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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgatttattagatactaatacttataagactatataaaaaataaactatgtgctttagagattaattatctttgtactttatgtttctatagATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGGAATCCTTGTCCGCGGGCATATTACCGCTGCACGATGGCCACGGGCTGTC

Basic information

species Arabidopsis thaliana
transcript AT1G62300.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G62300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g14440.1 (Oryza sativa), 3'ss of exon 3
gtaagttgatttattagatactaatacttataagactatataaaaaataaactatgtgctttagagattaattatctttgtact--ttatgtttctat--agATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGGAATCCTTGTCCGCGGGCATATTACCGCTGCACGATGGCCACGGGCTGTC
             | |||  | |  |||   ||  | | ||  |  | |  |  | |    | ||||     |   ||   | |  || || |||  |  ||||   |||||| || |||||||| || || || ||||||||||| || || || |||||||| || || || ||||||||||| |||||||| ||||| |
------------gtaagaccccaccactagcaa--ccacatcgatcacaggcattttctcatcgagacgtgctgaattccaaatcgttttggttccgtgcagATCGCCGATGGGTGCCAATGGAGGAAGTACGGTCAGAAGATGGCGAAGGGAAACCCTTGTCCACGCGCGTACTACCGCTGCACCATGGCCACCGGCTGCC

upper sequence: AT1G62300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G43260.1 (Glycine max), 3'ss of exon 2
----gtaagttgatttattagatactaatacttataagactatataaaaaataaactatg--tgct-ttagagattaattatctttgtactttatgtttctatagATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGGAATCCTTGTCCGCGGGCATATTACCGCTGCACGATGGCCACGGGCTGTC
    ||| ||  | ||     || ||   | ||| ||   | |     | |||   |||   ||||  |||| ||||||| |||||  |  | |  |    | |||||   |||||||||||||||||||| ||||| ||||||||||| ||||||||||| ||||||||  | ||||| || ||| | ||||  || |  ||||
ttttgtatgtgaagttgc---attctttgagttaaaaatttctggtcgatatatcttatacctgctactagatattaattttcttttca--tcaattcatgacagATATCAGATGGATGTCAATGGAGAAAGTATGGACAGAAGATGGCAAAAGGGAATCCATGTCCGCGATCTTATTATCGTTGCTCAATGGGGACTGCTTGTC

upper sequence: AT1G62300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G46280.1 (Glycine max), 3'ss of exon 4
----gtaagttgatttattagatactaatacttataagactatataaaaaataaactatgtgctttagagattaattatctttgtactttat--gtttctatagATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGGAATCCTTGTCCGCGGGCATATTACCGCTGCACGATGGCCACGGGCTGTC
    |||| ||   |   |  |   |   ||  || |   | |      |  |||  |  |   |||    |||||| | | ||   |  ||   ||   | ||||    |||||||| ||||||||||| ||||| ||||||||||| |||||||||||||| ||  | || ||||| || ||||| |||   || || ||||
ggatgtaatttacgtgggtgaa-gtttgcacgcattaatttcttgtttcatgaaaacacat---ttacgtgttaattttatgtgggatgaatttattataacagATTGCAGATGGATGCCAATGGAGAAAGTATGGGCAGAAGATGGCGAAAGGGAATCCTTGGCCAAGAGCCTATTATCGTTGCACAATGAGTACTGGTTGTC

upper sequence: AT1G62300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G17800.1 (Glycine max), 3'ss of exon 5
gtaagttgatttattagatactaatacttataagactatataaaaaataaactatgtgctttagagattaattatctttg---------tactttatgtttctatagATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGGAATCCTTGTCCGCGGGCATATTACCGCTGCACGATGGCCACGGGCTGTC
     |  || ||| | |||   ||   |  |   |  ||  |||||| || |||   | ||  |||  || ||| |  |         | | |||| | | |  ||||  | ||||| |||||||||||||||||||| || |||||  | || || ||||||||||| ||||| ||||| |||||||  ||||  || |  ||||
-----tatatatat-atatatatatttgtgcattgcactaataaaaatgaaatattgacattgaagaa-aactatttacgataatgcattgccttatatattttcagATGGGTGATGGGTGTCAATGGAGAAAATATGGACAAAAGATATCAAAGGGCAATCCTTGTCCTCGGGCCTATTATCGCTGCAACATGGGAACTGCATGTC

