||||| |||||| ||||||| ||| |
gtgggtcttaccttttcta---gtgataacctagga--cttactttaaaagcagcatacgtaaaccttttgttttcatctgc--agAATGACAAGTCAAAAATCAAGACAGTGATAGAAGAGTTGGATGAGAAGAAGAAAGAGACCTTGAAAGTCACATGGCTTAAAGTAAACAA

upper sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G006452_T02 (Zea mays), 3'ss of exon 10
gttagttttggagggtctgtgcaacatagtttaaaaagcttaaaacacatttacgaactatgttt-ttttttttttcattttcttagACTGACAAATCAAAAATCAAGAAAGTTATTGAGGAGCTTGATGAGAAGAAAAAAGAAACACTGAAAGTTACATGGGTTAAAGTTAACCA
    || |         ||| ||   |   || | || || |||  |  ||||  | ||  |    |   || | |||| | |  ||| ||||||  |||||||||||||||| || |||||| | ||||||||||| || |||||| |||| || || ||| | ||||| ||| |
----gtatctcctatcatgtacagtttt-cttgataaactgaaagtagttttaatatctgggcacataccttgtctcatctgc--agAATGACAAGGCAAAAATCAAGAAAGTGATAGAGGAGTTGGATGAGAAGAAGAAGGAAACATTGAAGGTCACTTGGCTCAAAGTAAACAA

upper sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 17
gttagttttggagggtctgtgcaacatagtttaaaaagcttaaaacacatttacgaactatgtttttttttttttcattttcttagACTGACAAATCAAAAATCAAGAAAGTTATTGAGGAGCTTGATGAGAAGAAAAAAGAAACACTGAAAGTTACATGGGTTAAAGTTAACCA
             |   | | |||  || |||  | |  ||  |||    ||    |  ||| ||  | | |||   ||||| |||| |||||| || ||||||||||| || ||||| ||||| ||||||||||| || || ||||| || ||||| ||| | ||||| ||  |
-------------gtgattttcaatcta-tttccacattttctaactttcttgtataa-atgcttaatctatttattttttcctagAATGACAAGTCTAAAATCAAGAAGGTGATTGAAGAGCTAGATGAGAAGAAGAAGGAGACACTTAATGTTACCTGGATCAAAGTGAATAA

upper sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv16s0022g00060.t01 (Vitis vinifera), 3'ss of exon 16
gttagttttggagggtctgtgcaacatagtttaaaaagcttaaaacacatttacgaactatgtttttttttttttcattttcttagACTGACAAATCAAAAATCAAGAAAGTTATTGAGGAGCTTGATGAGAAGAAAAAAGAAACACTGAAAGTTACATGGGTTAAAGTTAACCA
              || |||    |  | | |    |  |     || | | | ||  | |  || |  |  | |   |||  |||| |||||| |||||||||||||  || ||||| ||||| ||||| ||||| || |||||| | || ||||| |||  |||||||||| |
--------------gtttgtagctctcaatctgttgacatgttgtcatact-atgattt-tacttatgataatatgcctttaatagAATGACAAGTCAAAAATCAAGATGGTGATTGAAGAGCTGGATGAAAAGAAGAAGGAAACATTAAAGGTTACTTGGACTAAAGTTAACAA

upper sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: EFJ04936 (Selaginella moellendorffii), 3'ss of exon 16
gttagttttggagggtctgtgcaacatagtttaaaaagcttaaaacacatttacgaactatgtttttttttttttcattttcttagACTGACAAATCAAAAATCAAGAAAGTTATTGAGGAGCTTGATGAGAAGAAAAAAGAAACACTGAAAGTTACATGGGTTAAAGTTAACCA
                               |||     |    | |  |||     |  |||    |   |   | |  |   ||  ||| ||| | |||||| |    || ||   |||||||||||||||||||||||| || || |||||||| |||    | || ||| |
------------------------------gtaagctaatcgtgaaatttttctttgccgtgtgacgtgcatcggc-tgctggcagGATGATAAAGCGAAAATCGAAGCGGTGATCAGGGAGCTTGATGAGAAGAAAAAAGAGACTCTAAAAGTTACTTGGCAACACGTGAACAA

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|164048144|gb|ES104022.1|ES104022
EST:     AGCTGAAGATGAATATAATGCTCTTATGACCAAGAAAAAATATAATCGAG                         ACTGACAAATCAAAAATCAAGAAAGTTATTGAGGAGCTTGATGAG
genomic: AGCTGAAGATGAATATAATGCTCTTATGACCAAG-AAAAATATAATCGAGgttagttttg ... attttcttagACTGACAAATCAAAAATCAAGAAAGTTATTGAGGAGCTTGATGAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaagcttaaaacacatttacgaactatgtttttttttttttcattttcttagACTGACAAATCAAAAATCAAGAAAGTTATTGAGGAGCTTGATGAGAAGAAAAAAGAAACACTGAAAGTTACATGGGTTAAAGTTAACCA
                          ctatgttttttttttt  CT-rich tract
                        aactatgttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttttggagggtctgtgcaacatagtttaaaaagcttaaaacacatttacgaactatgtttttttttttttcattttcttagACTGACAAATCAAAAATCAAGAAAGTTATTGAGGAGCTTGATGAGAAGAAAAAAGAAACACTGAAAGTTACATGGGTTAAAGTTAACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA