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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taattgttttagtaagtttacttggatatgtttatactcaagttcaattggatgatgctgttgaattaatggatgtatctgatctcaatttatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG

Basic information

species Arabidopsis thaliana
transcript AT1G79550.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g45710.1 (Oryza sativa), 3'ss of exon 2
------taattgttttagtaagtttacttggatatgtttatactcaagttcaattggatgatgctgttgaattaatggatgtatctgatctcaatttatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG
      |||  || ||  || | ||      || |  ||   | |   ||   |||  |  |  |||    |      ||| |    || |    ||    ||||||| |||||||||||||| || || ||||||||||| ||||||||||| ||  | |||||||| |||||||||||||| 
agcagctaaccgtgtttctatgcttgggataatgttctttcgccccccttt--ttgttttctcttgtcctctgttgtaatgcaatcaattttgtctt----ttcagGGTCGCCCAAAAGGTGTAACCCCGAAGTACAGCTTGAAGCCTCTTGTTCCGCGCTTGTCTGAGCTTCTTGGTGTTGAT

upper sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G382914_T02 (Zea mays), 3'ss of exon 2
taattgttttagtaagtttacttggatatgtttatactcaagttcaattggatgatg-ctgttgaattaatggatgtatctgatctcaatttatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG
 | |  |  ||  ||||  || |   |  | ||      |    ||||    |  || || ||   ||  |     |      | |  ||     |||||||| || ||||||||||| || || ||||||||||| ||||||||||| ||  | |||||||| || ||||| ||||| 
-actaatagtaacaagtcaaccttttttgggttgagtgtagcaacaataattttttgtcttttatttttgtaataatgcaatttgttgatgccattttcagGGTCGTCCAAAAGGTGTCACCCCAAAGTACAGCTTGAAGCCTCTTGTTCCACGCTTGTCTGAGCTCCTTGGAGTTGAA

upper sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G41550.1 (Glycine max), 3'ss of exon 2
taattgttttagtaagtttacttggatatgtttatactcaagttcaattggatgatgctgttgaattaatggatgtatctgatctcaatttatg--tttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG
 |   |||    | | | || |  ||    |  ||  |||        |||    |  |  ||| || |    ||  | ||   | | | |     |||||||| || ||||||||||| || ||||| ||||| || |||||||||||||| ||  ||||| ||||||||||  |||||
gaggagttactattattctattaagac-catgaatg-tcagaaaagtgtggtgagtagtagtgacttgaaaagtgattttgccttgactatgctgttttcagGGACGTCCAAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCAAGGCTGTCTCAACTTCTTGGAATTGAG

upper sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G17600.1 (Glycine max), 3'ss of exon 2
taattgttttagtaagtttacttggatatgtttatactcaagttcaattggatgatgctgttgaattaatggatgtatctgatctcaatttatg--tttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG
|  ||  ||||     |    |||| | | ||  |  |  |||   ||| ||   || |  ||| || |   |||  | ||   | | | |     |||||||| || || |||||||| || ||||| ||||| || |||||||||||||| ||  ||||| ||||||| ||  |||||
ttttttatttaacttttgcttttgggtgtattagttatagagtgtgatttga--gtggttgtgacttgaaaaatggttttgccttgactatgctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCAAGGCTGTCTCAACTTCTCGGAATTGAG

upper sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv19s0085g00370.t01 (Vitis vinifera), 3'ss of exon 1
----taattgttttagtaagtttacttggatatgtttatactcaagttcaattggatgatgctgttgaattaatggatgtatctgatctcaatttatgttt-cagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG
    |  ||  |||  | | |||   |||||   ||| |  |  | |  | ||   | |     |  |||| ||| |  |      ||| ||||   |||| ||||| |||||||| |||||||| |||||||||||||| || ||||||||||| ||  |||||||||||||||| ||||||
gtttttgtttctttcctgactttctatggattcatttct--tggaatatattt---ttacttgttctaatttatgaaactgatgattctgaattgtcgttttcagGGGCGCCCAAAGGGTGTTACACCTAAGTACAGCTTGAAACCTCTTGTGCCAAGGCTGTCTGAACTTCTTGGAGTTGAG

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|47828512|gb|CK118196.1|CK118196
EST:     TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTG                         GGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
genomic: TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTGgtatgatatc ... tatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
EST: gi|116446998|gb|EG489590.1|EG489590
EST:     TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTG                         GGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
genomic: TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTGgtatgatatc ... tatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
EST: gi|47831797|gb|CK121481.1|CK121481
EST:     TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTG                         GGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
genomic: TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTGgtatgatatc ... tatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
EST: gi|47829445|gb|CK119129.1|CK119129
EST:     TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTG                         GGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
genomic: TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTGgtatgatatc ... tatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
EST: gi|124748412|gb|EH838542.1|EH838542
EST:     TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTG                         GGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCT
genomic: TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTGgtatgatatc ... tatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCT
EST: gi|116434727|gb|EG477319.1|EG477319
EST:     TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTG                         GGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
genomic: TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTGgtatgatatc ... tatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
EST: gi|47831355|gb|CK121039.1|CK121039
EST:     TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTG                         GGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
genomic: TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTGgtatgatatc ... tatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
EST: gi|47828442|gb|CK118126.1|CK118126
EST:     TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTG                         GGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
genomic: TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTGgtatgatatc ... tatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
EST: gi|116434726|gb|EG477318.1|EG477318
EST:     TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTG                         GGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
genomic: TCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTGgtatgatatc ... tatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCC
EST: gi|125192497|gb|EL207451.1|EL207451
EST:     CAAGTACTTGATGGGTAATGGAATCTAGGGTTGTTCTCTGCAGTCACTTG                         GGCCGCCCAAAAGGTGTTACTCCTAAGTA
genomic: CAAGTACTTGATGGGTAATGG-ATCTAGGGTTGTTCTCTGCAGTCACTTGgtatgatatc ... tatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattggatgatgctgttgaattaatggatgtatctgatctcaatttatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG
                                         aatttatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taattgttttagtaagtttacttggatatgtttatactcaagttcaattggatgatgctgttgaattaatggatgtatctgatctcaatttatgtttcagGGCCGCCCAAAAGGTGTTACTCCTAAGTACAGCTTAAAGCCTCTTGTGCCCAGATTGTCTGAACTTCTTGGTGTTGAG

- - -gttttag
- - - - - - - - - - - - - - - - - -actcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atctcaa