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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataatgcttacaatatggctgatatcgctacaccaaaaccctattaatccataccataaaaaatgcaacgcaaactcttgaggcctaaatcttatagattaacatacagttgtatatatctgatgaagcgtttatatatgtgatacattgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTTCCATTCTTCTACTCTCGCTCCTTTGATCTCTCATGGCAGTTCTACGGAG

Basic information

species Arabidopsis thaliana
transcript AT3G52880.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52880.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv08s0007g03610.t01 (Vitis vinifera), 3'ss of exon 9
gtaaataatgcttacaatatggctgatatcgctacaccaaaaccctattaatccataccataaaaaatgcaacgcaaactcttgaggcctaaatcttatagattaacatacagttgtatatatctgatgaagcgtttatatatgtgatacattgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTTCCATTCTTCTACTCTCGCTCCTTTGATCTCTCATGGCAGTTCTACGGAG
                                                          | |      ||| | |   | || | |||     |   |||| ||||  |||    | | ||    |||   || |  | ||  | ||     ||   |||||| ||||| ||   ||||| |||   | | || ||||| || ||||| ||||||| ||||||||||||  |||||||||| || ||||||||||| || |
----------------------------------------------------------ctttttttctgccatgatcattccttaggtgctcaaaatatacattag-atatgcatttttaggagtgaatcagtgaat-tacttctggcttgtttatgcagGCAATCAAGGCAAGTGAGGAAGGGAAATCAGTTGAGGAGTATGACTACCTTCCATACTTCTACTCTCGTGCCTTTGATCTGTCCTGGCAGTTCTATGGTG

upper sequence: AT3G52880.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S90_28V6.4 (Physcomitrella patens), 3'ss of exon 10
gtaaataatgcttacaatatggctgatatcgctacaccaaaaccctattaatccataccataaaaaatgcaacgcaaactcttgaggcctaaatcttatagattaacatacagttgtatatatctgatgaagcgtttatatatgtgatacattgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTTCCATTCTTCTACTCTCGCTCCTTTGATCTCTCATGGCAGTTCTACGGAG
                          ||| | ||  ||     | | |   || |     |    |||| |     |  |   | ||  |    ||| |  || |  ||| | || |   ||||||||     | || |  ||   | | |||  |||||||||||||||| ||||||   |||| ||  ||||| || ||||| || || |||||||||||||| ||||||||  |||| || |||||||||||||| |
-------------------------gtat-gttatcccgtttgcttgtacttcgacgatcttttgaatgaag----aggttcagtggtttgtgacttctctatgaggata-attttt---tatctgata----gcttgtgaat-caaca-atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTCCCATTCTTCTACTCCCGCTCCTTCAATCTGTCGTGGCAGTTCTACGGCG

upper sequence: AT3G52880.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S211_74V6.2 (Physcomitrella patens), 3'ss of exon 10
gtaaataatgcttacaatatggctgatatcgctacaccaaaaccctattaatccataccataaaaaatgcaacgcaaactcttgaggcctaaatcttatagattaacatacagttgtatatatctgatgaagcgtttatatatgtgatacattgtgg-cagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTTCCATTCTTCTACTCTCGCTCCTTTGATCTCTCATGGCAGTTCTACGGAG
|||  || ||||     |||| || |||||  |  |   ||     | |||  ||   | |      | |      |   |||| |   ||    ||  |  ||||  |||   || | |   || ||  |  |||  |  |    |   ||||||  ||||| |||||||| || |||   |||| ||  ||||| || ||||| || || || |||||||||||||||||||| ||||| || |||||||| || || |
gtatgtagtgctc----tatg-cttatatc--tgaattgaa---tcagtaaatcactacgtg---ccttctttatgacaccttggg---tatgctttgcac-ttaatttac---tggaaagtcctaatacattgttc-tgca---aactgattgtgaacagGCTATCAAAGCTGCAGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTGCCTTTCTTCTACTCTCGCTCCTTCGATCTGTCGTGGCAGTTTTATGGCG

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|86078827|gb|DR374584.1|DR374584
EST:     GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
genomic: GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
EST: gi|47828341|gb|CK118025.1|CK118025
EST:     GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
genomic: GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
EST: gi|125217538|gb|EL231621.1|EL231621
EST:     GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAG
genomic: GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAG
EST: gi|47828077|gb|CK117761.1|CK117761
EST:     GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
genomic: GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
EST: gi|125272888|gb|EL286973.1|EL286973
EST:     TGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAGGCGTAGCGGTGGAGGAATACGACTATCTT
genomic: TGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
EST: gi|47829815|gb|CK119499.1|CK119499
EST:     GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
genomic: GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
EST: gi|125020210|gb|EL092479.1|EL092479
EST:     GTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
genomic: GTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
EST: gi|47830852|gb|CK120536.1|CK120536
EST:     GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAG                         GCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT
genomic: GGGTCGAGCATGTTGACCATTCCCGCAAATCAGCAGAGCAAGCTGTTAAGgtaaataatg ... attgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatacagttgtatatatctgatgaagcgtttatatatgtgatacattgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTTCCATTCTTCTACTCTCGCTCCTTTGATCTCTCATGGCAGTTCTACGGAG
                             tttatatatgtgata  TA-rich tract