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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatgaatatttgataccggagtagttcctttatttcataccatgttttttcctcttcatgtttgataataagattgagaaactgtagGTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTATATGTACACTGATCTTGCAACTATTTATGAACGTGCTGGGCGTATAGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G76030.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 9
---------gtaaaatgaatatttgataccggagtagttcctttatttcataccatgttttttcctcttcatgtttgataataagattgagaaactgtagGTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTATATGTACACTGATCTTGCAACTATTTATGAACGTGCTGGGCGTATAGAAG
          | |  |     |   |||   ||  | || ||  | ||      ||  |  ||     | ||     |   |||   ||   |  ||||||| || || ||||||||||| || || || || ||||| ||||| || |||||||| |||||||| ||||| || ||||| || ||||||||||| ||||
acatctccttttatgttcgactgcaataaatgataaattgctgaaattttatttattgtgattggcactaatacaacacggtaattgtgcttatatgtagGTATCAGCAGCCCGAGAAGAAGTGCCAGGTAGGCGTGGGTATCCTGGATATATGTATACTGATCTGGCAACCATATATGAGCGAGCTGGGCGTATTGAAG

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 9
-----gtaaaatgaatatttgataccggagtagtt---cctttatttcataccatgttttttcctcttcatgtt-tgataataagattgagaaact-gtagGTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTATATGTACACTGATCTTGCAACTATTTATGAACGTGCTGGGCGTATAGAAG
      ||| || ||  |||| ||     ||| |       | | || ||  |||||||  |  |  | ||  |   | |     |||| |    | ||||||||| || |||||||||||||| || || || ||||| ||||| || |||||||| |||||||| ||||| || ||||| |||||||||||||| ||||
agtatttaagatcaacctttg-tatttaggtaatcaaatggtaaattgatttcatgtttgatgtttctaataatgctacatgggcattgtgctttttgtagGTTTCTGCAGCCCGAGAAGAGGTGCCAGGTAGGCGTGGTTATCCTGGATATATGTATACTGATCTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAG

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 9
----------gtaaaatgaatatttgataccggagtagttcctttatttcataccatgttttttcctcttcatgtttgataataagattgagaaactgtagGTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTATATGTACACTGATCTTGCAACTATTTATGAACGTGCTGGGCGTATAGAAG
           ||| || ||  |||  ||   |  || ||   | |     |    |  || || ||  | ||| |  ||    |   ||      |||||||||| || |||||||||||||| || || || ||||| ||||| || |||||||| |||||| | ||||| || ||||| |||||||||||||| ||||
ttttatatatttaagattaaccttttctattagc-taattaaatgacaaattgatgtcgttgtttctaataatgctacatgggcattgtgcttttttgtagGTTTCTGCAGCCCGAGAAGAGGTGCCAGGTAGGCGTGGTTATCCTGGATATATGTATACTGATTTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAG

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 9
----gtaaaatgaatatttgataccgg-agtagttcctttatttca----taccatgttt--tttcctcttcatgtttgataataagattgagaaactgtagGTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTATATGTACACTGATCTTGCAACTATTTATGAACGTGCTGGGCGTATAGAAG
     ||   |  | | |  |||| |  | | |    | |||| ||    | |||   ||  ||||  || | ||  ||  |||     |    | ||| |||| || || ||||| || || || || ||||| ||||| ||||| || |||||||| |||||||||||||| |||||||| |||||||| ||||||||||
cttcataggttttaaaatc-atacggataatcgaatttctattgcaccattcccacacttactttcacctacttgactggaaatgtctgttttga-ctgcagGTATCTGCAGCCCGGGAGGAAGTACCTGGAAGGCGTGGGTATCCTGGGTATATGTATACTGATCTTGCAACAATTTATGAGCGTGCTGGACGTATAGAAG

