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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatagaagatagtgttgtttttgtagcttgttaatcaaggaaagacttttcttgctgtgtactcaagccatagagttttgtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAACAATGCTTCGGCTTCTTTTGAGAACCAGTTATCAGAAGAAGCAAGTGACG

Basic information

species Arabidopsis thaliana
transcript AT4G27440.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G23140.1 (Glycine max), 3'ss of exon 5
gtaatatagaagatagtgttgtttttgtagcttgttaatcaaggaaagacttttcttgctgtgtactcaagccatagagttttgtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAACAATGCTTCGGCTTCTTTTGAGAACCAGTTATCAGAAGAAGCAAGTGACG
                                   | ||   | | |  | ||  ||    |||  |  | |  | | ||| |   ||   |||| ||||||||||||||| |||| |||||||| ||||| |||||||||||    || || ||||| ||||| ||||| || ||  |||| || || || |
----------------------------------gtgattttgaagaatccttgtttctcatgt--ttgaactgttgtgttct---tgtgtagGTTGTGAGTGATCCAAGCCTGACAAAATCAGGTGTTTACTGGAGCTGGAATGCAGCCTCTGCTTCGTTTGAAAACCAATTGTCCCAAGAGGCCAGCGATG

upper sequence: AT4G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G35050.2 (Glycine max), 3'ss of exon 4
gtaatatagaagatagtgttgtttttgtagcttgttaatcaaggaa---agacttttcttgc-tgtgtactcaagccatagagttttgtttgat-cagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAACAATGCTTCGGCTTCTTTTGAGAACCAGTTATCAGAAGAAGCAAGTGACG
|||||||  |  |||    |  |   | || |  | | |  | ||      | |||||     | | || |       |   ||| | ||| ||  |||| || |||||||||||| | || ||||| || ||||| |||||||||||||| || || ||||| ||||| |||||||| ||  | || || |||||  
gtaatatcaataataaccct-ctagggaagataatgactacaagagtatgaagttttcaaatatctttatttctcatgtgtggttgtcttttatatagGTTGTAAGTGATCCAAGCCTAACAAAATCTGGTGTTTACTGGAGCTGGAACAAAGCATCAGCTTCGTTTGAAAACCAGTTGTCTCAGGAGGCCAGTGATA

upper sequence: AT4G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G38160.1 (Glycine max), 3'ss of exon 4
gtaatatagaagatagtgttgtttttgtag--cttgttaatcaaggaaagacttttcttgctgtgtactcaagccata-----gagttttgtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAACAATGCTTCGGCTTCTTTTGAGAACCAGTTATCAGAAGAAGCAAGTGACG
 |    ||    |     || ||     ||  | |||   |       |   | || |||  |  | ||     |  |     ||  | |  |||   |||| ||||||||||||||| | || |||||||| ||||| ||||||||||||   || || ||||| ||||| ||||| || ||  ||||||| || || |
atcccttaattaagcagtttattcaaacaggccatgtatgttgttagcaacgtgtttttgaagaatccttgtttctcatgtttgaactgttcttgtgtagGTTGTGAGTGATCCAAGCCTAACAAAATCAGGTGTTTACTGGAGCTGGAACGCGGCCTCTGCTTCGTTTGAAAACCAATTGTCCCAAGAAGCCAGCGATG

upper sequence: AT4G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0014g03160.t01 (Vitis vinifera), 3'ss of exon 4
gtaatatagaagatagtgttgtttttgtagcttgttaatcaaggaaagacttttcttgctgtgtactcaagccatagagttttgtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAACAATGCTTCGGCTTCTTTTGAGAACCAGTTATCAGAAGAAGCAAGTGACG
|||| | | ||   | | |    |||||   |  || ||| ||| |||         |   |  | |  |    | |  || || |     |||| || ||||| ||||||||||| || ||||| || || ||||||||||||||    || ||||| |||||||||||||| ||  | ||||| ||||| |
gtaagagaaaaaggact-taccctttgttaataattgatcgagggaaggg-------ggcataaatttga-ttgttggtttatgata---tagGTTGTCAGTGAGCCAAGCTTGACAAAGTCAGGTGTGTACTGGAGCTGGAACAAGAACTCAGCTTCATTTGAGAACCAGTTGTCTCAGGAAGCTAGTGATG

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|116431477|gb|EG474069.1|EG474069
EST:     TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
genomic: TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
EST: gi|125277580|gb|EL291665.1|EL291665
EST:     GAGTCAGGCAAAAGAACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
genomic: GAGTCAGGCAAAAG-ACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
EST: gi|125232759|gb|EL246844.1|EL246844
EST:     GGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
genomic: GGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
EST: gi|164228909|gb|EL973718.1|EL973718
EST:     TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAG                         GTGGTGAGTGATCCAAG
genomic: TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAG
EST: gi|164115715|gb|ES195450.1|ES195450
EST:     ACTAAAGGATATGTCGTTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGG
genomic: ACTAAAGGATATGTC--TCCGAAACAGAGTCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGG
EST: gi|124743196|gb|EH834358.1|EH834358
EST:     TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAG                         GTGGTGAGTGATCCA
genomic: TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCA
EST: gi|116443985|gb|EG486577.1|EG486577
EST:     TCACTAAAGGATATGTTTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
genomic: TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
EST: gi|125075101|gb|EL138796.1|EL138796
EST:     AAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCCGGAAC
genomic: AAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
EST: gi|163982555|gb|EL992270.1|EL992270
EST:     GAGTCAGGCAAAAGACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
genomic: GAGTCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
EST: gi|125239104|gb|EL253189.1|EL253189
EST:     AAAAGAACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
genomic: AAAAG-ACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
EST: gi|124778102|gb|EH868045.1|EH868045
EST:     TCAGGCAAAAGACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
genomic: TCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
EST: gi|124929995|gb|EL007485.1|EL007485
EST:     AAAAGACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
genomic: AAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
EST: gi|164063382|gb|ES176059.1|ES176059
EST:     TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAA-GACTTGCTCAG                         GTGGTGAGTGAT
genomic: TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGAT
EST: gi|86080046|gb|DR375803.1|DR375803
EST:     TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
genomic: TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
EST: gi|164030285|gb|ES121669.1|ES121669
EST:     TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGG
genomic: TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGG
EST: gi|116416037|gb|EG458629.1|EG458629
EST:     TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
genomic: TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
EST: gi|125031860|gb|EL104129.1|EL104129
EST:     AGGCAAAAGACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
genomic: AGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
EST: gi|164183134|gb|ES091082.1|ES091082
EST:     GTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTAGAAC
genomic: GTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAAC
EST: gi|124709645|gb|EH801047.1|EH801047
EST:     TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAG                         GTGGTGAGTGAT
genomic: TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGAT
EST: gi|124897098|gb|EH973312.1|EH973312
EST:     TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAG                         GTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTG
genomic: TCACTAAAGGATATGTCTCCGAAACAGAGTCAGGCAAAAGACTTGCTCAGgtaatataga ... gtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaggaaagacttttcttgctgtgtactcaagccatagagttttgtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAACAATGCTTCGGCTTCTTTTGAGAACCAGTTATCAGAAGAAGCAAGTGACG
                                         ttttgttt  CT-rich tract
                                         ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatagaagatagtgttgtttttgtagcttgttaatcaaggaaagacttttcttgctgtgtactcaagccatagagttttgtttgatcagGTGGTGAGTGATCCAAGCTTGACGAAATCAGGGGTTTATTGGAGCTGGAACAATGCTTCGGCTTCTTTTGAGAACCAGTTATCAGAAGAAGCAAGTGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG