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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttagctttgacctagcgtaggataagtttttgaggttttagtttgttataaaaaccaactgccaaggtcttcaacagaaattttattctgttgtgcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAAAAAACTGGAAAG

Basic information

species Arabidopsis thaliana
transcript AT1G59610.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 14
ctttagctttgacctagc--gtaggataagtttttgaggttttagtttgttataaaaaccaac-tgccaaggtcttcaacaga-aattttattc--tgttgtgcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAAAAAACTGGAAAG
      |||||| | |    ||   || |    ||   |||||   |  || ||||||   || ||| ||  |    |   |  |||||| | |  | || | |||| ||| |  |||||||||||||||| |||||||| ||||||||| | |||||||| || ||||| ||||  ||||||
----ccctttgaaccatttggtgaaatgaaacattt--gttttgtctcattgtaaaaaagtacatgcaaatataaatattcgttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 14
ctttagctttgacctagcgtaggataagtttttgaggttttagtttgttataaaaaccaactgccaaggtcttca---acagaaatt---ttattctgttgt--gcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAAAAAACTGGAAAG
    |||| ||    |    | ||     ||| || |||  | | ||  | ||  |   | | | ||  | || |   ||  ||| |   ||  | | ||||   |||| |  ||| | |||||||||||||| || ||||| ||||| |||||||||||||| || |||||||| || ||||||
---gagctatgcttaaatacatgaa----tttggaagttacaatgtgcca-aagtatatatttcaaaattattaataaactaaaactacttttctttattgttttcagGATTTTTATTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAAAAGACAGGAAAG

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 14
ctttagctttgacctagcgtaggataagtttttgaggttttagtttgttataaaaaccaactgccaaggtcttca---acagaaatt---ttattctgttgt--gcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAAAAAACTGGAAAG
    ||||    | ||     | || | |||  || ||| || | ||  | ||  |   | | | ||  | || |   ||  ||| |   ||  | | ||||  ||||| |  ||  | |||||||||||||| || ||||| ||||| |||||||||||||| || ||||| || || ||||||
----agctaatgcttaaat--gcatgaatttg-gaagttgtaatgtgcca-aagtatatatttcaaaattattaataaactaaaactacttttctttattgtttgcagGATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAG

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 14
-ctttagctttgacctagcgtaggataagtttttgaggttttagtttgttataaaaaccaactgccaaggtcttcaacagaaattttattctgt---tgtgcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAAAAAACTGGAAAG
    | || |  |    || |    |    | |  |  | |   | | |        |   ||  |    ||| ||||     ||||| | | |   | | |||| |   || |||||||||||| ||| || ||||| ||||| ||||||||||||||| | |||||||| ||||| |||
ataatggcatgtattgtgcatcttctcttgtatcaacatctctctctctctctctctctctctctctctctctccaacc----ttttactttatacatatacagGCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAG

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 14
---------------------------------------------------------------------------------------ctttagctttgacctagcgtaggataagtttttgag---gttttagt--ttgttataaaaaccaactgccaaggtcttcaacagaaattttattctgttgtgcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAAAAAACTGGAAAG
                                                                                          |  |||      | | |  |   ||| || |||   | ||   |  ||| ||||   |   | |         |   |  ||  ||||||| |  | |||||| |  ||| |||||| ||| || || |||||||| ||||||||||||||||||||| | ||||| |||| | | |||
gtgcttgagcgaacaatcagcattttaacttttgtggttctaaaaaatatggaattgtactatctacctgcagtcaacagttgttggacatgccttctctacatcatcagtagagtgttggagaaggcttgcataattggtatatttatttattttattaacttgtcatcgattttttatttttatctgcagGATTTTTATTGAAGAGAAGCGCCAAAACAAATGGATGGAGTAGGCGATGGTTTGTTTTAAATGAGAAAAGTAGTAAG

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|125041524|gb|EL113793.1|EL113793
EST:     GGAGGTGTCTGGTCTGAAGACTGCTGGACCTGAGGGAGAGATAACTGCAG                         GGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGG
genomic: GGAGGTGTCTGGTCTGAAGACTGCTGGACCTGAGGGAGAGATAACTGCAGgtccttattc ... tgttgtgcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGG
EST: gi|124887224|gb|EH966126.1|EH966126
EST:     TGCTGGACCTGAGGGAGAGATAACTGCAG                         GGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGT
genomic: TGCTGGACCTGAGGGAGAGATAACTGCAGgtccttattc ... tgttgtgcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGT
EST: gi|125318670|gb|EL332755.1|EL332755
EST:     GGAGGTGTCTGGTCTGAAGACTGCTGGACCTGAGGGAGAGATAACTGCAG                         GGTACTTAATGAAGAAAAGTGCAAAGACAAA
genomic: GGAGGTGTCTGGTCTGAAGACTGCTGGACCTGAGGGAGAGATAACTGCAGgtccttattc ... tgttgtgcagGGTACTTAATGAAGAAAAGTGCAAAGACAAA
EST: gi|124769356|gb|EH859486.1|EH859486
EST:     GGAGGTGTCTGGTCTGAAGACTGCTGGACCTGAGGGAGAGATAACTGCAG                         GGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGAT
genomic: GGAGGTGTCTGGTCTGAAGACTGCTGGACCTGAGGGAGAGATAACTGCAGgtccttattc ... tgttgtgcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGAT
EST: gi|125204369|gb|EL219323.1|EL219323
EST:     GGAGGTGTCTGGTCTGAAGACTGCTGGACCTGAGGGAGAGATAACTGCAG                         GGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGT
genomic: GGAGGTGTCTGGTCTGAAGACTGCTGGACCTGAGGGAGAGATAACTGCAGgtccttattc ... tgttgtgcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttataaaaaccaactgccaaggtcttcaacagaaattttattctgttgtgcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAAAAAACTGGAAAG
                                     ttttattct  CT-rich tract
                             aacagaaattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttagctttgacctagcgtaggataagtttttgaggttttagtttgttataaaaaccaactgccaaggtcttcaacagaaattttattctgttgtgcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAAAAAACTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - -gtttttg
- - - - - - - - - - - - - - - - - -ggtttta
- - - - - - - - - - - - - - - - - - - - - - - - - taaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acagaaa