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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttgatttgatatgttcttcattattttgttcaaattctggtttaatgtttgttgatgattccttaaacttgttgttgcttttgcgcagTTGTTGATTAAAGGATCTGCTGAACGTGGTGCTAAGAGAATCAGAGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTTGGATTTG

Basic information

species Arabidopsis thaliana
transcript AT1G09780.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g40420.1 (Oryza sativa), 3'ss of exon 4
-----------------gttttgatttgatatgttctt---cattattttgttcaaattctggtttaatgtttgttgat-------------gattccttaaacttgttgttgcttttgc--gcagTTGTTGATTAAAGGATCTGCTGAACGTGGTGCTAAGAGAATCAGAGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTTGGATTTG
                   | |  |||| |||  ||||    | |||   |  | |||  |  ||||     |||||||              |||| ||     | ||||   |  ||     ||||| |  | || ||  |   ||    ||| || || | |||| | || || |||||||||||||| |||||||||||||||||  | || ||||| ||||
gtataaaagtactcttttctatagtttgctatcatcttgtatagtatgaggcactaatgtttctttacaacatgttgatctgtccagtatctaattctttttgtcttttgtcattcctgtttatagTTGCTCCTGAATGGTGCAAGTGCGAATGGAGCGAAAAAAATCCGTGTTCACATTCTTACTGATGGACGTGATGTTTTGGATGGCACAAGCGTTGGTTTTG

upper sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 4
gttttgatttgatatgttcttcattattttgttcaaattctggtttaatgtttgttg-atgattcctta-aacttgttgttgcttttgcgcagTTGTTGATTAAAGGATCTGCTGAACGTGGTGCTAAGAGAATCAGAGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTTGGATTTG
       |||| ||   | ||| || ||   || |    |||||| | |   ||    | ||||   || || || ||   |  | |   |||||  |  | |||||      |||  | || || || | |||| | || || || ||||||||||| |||||||||||||||||    ||| |||| || |
------gtttgctaa--tattctttcttcaatttag--cctggttcagttactgccacaagatttactataatttttttggggctctatccagTTACTTCTGAAAGGTGTCAGTGAGAGAGGGGCGAAAAAAATCCGTGTGCACATCCTTACTGATGGACGTGATGTTTTGGATGGAAGCAGTATTGGTTTCG

upper sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G833389_T01 (Zea mays), 3'ss of exon 4
gttttgatttgatatgttcttcattattttgttcaaattctggtttaatgtttgttg-atgattcctta-aacttgttgttgcttttgcgcagTTGTTGATTAAAGGATCTGCTGAACGTGGTGCTAAGAGAATCAGAGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTTGGATTTG-----------------------------------------------------------------------------------------
       |||| ||   | ||| || ||   || |    |||||| | |   ||    | ||||   || || || ||   |  | |   |||||  |  | |||||      |||  | || || || | |||| | || || || ||||||||||| |||||||||||||||||    ||| |||| || |                                                                                         
------gtttgctaa--tattctttcttcaatttag--cctggttcagttactgccacaagatttactataatttttttggggctctatccagttacttctgaaaggtgtcagtgagagaggggcgaaaaaaatccgtgtgcacatccttactgatggacgtgatgttttggatggaagcagTATTGGTTTCGTGGAGACCCTAGAGAATGATCTTTTGGAGCTTAGAGCGAAGGGTGTTGATGCACAAATTGCATCTGGTGGTGGAAGGATGTATGTTACG

upper sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 3
gttttgatttgatatgttcttcattattttgttcaaattctggtttaatgtttgttgatgattccttaaacttgttgttgcttttgcgcagTTGTTGATTAAAGGATCTGCTGAACGTGGTGCTAAGAGAATCAGAGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTTGGATTTG
            |   || ||     ||    |    ||    | |  ||| |   | | |||| ||  |  |     |  |||||  ||||||||| ||||||||  |   || || |||| ||| ||| || | |||||||||||||| ||||| |||||||||||||||||||| ||||| || ||||
-----------gtg-attatttggggttggagttgtttttccttcttgtgtatacagtttattctttctaacta--agtatttttgtacagTTGTTGCTTAAAGGAGTTAGCGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATGGTTCAAGTGTGGGGTTTG

upper sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G45120.1 (Glycine max), 3'ss of exon 4
gttttgatttgatatgttcttcattattttgttcaaattctggttta-atgtttgttgatgattccttaaacttgttgttgcttttgcgcagTTGTTGATTAAAGGATCTGCTGAACGTGGTGCTAAGAGAATCAGAGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTTGGATTTG
              || |  |      || |  |   || |  || |  ||| |   | | |||| ||  |  |     | ||||||  ||||||||| ||||||||  |  ||| || |||| ||| ||| || | |||||||||||||| ||||| ||||||||||||||||                  
-------------gtgattatttggggttggagctgtttttccttcatgtgtattcagtttattctttctaacta--actacttttgtacagTTGTTGCTTAAAGGAGTTAGTGAGCGAGGTGTTAAAAGAGTCCGTGTCCATATTCTTACAGATGGCCGTGATGTTTTGGATG------------------

upper sequence: AT1G09780.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 3
gttttgatttgatat-gttcttcattattttgt--tcaaattctggtttaatgtttgttgatgattccttaaacttgttgttgcttttgc-----gcagTTGTTGATTAAAGGATCTGCTGAACGTGGTGCTAAGAGAATCAGAGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTTGGATTTG
  | || |||| | | |   |  ||||  ||||  |   ||   | |||    ||    |  ||   | | | | | || | |||||| |     ||||||  |  | |||||| ||  |||   |||||| || |||||| | |||||||| ||||||||||| |||||||||||||||||||| |||||||| ||||
-gtatgttttgttgttgaattctattaccttgtgattggatatagttttgtatttcccaggggagatcatgatcctctt-tggctttttctcttggcagTTACTTTTAAAAGGAGCTAGTGAGAATGGTGCAAAAAGAATCCGTGTCCATATCCTTACTGATGGGCGTGATGTTTTGGATGGTTCCAGTGTTGGGTTTG

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|301501920|gb|HO207460.1|HO207460
EST:     TTGGACTTCTCAGTGACGGTGGAGTTCACTCTCGTCTCGATCAACTACAG                         TTGTTGATTAAAGGATCTGCTGAACGTGGTGCTAAGAGAATCAGAGTCCAT
genomic: TTGGACTTCTCAGTGACGGTGGAGTTCACTCTCGTCTCGATCAACTACAGgttttgattt ... ttttgcgcagTTGTTGATTAAAGGATCTGCTGAACGTGGTGCTAAGAGAATCAGAGTCCAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctggtttaatgtttgttgatgattccttaaacttgttgttgcttttgcgcagTTGTTGATTAAAGGATCTGCTGAACGTGGTGCTAAGAGAATCAGAGTCCATATTCTTACTGATGGTCGTGATGTTTTGGATGGTTCTAGTGTTGGATTTG
                tgttgat  putative branch site (score: 4)
                                         ttgctttt  putative PPT
       tttaatgttt  TA-rich tract