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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctctagatcatagatcggcgcatattattgtgtctcgtagtttgcaaattgtgttgctttgtgggagattgttgtcttatatgatgtatgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGCAAACCCACGTCAGTTCAAGATCCCAGACTGGTTCTTGAACAGGCAGAAG

Basic information

species Arabidopsis thaliana
transcript AT4G09800.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G36610.3 (Glycine max), 3'ss of exon 2
atctctagatcatagatcggcgcatattattgtgtctcgtagtttgcaaattgtgttgctttgtgggagattgttgtcttatatgatgtatgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGCAAACCCACGTCAGTTCAAGATCCCAGACTGGTTCTTGAACAGGCAGAAG
            |   |      || |  ||| ||    | | | |  ||||       |||   ||  |||||||   | |  ||| | |||||  |||||||||||||||  ||||||||||| | ||||   | |||||  | || || |||||  | ||||||||||||||||||||||| ||||||||  |||||
-----------gtgcttttttttat-tggttgagttcaattgctcgttaattcgcacatttttgtggttattgttgaaat-tgggatttttgtttgtcagGGCTGGTGAGTTGACTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTGGCGAACCCTAGGCAGTTCAAGATCCCAGACTGGTTTTTGAACAGAAAGAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0072g00060.t01 (Vitis vinifera), 3'ss of exon 3
---atctctagatcatagatcggcgcatattattgtgtctcgtagtttgcaaattgtgttgctttgtgggagattgttgtcttatatgatgtatgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGCAAACCCACGTCAGTTCAAGATCCCAGACTGGTTCTTGAACAGGCAGAAG
      |  | ||  ||  |  |    |||  || | ||| |||   ||  || | | |       |  ||  ||| | ||| |  || | ||    |  |||||||||||| ||||||||||||||| | || |||||||||   || ||||| || ||  | || ||||| || || |||||||| ||||| ||| | |||
gagggattcatatt-tatgtttgtctttatgtttttatct-gtaacatgttaagtttttcaaagcatctgat-ttgctatctgaattggtttaatgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGCTAATCCTAGGCAATTCAAAATTCCTGACTGGTTTTTGAATAGGAAAAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EDP08449 (Chlamydomonas reinhardtii), 3'ss of exon 1
atctctagatca--tagatcggcgcatatt--attgtgtctcgtagtt-tgcaaattgtgttgctttgtgggagattgttgtcttatatgatgtatgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGCAAACCCACGTCAGTTCAAGATCCCAGACTGGTTCTTGAACAGGCAGAAG-----
      || ||   | | || ||    | |  || | || ||   | |  |    |       |||   |||     | |  |       |  || || | |||||      ||||  || || | |||| | ||   | | |||   ||||| || ||||| ||   || ||||||||| ||||||||| ||||||||||||||     
-----aaggtccactggctctgcatgcagtgcatggcgtttcagggctgcggctgtcccaccacttaacgggcatccgctcacacgggcaaactacgtgtcacagG-----CGAGTGCTCGGCCGATGAGCTGGAGCGCATGATGGGCATCGTCGCGAACCCCCGCGCGTACAAGATCCCCGACTGGTTCCTGAACAGGCAGAAGGACCA

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S14_438V6.1 (Physcomitrella patens), 3'ss of exon 2
atctctagatcataga-tcggcgcatattattgtgtc-tcgtagtttgcaaattgtgttgctttgtgggagattgttgtcttatatgatgtatgtttaa--cagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGCAAACCCACGTCAGTTCAAGATCCCAGACTGGTTCTTGAACAGGCAGAAG
        || ||  | ||          |    | | ||   ||   |  |         || |       |  |  |    | || || |  |  ||  ||||||||||||| | || ||||||||  | || ||  | |||   || ||||| ||||| || ||||||||| ||||||| ||||||||||| ||| |||| 
--taaggaataatgtagtccttctgcgacaaaaagccatccgtgtgcaccgacgacac-aattcgcaaaccttgctcattaagtttggtgga-atcgaattcagGGCTGGTGAGCTCTCCGCTGCTGAACTCGAGAATTTGATGGTTATTGTTGCCAACCCTCGCCAGTTCAAGGTCCCAGATTGGTTCTTGAATAGGAAGAAA

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S215_71V6.1 (Physcomitrella patens), 3'ss of exon 2
atctctagatcatagatcggcgcatattattgtgtctcgtagtttgcaaattgtgttgctttgtgggagatt--gttgtcttatatgatgtatgtttaa--------cagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGCAAACCCACGTCAGTTCAAGATCCCAGACTGGTTCTTGAACAGGCAGAAG
         | || | |    | || |||  || ||  ||  ||||     | |     || ||| ||  |     ||||| || |  ||| | | |||        |||||| || ||| | || || || ||| | || ||| | |||   || ||||| ||||| || ||||||||||| ||||| ||||||||||||||| | || 
--------cttattgtttatgggat-ttagggtttcgtgtcttttgtgt-ctctacgagttcgtgagaactccgaatgtctcatctcgtgtttctctaaatcacgtgcagGGCCGGCGAGCTTTCCGCAGCAGAGCTGGAGAACTTAATGGTGATAGTTGCTAACCCTCGCCAGTTCAAGATTCCAGATTGGTTCTTGAACAGGAAAAAA

