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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatccacatgagccgttccataattttcatttatttattttgattgtttctggatattgagtttcagatgcttatgttttgtggcagTTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGTGAATGGGATCAATTTGAGTGGTCAAAAACTGCAATTCATGTTAGTGCAA

Basic information

species Vitis vinifera
transcript Vv06s0004g02700.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------------------------------------gtcatccac-atgagccgttccataattttcatttatttattttgattgtttctggatattgagtttcagatgcttatgttttgtggc--agTTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGTGAATGGGATCAATTTGAGTGGTCAAAAACTGCAATTCATGTTAGTGCAA
                                                                                                   |  || || || || | | | || ||  | |   | |||  |      | | |    ||| |  |||| ||    |||  || |     ||||||| ||  | |||  |||| || | || |||||||||||||| || | ||| |||||| ||||||||||||||||||  || |||||||| ||||  |
gtaattacttagacaactagcatgtgtaaactgattgcattgaataagcatacaattgctttgttcaaaatagtcttcagaatagaaaaaaaaaacttatgttcaactataaggcat-ctatcatgcttaaacagttaactgagacatctat---cattca-cttcaaatttacatgccttattatatagTTTTCAGAAAACTTCACAATTATGTTGTTCCACTATGATGGTCGGACTAATGACTGGGATGAATTTGAGTGGTCAAAAAGGGCCATTCATGTGAGTGTCA

upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 6
gtcatccacatgagccgttccataattttcatt-tatttattttgattgtttctggatattgag---tttcagatgctta------tgtttt------gtggcagTTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGTGAATGGGATCAATTTGAGTGGTCAAAAACTGCAATTCATGTTAGTGCAA
          || | | ||  | | ||| | || |||||| ||| |      |  || ||||     | |||  ||| ||      | ||||      || ||||||||||||  ||||    ||  || | |||||||||||||||||    |||||||||||| ||||||||||||||||    || || |||||||||| | 
-----atgtttgtgtcattggacactttactttgtatttaatttaaacacaccatgaaattgtaacttgtcaattgcctaatcttttatttttctgctgttgcagTTTTCTGATAATTTTGCTATCCTGTTATTTCACTATGATGGTCGGGTGAGTGAATGGGATGAATTTGAGTGGTCAAAGCGAGCTATACATGTTAGTGTAC

upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM5G801369_T01 (Zea mays), 3'ss of exon 6
gtcatccacatgagccgttccataattttcatttatttattt--tgattgtttctggatattgagtttcagatgcttatgttttgtggcagTTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGTGAATGGGATCAATTTGAGTGGTCAAAAACTGCAATTCATGTTAGTGCAA
          | || | | | | |   || |  |||        ||||   || | | | || || |||| ||   | |  | |    |||||||| ||  | |||  |||| || | || || ||||||||||| |||| ||| |||||| ||||||||||||||||||  ||  | ||||| ||||  |
---------gtaagacatcctaaatgcttaaaatatgcgaggaatgatatattgtagtttttcagattcacatatgtcttctcta---cagTTTTCAGATAACTTCACAATTATGTTGTTCCATTATGATGGTCGGACAACTGAGTGGGATGAATTTGAGTGGTCAAAAAGGGCCGTCCATGTGAGTGTCA

upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 6
gtcatccacatgagccgt-tccata-attttcatttattt--attttgattgtttctggatatt----gagtttcagatgcttatgttttgtggcagTTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGTGAATGGGATCAATTTGAGTGGTCAAAAACTGCAATTCATGTTAGTGCAA
|| ||  | ||   |    | |||| ||    ||||||||  || |  |   |||||   | |      | || | ||   | |  || |   | |||||||||| |||||   ||||||||| ||||| ||||||||||| || ||||||||||||||||||||||||||||  | |||||| |||||||||||||
gttattgagattgactaccttcatatataagaatttatttgtatatctaccatttcttattttcttcaaaattgctgactatcaaattgttctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAATGCAATCCATGTTAGTGCAA

upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 6
gtcatccacatgagccgt-tccata-attttcatttattt--attttgattgtttctggatatt----gagtttcagatgcttatgttttgtggcagTTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGTGAATGGGATCAATTTGAGTGGTCAAAAACTGCAATTCATGTTAGTGCAA
|| ||  | ||   |    | |||| || |  ||||||||  || |  |   ||||    | |        || | ||   | |  || |   | |||||||||| |||||   ||||||||| ||||| ||||||||||| || ||||||||||||||||||||||||||||  | |||||| ||||| || ||||
gttattgatattgactaccttcatatatatgaatttatttgtatatctaccatttcatattttcttcaagattgctgactatcaaattgttctgtagTTTTCTGATGATTTTGCAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAA

upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 6
-gtcatccacatgagc-cgttccataattttcatttatttattttgattgtttctggata---ttgagtttcagatgcttatgttttgtgg-cagTTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGTGAATGGGATCAATTTGAGTGGTCAAAAACTGCAATTCATGTTAGTGCAA
  ||  | | || |||  ||    ||      |||  ||||| |  ||| ||| ||||||   |    |||    |  |  |||  | |   ||||||||||| ||||||||||||||||| || || |||||||| || |||| ||||||||| |||||||||||||| || |  || |||||| ||||| |||
gttctgcaatatcagcatgtgttttagcaagtattgttttatat--attctttgtggatacactcagattttttgttttcttgtcatatcttcagTTTTCTGAAGATTTCCAAATTTTGCTCTTCCATTATGATGGCCGGACAACTGAATGGGACCAATTTGAGTGGTCGAAGAGCGCGATTCATATTAGTACAA

upper sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 6
gtcatccacatgagccgttccataattttcatttatttattttgattgtttctggatattgagtttcagatgcttatgttttgtggcagTTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGTGAATGGGATCAATTTGAGTGGTCAAAAACTGCAATTCATGTTAGTGCAA
    ||  ||  |     |||    || |   | |  ||||| || | ||      ||  || |||    | | |     |||   ||||||||||| ||||||||||| ||| | || || |||||||| ||||||| ||| ||||| || ||||||||||| |||| |||||| ||| | |||||||
--gttctgcaacaatttctcccctcttgtttgtaaactattt-gagtattgacacttaaagatttttgctttcatcatcattgcttcagTTTTCTGAAGATTTCCAAATATTGTTATTCCATTATGATGGCCGAACAACTGAGTGGGACCAGTTTGAGTGGTCTAAAAATGCAATACATATCAGTGCAA

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|37184080|gb|CF603434.1|CF603434
EST:     TTACAGTTGGTCTTGATCAACGGAAAAATATTGATGAATCAGTTAAAAAG                         TTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGT
genomic: TTACAGTTGGTCTTGATCAACGGAAAAATATTGATGAATCAGTTAAAAAGgtcatccaca ... tttgtggcagTTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGT
EST: gi|161717256|gb|FC067262.1|FC067262
EST:     TTACAGTTGGTCTTGATCAACGGAAAAATATTGATGAATCAGTTAAAAAG                         TTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAAACA-G
genomic: TTACAGTTGGTCTTGATCAACGGAAAAATATTGATGAATCAGTTAAAAAGgtcatccaca ... tttgtggcagTTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAA-CAAG
EST: gi|110687082|gb|EE064179.1|EE064179
EST:     TTACAGTTGGTCTTGATCAACGGAAAAATATTGATGAATCAGTTAAAAAG                         TTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGT
genomic: TTACAGTTGGTCTTGATCAACGGAAAAATATTGATGAATCAGTTAAAAAGgtcatccaca ... tttgtggcagTTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttattttgattgtttctggatattgagtttcagatgcttatgttttgtggcagTTTTCTGAGGATTTCCAAATTTTGCTTTTTCACTATGATGGTCGAACAAGTGAATGGGATCAATTTGAGTGGTCAAAAACTGCAATTCATGTTAGTGCAA
     ttttgat  putative branch site (score: 4)
                                       ttatgtttt  TA-rich tract