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 9
-gtaaaat-gaatatttgat-accggagtagttcctttatttcataccatgttttttcctcttcatgtttgata---ataagattgagaaact---gtagGTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTATATGTACACTGATCTTGCAACTATTTATGAACGTGCTGGGCGTATAGAAG
  |  | | |  || ||  | |    |||| ||       |  ||| |  |  | |   |  | | | |  ||     |    || |   |||     |||| || ||||| || ||||| || |||||  | ||||| || || |||||||||||||| |||||||| || ||||||||||||||||| ||||| || |
gctgcactcggttacttagttaatcaagtattttgaaacctcgatatcgagggtctatgtaatgacgatatatttttgtcgttttcaattacttaaacagGTGTCTGCTGCTCGTGAAGAAGTACCCGGTCGTCGTGGGTACCCTGGTTATATGTACACCGATCTTGCCACCATTTATGAACGTGCTGGACGTATTGAGG

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------------------------gtaaaatgaatatttgataccggagtagttcctttatttcataccatgttttttcctcttcatgtttgataataagat-----tgaga-----aactgt------agGTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTATATGTACACTGATCTTGCAACTATTTATGAACGTGCTGGGCGTATAGAAG
                                                                      | ||  | | | ||  | |         |   |||  ||  | | | || |   ||| ||  | |   | ||| | ||     |  ||     |||| |      ||||||| || || || ||||| || || ||  | ||||||||||| ||||| |||||||| |||||||| |||||||| |||||||||||||| || || |
gtaccagtctttaccttaaagatctgcttgcccttgtggtatggtacttctgactctgtttttggtttttgaaatgttagtgttctaaaaaatgcccctctattttgttggttctaagtctgcacct-ttagtatgccagaatgacatattcttatgatccttaactatgcgaacagGTTTCTGCAGCTCGTGAAGAAGTACCTGGGCGTCGTGGATATCCTGGTTACATGTACACGGATCTTGCCACTATTTACGAACGTGCTGGGCGAATTGAGG

upper sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------------------------------------------------------------------gtaaaatgaatatttgataccggagtagtt--cctttatttcataccat--gttttttcctcttcatgtttgataataagattgagaaactgtagGTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTATATGTACACTGATCTTGCAACTATTTATGAACGTGCTGGGCGTATAGAAG
                                                                                                      |   | | | |||||  | |     ||||    |||| || | ||| |  || |  | |   |  | |    |   ||   |   ||    |||||||| ||||| || ||||| || || ||  | ||||||||||| ||||| ||||| |||||||| || || ||||||||||||||||| || || ||||
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttcagtgtgctacaaattttttccactctcaattcttcaaa----tagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG

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|116457675|gb|EG500267.1|EG500267
EST:     TCCTTGTTATATTGACGGATATGAGTTCTTATGCTGATGCTCTTCGTGAG                         GTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTAT
genomic: TCCTTGTTATATTGACGGATATGAGTTCTTATGCTGATGCTCTTCGTGAGgtaaaatgaa ... gaaactgtagGTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTAT
EST: gi|124918592|gb|EH992416.1|EH992416
EST:     CCTTGTTATATTGACGGATATGAGTTCTTATGCTGATGCTCTTCGTGAG                         GTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTAT
genomic: CCTTGTTATATTGACGGATATGAGTTCTTATGCTGATGCTCTTCGTGAGgtaaaatgaa ... gaaactgtagGTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTAT
EST: gi|125161475|gb|EL188581.1|EL188581
EST:     TTCTTATGCTGATGCTCTTCGTGAG                         GTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTAT
genomic: TTCTTATGCTGATGCTCTTCGTGAGgtaaaatgaa ... gaaactgtagGTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTAT
EST: gi|86066844|gb|DR362601.1|DR362601
EST:     TCCTTGTTATATTGACGGATATGAGTTCTTATGCTGATGCTCTTCGTGAG                         GTTTCCGCTGCCCGAGAAGAGGTTCC
genomic: TCCTTGTTATATTGACGGATATGAGTTCTTATGCTGATGCTCTTCGTGAGgtaaaatgaa ... gaaactgtagGTTTCCGCTGCCCGAGAAGAGGTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcataccatgttttttcctcttcatgtttgataataagattgagaaactgtagGTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTATATGTACACTGATCTTGCAACTATTTATGAACGTGCTGGGCGTATAGAAG
                           gtttgat  putative branch site (score: 5)
                            tttgataataagatt  TA-rich tract