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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatctttaaacgatgattccttgcaaattacattctttggctacaaaatcctcactgtatagttgttgtacacagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG

Basic information

species Arabidopsis thaliana
transcript AT4G18710.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 3'ss of exon 8
-----gtaagaatctttaaacgatgatt-ccttgcaaattacattctttggctacaaaatc-ctcactgtata-gttgttgtacacagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG
     | ||||      |  |  |  |    ||||   |   |||   |     ||   || || ||  | || | | || |   |||||||||||||||||||| || || ||||| ||||| ||||| ||  | || ||||| || ||||||||||||||||| || || || |||||||||
gtactgcaagacatgccatgcagttctaattttgctcctactattgagtatgggcatcttctctaaccttgtatgatattct-tgcagGTTCTTGGTACACCAACCCGTGAGGAAATACGTTGCATGAACCCGAACTATACAGAGTTTAGGTTTCCACAGATAAAAGCTCACCCTTGGCACAAG

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G472625_T01 (Zea mays), 3'ss of exon 8
gtaagaatctttaaacgatgattccttgcaaattacattctttggctacaaaatcctcactgtatagttgttgtac--acagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG
        ||  |||   |       |  | |||  ||||||   |       |      ||  ||  || ||| |    ||||||||||||| ||||| || || || || || || ||||||||  | || || || ||||||||||| ||||||||||| ||||| |||||||||
-----gtactgcaaaatgttccaaagtagacattctattcttctaccggggtgtttcttatggttatgtgatgtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAG

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
gtaagaatctttaaacgatgattccttgcaaattacattctttggctacaaaatcctcactgtatagttgttgtac--acagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG----
        ||  |||   |       |  | |||  ||||||   |       |      ||  ||  || ||| |    ||||||||||||| ||||| || || || || || || ||||||||  | || || || ||||||||||| ||||||||||| ||||| |||||||||    
-----gtactgcaaaatgttccaaagtagacattctattcttctaccggggtgtttcttatggttatgtgatgtgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
gtaagaatctttaaacgatgattccttgcaaattacattctttggctacaaaatc-ctcactg-tatagttgttgtacacagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG
    | ||    ||| | |       |  |||||  |||| |  ||  | |  |  || | || |||      ||     ||||||||||||| ||||| || || || || || || ||||||||  | || || || ||||||||||| ||||||||||| ||||| |||||||||
----gtattgcaaaatgtt--ccaaatagaaattctattcctctgccgcgacgttacttattggtatgtgatatgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G09090.1 (Glycine max), 3'ss of exon 8
---------gtaagaatctttaaacgatgattccttgcaaattacattctttggctacaaaatcctcactgtatagttgttgtac-acagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG
         ||   ||  | ||    ||| |   |||  |  | |  || ||| |   | ||  | |  | || | || |||||   ||||| ||||| ||||| |||||||| ||| | || |||||||||||  ||||||  || || ||||||||||||||||| ||||| || |||||||||
gtgcaattggtgttaacatgtattttatgttcttttgtca--tgccatccttgtcattataagtcactttataaaatt-ttgtattgcagGTGCTTGGCACACCCACTCGAGAGGAAGTACGCTGTATGAATCCCAATTACAATGACTTTAGGTTTCCACAGATAAAAGCACACCCATGGCACAAG

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G30060.2 (Glycine max), 3'ss of exon 8
---------gtaagaatctttaaacgatgattccttgcaaattacattctt-----tggctacaaaatcctcactgtatagttgttgtacacagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG
          |   ||  | ||    ||| ||  || ||    |   |  |     |   |   || ||  |  | || | ||||  || |  ||| ||||| ||||| |||||||| ||| | || |||||||||||  ||||||  || || ||||||||||||||||| ||||| || |||||||||
gtgcaattgatgttaacatgtattttatgtttgttttcatgccatccttgtcatcataatttataagtcacctttataaaattgtattata--gGTGCTTGGCACACCCACTCGAGAGGAAGTACGCTGTATGAATCCCAATTACAATGACTTTAGGTTTCCACAGATAAAAGCACACCCATGGCACAAG