upper sequence: AT1G62300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0090g00840.t01 (Vitis vinifera), 3'ss of exon 4
-gtaagttgatttattagatactaatac-ttataagactatataaaaaataaactatgtgctttagagattaattatctttgtactttatgtttctata--gATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGGAATCCTTGTCCGCGGGCATATTACCGCTGCACGATGGCCACGGGCTGTC
  | | |     | |    |  |  ||  ||  |||| |   ||      ||| |||     | |  | || |  ||      |  |||     |||||  |||   ||||||||| ||||||||||| ||||| || |||||||| ||||| || || || || || || ||||| || ||||| ||||| || |  ||||
tttcaatcacaatctggactgtttgtagattggaagattcagtactc--caaattataaaaataaatgtttgaccattggccgatcttaatccactatacagATCTCCGATGGATGCCAATGGAGAAAGTATGGACAAAAGATGGCGAAAGGAAACCCATGCCCTCGAGCTTATTATCGATGCACCATGGCAACTGCTTGTC

upper sequence: AT1G62300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S158_166V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------gtaagttgatttattagatactaatacttataagactatataaaaaataaactat--gtgctt--tagagattaattatctttgt------actttatg-----tttctatagATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGGAATCCTTGTCCGCGGGCATATTACCGCTGCACGATGGCCACGGGCTGTC
               ||  || |  |  |||  | | || |  |  |    |        | |    | |    ||||   || | ||  |    | | |      ||   |||     ||| |  |||| | ||| ||||| || ||| | || || || ||||||||||| ||||||||||| ||||| || ||||| ||||| |||||  | ||  | || || |
gtacgttctcattttgtttgtgggatccttacctgc-aacatgtgcagagttcggcgcctacttgcgtgttgacgcttgccagcgtttgttcggttctatgaagtaacaccatgaatcgttttttcagATGAACGACGGATGCCAGTGGCGGAAGTACGGTCAGAAGATGGCTAAAGGGAATCCCTGTCCTCGTGCATACTACCGTTGCACTGTTGCGCCTGGGTGCC

upper sequence: AT1G62300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S246_89V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------gtaagttgatttattagatact--------aatacttataagactatataaa-------aaataaactatgtgctttagagatta-attatctttgtactttatgtt-tctatagATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGGAATCCTTGTCCGCGGGCATATTACCGCTGCACGATGGCCACGGGCTGTC
                  | |  |  || |  || ||||        | | ||| |    ||  | |         ||  |    || ||  | ||    |  |||| | | ||    ||| || | |  |||| | ||| ||||| || |||||||||||||| ||||||||||| |||||||||||||| || || |||||||||||||||||  |     | |||||||
gtgagaacttggagttctttaaatacttcaacagctactctcatcgcattgcttttgtagcttcaaagccagctttaagcagttgatatgtgtaagtccctggattaacatggtgagatattttgttttcagATTAACGACGGATGCCAGTGGAGAAAATATGGTCAGAAGATGGCTAAAGGGAATCCTTGCCCTCGCGCATATTACCGCTGCACTGTTATGTCTGGCTGTC

upper sequence: AT1G62300.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S47_251V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------gtaagttgatttattagatactaatacttataagactatataaaaaata--aactatgtgcttta---gagattaattatct----ttgtactttatgtttctatagATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGGAATCCTTGTCCGCGGGCATATTACCGCTGCACGATGGCCACGGGCTGTC
                      | |   |  | ||   | |  ||| | | |  |    ||  |     |   | |  |  | ||||   | |    || ||||    |  |  ||||| | | | ||||| |  || ||||| || ||||| |||||||| ||||||||||| |||||||| || ||||| || ||||| ||||| |||||  | ||  |||||||||
gtacgttcctgtccttttcatagaacccttctctacacgcttttaaaattcagcaccggattcagtgcttttcatcgttaaggtttaatcgggtcccatgatctcacatgatgatttatctgttt-tagATCAATGACGGATGCCAGTGGAGGAAATATGGTCAGAAGATGGCGAAAGGGAACCCCTGTCCTCGTGCATACTACCGATGCACCGTTGCGCCGGGCTGTC

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|124816496|gb|EH901362.1|EH901362
EST:     CTCCGTTCGTGCCCGATCGGAAGCTCCGATG                         ATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGG
genomic: CTCCGTTCGTGCCCGATCGGAAGCTCCGATGgtaagttgat ... gtttctatagATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaataaactatgtgctttagagattaattatctttgtactttatgtttctatagATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGGAATCCTTGTCCGCGGGCATATTACCGCTGCACGATGGCCACGGGCTGTC
                      gattaat  putative branch site (score: 3)
                                            tgtttct  putative PPT
                       attaattatctttgta  TA-rich tract