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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtggtgatatcttcctctacctagtttttcagctttgctatcagggaattatttagctattggaatcaattgttttttatcatgtctaatattgtggctcaaatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT

Basic information

species Arabidopsis thaliana
transcript AT1G09640.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os06g37440.1 (Oryza sativa), 3'ss of exon 7
gtgtgtggtgatatcttcctctacctagtttttcagctttgctatcagggaattatttagct-attggaatcaattgtttt----ttatcatgtctaatattgtggctcaaatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT
                 | |||   ||   ||| |||  |    | ||| |   | |||  | |||  | |   |||||||    ||| ||     | |||   | ||    | |||| |||||||||||||||||||||||||| ||||| || ||||||||||||||||||||||||||||||||||  || || ||||| ||| | ||||||||
-----------------cttcttgttacaattttagcaatatatttaggcatgaacttaatttattccattttcttgtttttgaattaacagagacattatcacgtctatttttcagGTTTCTGGGACATGTATGACCCAGAGGGTTACTCTCTGTGGTTCTGTGACTACAAGTACAACGATGAGAACACCGTATCGTTTGTGACGATGAACAAGGT

upper sequence: AT1G09640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 7
gtgtgtggtgatatcttcctctacctagtttttcagctttgctatcagggaattatttagctattggaatcaattgttttttatcatgtctaatattgtggctcaaatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT
     | ||  | |||||  |  | |  ||| ||| ||   | | |      | | || |  | ||   | ||||||  |  |   | |||  |  |||      | |||||| |||||||| |||||||||||||| || ||||| || |||||||| |||||||| ||||| ||||||||||  ||||| || || ||  | ||||||||
----ttagttctctcttctacaccattatttctcatctacaccaacttctgttgagtttga-actgctgtgaattgtactcaagt-tatcttctcatgt------attgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTCTGCGACTACAAATACAATGATGAGAACACCGTGTCCTTCGTGACCATGAACAAGGT

upper sequence: AT1G09640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 6
gtgtgtggtgatatcttcctctacctagtttttcagctttgctatcagggaattatttagctattg-gaatcaattgttttttatcatgtctaatattgtggctca---aatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT
           ||| |  || |   ||   ||     ||||  ||| |      | ||  || ||| | || || |  | |  ||       || ||     ||||   | |||||| |||||||| |||||||||||||| || ||||| || ||||| ||||||||||| ||||| || |||||||  ||||| || || ||  | ||||||||
----------ttatatctctttgattaccatta----tttgtcatctgctcccaactt--ctgttgtgtatgaagttctgtgaattgaactcaacatgtcttctcacttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACTACAAATACAATGACGAGAACACTGTGTCCTTCGTGACCATGAACAAGGT

upper sequence: AT1G09640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 7
gtgtgtggtgatatcttcctctacctagtttttca-gctttgctatcagggaattatttagctattggaatcaattgttttttatcatgtctaatattgtggctcaaatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT
    |   | | |    ||  ||    ||| |  | | |||| | |       ||| | ||   |  | |  | |    |    |||  ||  || |  |        | |||| |||||||||||||||||||||||||| ||||| || ||||||||||||||||||||||| || |||||||  ||||| ||||| ||  | ||||||||
----gcatttaaacaccccattaagcggttctcaaagttttgtttttgatctgttagt-agtgctatgcacaagtcaactgaactcaactcccatgtatt--------ttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACTACAAGTACAATGACGAGAACACAGTGTCGTTTGTGACTATGAACAAGGT