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA06G06850.1 (Glycine max), 3'ss of exon 8
---------gtaagaatctttaaacgatgattccttgcaaattacattctttggctacaaaatcctcactgtatagttgttgtac-acagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG
         ||   ||    ||    ||| ||||||    ||  ||| |||    |   || ||  |  |||| | || |||||   ||||| ||||| ||||| || ||||| ||| | || |||||||||||  ||||||  || || ||||||||||||||||| ||||| || |||||||||
gtacaattggtgttaacacgtattgcatg-ttccttagtcatgccatccttgtcatcataactcacctttgtaaaatt-ttgtattgcagGTGCTTGGCACACCCACCCGAGAGGAAGTACGCTGTATGAATCCCAATTACAATGACTTTAGGTTTCCACAGATAAAAGCACACCCATGGCACAAG

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G06760.1 (Glycine max), 3'ss of exon 8
---------gtaagaatctttaaacgatgattccttgcaaattacattctttggctacaaaatcctcactgtatagttgttgtac-acagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG
         ||    || | ||    ||| ||||||    ||  ||| |||    |   |||||  |  |||| | || |||||   ||||| ||||| || || |||||||| ||| | || |||||||||||  ||||||  || || |||||||| |||||||| ||||| || |||||||||
gtacaattggtgttgatatgtattgtatg-ttccttagtcatgccatccttgtcattataaatcacctttgtaaaatt-ttgtattgcagGTGCTTGGCACGCCCACTCGAGAGGAAGTACGCTGTATGAATCCCAATTACAATGACTTTAGGTTTCCTCAGATAAAAGCACACCCATGGCACAAG

upper sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 3'ss of exon 8
--gtaag--aatctttaaacgatgattccttgcaaattacattctttggctacaaaatcctcactgtatagttgttgtacacagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG
  | ||    || ||||     |||   | || |  ||    |  |    |   |||| ||  |  | |   || ||    |||||||||||||||||||| || |||||||| || |||||||||||   ||| || ||||| ||||||||||||||||| ||||| || |||||||||
gtgcaatttgatttttagtgtttgaaatcatgtag-ttctggtgatcatttgttaaattcttgcattttgtctggtg---gcagGTTCTTGGTACACCAACGCGGGAAGAAATTCGCTGTATGAATCCGAGTTATACTGATTTTAGGTTTCCACAGATAAAAGCACACCCTTGGCACAAG

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|125054944|gb|EL125411.1|EL125411
EST:     TTATTTCCCGGAGAAAATGTTGTGGATCAGCTCGTTGAAATTATAAAA                         GTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTAC
genomic: TTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAAgtaagaatct ... ttgtacacagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTAC
EST: gi|124742043|gb|EH833205.1|EH833205
EST:     CATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAA                         GTTCTTGGTACACCAACTCGAGAAGAAATCCGTT
genomic: CATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAAgtaagaatct ... ttgtacacagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTT
EST: gi|116451981|gb|EG494573.1|EG494573
EST:     CATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAA                         GTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTAC
genomic: CATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAAgtaagaatct ... ttgtacacagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTAC
EST: gi|125078844|gb|EL141074.1|EL141074
EST:     GAAACTATAAAA                         GTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTAC
genomic: GAAATTATAAAAgtaagaatct ... ttgtacacagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTAC
EST: gi|116452048|gb|EG494640.1|EG494640
EST:     CATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAA                         GTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTAC
genomic: CATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAAgtaagaatct ... ttgtacacagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTAC
EST: gi|125223497|gb|EL237582.1|EL237582
EST:     CATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAA                         GTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTAC
genomic: CATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAAgtaagaatct ... ttgtacacagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTAC
EST: gi|125158332|gb|EL186977.1|EL186977
EST:     CATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAA                         GTTCTTGGTACACCAACTCGAGAAG
genomic: CATTATTTCCCGGAGAAAATGCTGTGGATCAGCTCGTTGAAATTATAAAAgtaagaatct ... ttgtacacagGTTCTTGGTACACCAACTCGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaaattacattctttggctacaaaatcctcactgtatagttgttgtacacagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG
                            tcctcac  putative branch site (score: 2)
     aattacatt  TA-rich tract