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S72_222V6.2 (Physcomitrella patens), 3'ss of exon 2
atctctagatcatagatcggcgcatattattgtgtctcgtagtttgcaaattgtgttgctttgtgggagattgttgtcttatatgatgtatg--tttaaca--gGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGCAAACCCACGTCAGTTCAAGATCCCAGACTGGTTCTTGAACAGGCAGAAG
      |||| |   ||    |    | | |   |   | |  ||   | ||| |       |  |   ||   | |  |  |  || |  |  || || |  ||||||| ||| | || || |||||| | || ||||| |||   |||||||| ||||| ||||| |||||||||||||||||||||||||||||| |||| 
---ctgagattaggaattc-tgtgagtgagtccatgatgaacgttttcagttgagagaaaccgatgacaatcactcttattcagcatctcggaattgaatatagGGCTGGCGAGCTCTCCGCAGCTGAGCTCGAGAACCTGATGGTCATCGTTGCTAACCCTCGTCAATTCAAGATCCCAGACTGGTTCTTGAACAGGAAGAAA

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ22352 (Selaginella moellendorffii), 3'ss of exon 2
-------------------------------------------------------------------------------------atctctagatcat--agatcggcgcatattattgtgtctcgtagtttgcaaattgtgttgctttgtgggagattgttgtct---tatatgatgtatgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGCAAACCCACGTCAGTTCAAGATCCCAGACTGGTTCTTGAACAGGCAGAAG
                                                                                      |  || |||| |   ||| |    || | |   | |    |  |||| |||      | || ||      ||| || | |   | | |    |   |  ||||||||||||||| |  ||||||| ||| | || |||||||||   |||||||| ||||| || |||||||||||||| ||||||||| | |||||| |||||
gtatgtttgccctttcttttcctcttgctctgctggtgagctgaaagatcttgttttctcgtcattttcttctatggatgactatcttccttgatctttcggattgattgat-tgagcttcttcattgatttgaaaaaaaaaat-ctgtgcttatcatttttctttgtttctttctcttccatcgaacagGGCTGGTGAGCTCACTGCTGCGGAGCTCGAGAACCTCATGGTGATCGTTGCCAACCCCCGCCAGTTCAAGATCCCCGACTGGTTCCTCAACAGGAAGAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 2
atctctagatcatagatcggcgcatattattgtgtctcgtagtttgcaaattgtgttgctttgtgggagattgttgtcttatatgatgtatgttt-aacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGCAAACCCACGTCAGTTCAAGATCCCAGACTGGTTCTTGAACAGGCAGAAG
  ||  |  |    ||| |    ||     |   ||    | ||   |||     |   |   |   |  ||  | | ||   |  | |  | |  ||||||||||||||| |  ||||||| ||| | || |||||||||   |||||||| ||||| || |||||||||||||| ||||||||| | |||||| |||||
-ccttgatctttcggattgattgattgagcttcttcattgatttgaaaaaaaaaatctgtgcttatcatttttctttgtttctttctcttcgatcgaacagGGCTGGTGAGCTGACTGCTGCGGAGCTCGAGAACCTCATGGTGATCGTTGCCAACCCCCGCCAGTTCAAGATCCCCGACTGGTTCCTCAACAGGAAGAAG

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|164153103|gb|EL993293.1|EL993293
EST:     GAAGGCTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
genomic: GAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
EST: gi|125264893|gb|EL278978.1|EL278978
EST:     CTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
genomic: CTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
EST: gi|86077988|gb|DR373745.1|DR373745
EST:     CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
genomic: CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
EST: gi|116431165|gb|EG473757.1|EG473757
EST:     CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
genomic: CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
EST: gi|164078765|gb|ES133277.1|ES133277
EST:     CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTGC
genomic: CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTGC
EST: gi|164184060|gb|ES091101.1|ES091101
EST:     CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAG                         GGAACTGGTGAGTTATCTGC
genomic: CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGG--CTGGTGAGTTATCTGC
EST: gi|86081140|gb|DR376897.1|DR376897
EST:     ACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
genomic: ACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGC
EST: gi|125049263|gb|EL121532.1|EL121532
EST:     CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTG
genomic: CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTG
EST: gi|164029431|gb|ES175245.1|ES175245
EST:     CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAG                         GGCTGGTGAGTTATCTGC
genomic: CGATTGGCTAACATTGTCTGCAAGAAGGCTGATGTCGACATGAACAAAAGgtttgagctt ... tgtttaacagGGCTGGTGAGTTATCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaattgtgttgctttgtgggagattgttgtcttatatgatgtatgtttaacagGGCTGGTGAGTTATCTGCTGCTGAGATTGATAACCTCATGACAATCGTTGCAAACCCACGTCAGTTCAAGATCCCAGACTGGTTCTTGAACAGGCAGAAG
                                 ttatatgat  TA-rich tract