upper sequence: AT1G09640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G059580_T03 (Zea mays), 3'ss of exon 5
gtgtgtggtgatatcttcctctacctagtttttcagctttgctatcagggaattatttagctattggaatcaattgttttttatcatgtctaatattgtggctcaaatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT
    | ||   || || | | ||   | ||  | ||||  | |  |  ||  ||  ||  || ||     ||  | | |    || || | |||| |  | ||    | |||| |||||||||||||||||||||||||| ||||| || ||||||||||||||||||||||| || |||||||  || || ||||| || || ||||||||
---agagggagta-ctgcttgta---aattaattagctg-gatggcttgggtttcctttcctttt----ccatgtttgtggagtcttgaccaataatccgtctatgtttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCTCTGTGGTTCTGTGACTACAAGTACAATGACGAGAACACCGTCTCCTTTGTGACCCTGAACAAGGT

upper sequence: AT1G09640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G122871_T02 (Zea mays), 3'ss of exon 6
gtgtgtggtgatatcttcctctacctagtttttcagctttgctatcagggaattatttagctattggaatcaattgttttttatcatgtctaatattgtggctcaaatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT
      || | ||       | |  || || || || |    |    ||   |  |||  || ||    |   | |  | ||  |    ||| || |  |  |    | |||| |||||||||||||| ||||||||||| |||||  | ||||||||||||||||||||||| ||||||||||  || || ||||| || || ||||||||
------ggcg-tactgcaagcaaattaattgtt-agatgaattgcttggatttcctttccctgttcatgtttgtggactcttgac----ctagtaatccgtgtgtgtttcagGTTTCTGGGACATGTACGACCCAGAGGGCTACTCTTTGTGGTTCTGTGACTACAAGTACAATGATGAGAACACCGTCTCCTTTGTGACCCTGAACAAGGT

upper sequence: AT1G09640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G134582_T01 (Zea mays), 3'ss of exon 7
gtgtgtggtgatatcttcct------ctacctagtttttcagctttgctatcagggaattatttagctattggaatcaattgttttttatcatgtctaatattgtggctcaaatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT
  || |||| |||||||  |       ||   ||||  | || ||||  ||| |  | |  |  |  | |  ||| ||| ||   |  | |   ||| || |         | |  ||| |||||||| ||||| ||||||||||| ||||| || ||||||||||||||||||||||| ||||||||||  ||||| ||||| ||  | ||||||||
--gtttggt-atatctttttggtgttttaagcagttcctaagttttg--atctgtcagtagtgcaa-tgtacgaaccaactgaactcaaac---tctcatgt---------attttagGTTTCTGGGATATGTACGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACTACAAGTACAATGATGAGAACACAGTGTCGTTTGTGACCATGAACAAGGT

upper sequence: AT1G09640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G122871_T03 (Zea mays), 3'ss of exon 6
gtgtgtggtgatatcttcctctacctagtttttcagctttgctatcagggaattatttagctattggaatcaat-tgttttttatcatgtctaatattgtggctcaaatgcagGAT-TCTGGGACATGTATGACCC-AGAGGGATACTCACTAT-GGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT
    |           | ||||   | ||| |    ||   | |  |   ||| ||      |  |    |  | ||    | | || |  |  |    |    ||   |  |||  | ||   || ||| | |    |   ||| |||   || || |||| | |  |    |    || | |    |||     | |  |  |  ||       
---cgacccagagggctactctttgtggttctgtgact--acaagtac--aatgatgagaacaccgtctcctttgtgaccctgaacaaggttggtggattcctgcagCGGATGGACCTGTGCCGCAAGTACGCCTTTGGGAAGATGCTCGTGATAGGCTCTGAGCCACCCTTCAAGCTGAAGGGCCTTTGGC----TCTTCCGTGGCCAGG-----

upper sequence: AT1G09640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S172_22V6.1 (Physcomitrella patens), 3'ss of exon 5
-----gtgtgtggtga-tatcttcctctacctagtttttcagctttgctatcagggaattatttagctattg-gaatcaattgttttttatcatgt-ctaatattgtggc----tcaaatg---cagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT
        | |  |||  || |   |  |  |||    |||| | || ||    | |   ||     ||| | ||||   |||    |   | ||| ||||  | ||||     |  |||    ||||||||||||| ||||  ||  | ||||| |  ||| | ||||||||||| ||||||||||| |||||||||   ||  | || || ||  | || |||||
gtacgtcttctaatgagcatatgatttaatttagagcctcag-tctgatactgagcacccat--gcttatggagaatgtcttgaccctcggcttgtgctaacgtggtggacgggttgaatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATTACAAGTACAATGATGAGAACCAAGTCACTTTCGTGACCATGAATAAGGT

upper sequence: AT1G09640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S71_218V6.1 (Physcomitrella patens), 3'ss of exon 7
----gtgtgtggtgatatcttcctctacctagtttttcagctttgctatcagggaattattt--agctattg-------gaatcaattgttttttatcatgt-ctaatattgtggctcaaatg-------cagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT
    || | |  | ||    || |      |||| |   | | ||  |  |   ||| ||||  |   |||         ||| | | || | | ||| | |  | || | |||| ||   ||       |||| || ||||| ||||  ||  | ||||| |  ||| | ||||||||||| ||||| |||||||||||||||   ||  ||||||| ||  | ||||||||
gtaagtttctattaatgaactcatgatttgagttat--ggttgtggcacaatttaatgatttgcactcattcttttcgcaaatgattggtgtctcatcttatgttcatgtggtggttctgttgagtgcaacagGTTTTTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATTACAAATACAACGATGAGAACCAAGTAACATTTGTGACTATGAACAAGGT

upper sequence: AT1G09640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ14564 (Selaginella moellendorffii), 3'ss of exon 6
gtgtgtggtgatatcttcctctacctagtttttcagctttgctatcagggaattatttagctattggaatcaattgttttttatcatgtctaatattgtggctcaaatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT
                                          ||  || |   | |  |   || |     || || |  || | ||  | ||| ||          ||||||||||||||| ||||||||||| ||||||||||| || |||||||| ||||||||||||||||||||||||| |||| | || || ||| | ||||||||
-----------------------------------------gtacaagtggtgtttccattgatcgcttgaaaatgctgattttgatcccaaatctt----------tgcagGATTCTGGGAGATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT

upper sequence: AT1G09640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
gtgtgtggtgatatcttcctctacctagtttttcagctttgctatcagggaattatttagctattggaatcaattgttttttatcatgtctaatattgtggctcaaatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT
                                            |    |   | |||  | ||||  |||  |||    |  | || ||| || |  |  ||    ||||||||||||||||||||||||||| ||||||||||| || |||||||| ||||||||||||||||||||||||| |||| | || || ||| | ||||||||
-------------------------------------------gtacaagtggtgttt--ccattg--atcgcttgaaaatgctgat-tctgatctcttccct----tgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT

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|86083543|gb|DR379302.1|DR379302
EST:     CCAAATTCTAACTTCCGCGAGGTTGCTATTAAAG                         GATTTTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACT
genomic: CCAAA-TCTAACTTCCGCGAGGTTGCTATTAAAGgtgtgtggtg ... tcaaatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACT
EST: gi|86079648|gb|DR375405.1|DR375405
EST:     GA-GCTTTACTCAAACACCAAATCTAACTTCCGCGAGGTTGCTATTAAAG                         GATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACT
genomic: GAGGCTTTACTCAAACACCAAATCTAACTTCCGCGAGGTTGCTATTAAAGgtgtgtggtg ... tcaaatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACT
EST: gi|301501927|gb|HO207467.1|HO207467
EST:     GAGGCTTTACTCAAACACCAAATCTAACTTCCGCGAGGTTGCTATTAAAG                         GATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACT
genomic: GAGGCTTTACTCAAACACCAAATCTAACTTCCGCGAGGTTGCTATTAAAGgtgtgtggtg ... tcaaatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctattggaatcaattgttttttatcatgtctaatattgtggctcaaatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT
                              gtctaat  putative branch site (score: 3)
                   ttttttatcatgtcta  TA-rich tract