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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggttttcatgtccagaatttcagaaactgtagtatttgtttctctttcttttactatagtactgataaaaataaatggggcaatgtttgtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g00180.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 1
-atggttttcatgtccagaatttcagaaactgtagtatttgtttctctttcttttactatagtactgataaaaataaatggggcaatgtttgtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAG
 |||  |  ||        |        | | |    || ||| | ||      |   || ||  |  | |  ||  ||       | |||   |  | || || || || || || ||||| || ||||||||||| || ||||| || || || ||||||||||| ||||||||||| |||||||||
catgtgtcccactctgtttaagcttatgattcttcctttggttacactcatcagtgaaattgtggtccttattatgcattctcttttattttgatggc-agAAACATCGTATCGACGGTCAATTTGGATTGCAAATTAGACCTCAAAGCTATAGCTTTGCAAGCTCGCAATGCAGAATATAATCCAAAG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 1
-atggttttcatgtccagaatttcagaaactgtagtatttgtttctctttcttttactatagtactgataaa----aataaatggggcaatgt-ttgtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAG
 |||  || ||         |||  |    | |  |  ||  ||    | || | || |  | | |   |      | ||  ||     || | || ||     || || || ||||| || ||||| || ||||||||||| || ||||| || || || |||||||| || ||||||||||| |||||||||
catgtgttccactct----gttttggc--ttatcatgcttcctttggatactctcaccaaggaaattgaagtcctcattatgtgttctcatctattttgatggcagAAACATCGTGTCGACGGTCAATTTGGATTGCAAATTAGACCTCAAAGCTATAGCTTTGCAAGCACGCAATGCAGAATATAATCCAAAG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G28780.1 (Glycine max), 3'ss of exon 2
atggttttcatgtccagaatttcaga--aactgtagtatttgtttctctttcttttactatagtactgataaaaataaa-tggggcaatgtttgtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAG
|| |  |||||||    ||||| |    || |        ||  |     | | |||   | | | ||  | |  |||| | |   | | ||| |    | || ||||||||||| || ||||| || || || |||||||| || ||  | |||||| | |||||||||||||||||||||||||| |||
attgcattcatgt---aaattttatgttaattacttagactggataatgatttcttatatttgcattggaatatctaaaattgtttactatttatactgccagAAATATTGTGTCAACGGTCAATTTGGACTGTAAATTGGAGCTTAAATCAATTGCACTTCAAGCTCGAAATGCAGAATACAATCCCAAG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 2
atggttttcatgtccag--aatttcagaaactgtagtatttgtttctctttcttttactatagtactgataaaaataaatggggcaatgtttgtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAG
  | || |       ||    ||  |    |  ||| ||   |     ||| || |    |  | | ||  ||  |||         |||||||      || ||||||||||| |||||||| || || || || ||||| |||||  | |||||| | |||||||| |||||||| |||||||| |||
--gattatggaaataagttgcttctattttcattagcatacatgataattttttctctatttatgcggagtaatctaataatcaagctgtttgtaccgtcagAAATATTGTGTCCACAGTCAATTTGGACTGTAAGTTGGACCTCAAAACAATTGCACTTCAAGCTCGGAATGCAGAGTACAATCCTAAG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 2
atggttttcatgtccagaatttcaga--aactgtagtatttgtttctctttcttttactatagtactgataaaaataaa-tggggcaatgtttgtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAG
|| |  |||||||    ||||| |    || |        ||  |     | | |||   | | | ||  | |  |||| | |   | | ||| |    | || ||||||||||| || ||||| || || || || ||||| || ||  | |||||| | |||||||||||||||||||||||||| |||
attgcattcatgt---aaattttatgttaattacttagactggataatgatttcttatatttgcattggaatatctaaaattgtttactatttatactgccagAAATATTGTGTCAACGGTCAATTTGGACTGTAAGTTGGAGCTTAAATCAATTGCACTTCAAGCTCGAAATGCAGAATACAATCCCAAG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 2
------atggttttcatgtccagaatttcagaaactgtagtatttgtttctctttcttttactatagtactgataaaaataaatggggcaatgtttgtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAG
      || ||    ||     |  ||| |   ||  ||| ||   |     |||   ||  | |  |   | | || |   ||   ||  |||||||  ||| || ||||||||||| |||||||| || || || || ||||| |||||  | |||||| | |||||||| |||||||| |||||||| |||
ctttggattgtgcaaataatttgc-ttttatttacattagcatacataatagttttccttctttttatgtggtttaata---atcaagc--tgtttgtacatccagAAATATTGTGTCCACAGTCAATTTGGACTGTAAGTTGGACCTCAAAACAATTGCACTTCAAGCTCGTAATGCAGAGTACAATCCCAAG

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|161713889|gb|FC062573.1|FC062573
EST:     CAACCGGTGGATCTCTCCAAGCATCCATCTGGAATCATACCCACGCTCCA                         GAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCAT
genomic: CAACCGGTGGATCTCTCCAAGCATCCATCTGGAATCATACCCACGCTCCAgtaagttccg ... gtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCAT
EST: gi|349817400|gb|FQ405404.1|FQ405404
EST:     CAACCGGTGGATCTCTCCAAGCATCCATCTGGAACCAGACCCACGCTCCA                         GAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCAT
genomic: CAACCGGTGGATCTCTCCAAGCATCCATCTGGAATCATACCCACGCTCCAgtaagttccg ... gtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCAT
EST: gi|30304500|gb|CB981294.1|CB981294
EST:     CAACCGGTGGATCTCTCCAAGCATACATCTGGAATCATACCCACGCTCCA                         GAATATTGTGTCTACAGTCAACTTAGATTGCTAATTGTATCTCAAGGCCAT
genomic: CAACCGGTGGATCTCTCCAAGCATCCATCTGGAATCATACCCACGCTCCAgtaagttccg ... gtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCAT
EST: gi|110721938|gb|EE097741.1|EE097741
EST:     CAACCGGTGGATCTCTCCAAGCACCCATCTGGAATCATACCCACGCTCCA                         GAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCAT
genomic: CAACCGGTGGATCTCTCCAAGCATCCATCTGGAATCATACCCACGCTCCAgtaagttccg ... gtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCAT
EST: gi|71881466|gb|DT030521.1|DT030521
EST:     CAACCGGTGGATCTCTCCAAGCATCCATCTGGAATCATACCCACGCTCCA                         GAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCAT
genomic: CAACCGGTGGATCTCTCCAAGCATCCATCTGGAATCATACCCACGCTCCAgtaagttccg ... gtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCAT
EST: gi|110724394|gb|EE100183.1|EE100183
EST:     CAACCGGTGGATCTCTCCAAGCACCCATCTGGAATCATACCCACGCTCCA                         GAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCAT
genomic: CAACCGGTGGATCTCTCCAAGCATCCATCTGGAATCATACCCACGCTCCAgtaagttccg ... gtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCAT
EST: gi|71881168|gb|DT030223.1|DT030223
EST:     CAACCGGTGGATCTCTCCAAGCATCCATCTGGAATCATACCCACGCTCCA                         GAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCAT
genomic: CAACCGGTGGATCTCTCCAAGCATCCATCTGGAATCATACCCACGCTCCAgtaagttccg ... gtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcttttactatagtactgataaaaataaatggggcaatgtttgtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAG
                tactgat  putative branch site (score: 2)
     ttttactatagtactg  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggttttcatgtccagaatttcagaaactgtagtatttgtttctctttcttttactatagtactgataaaaataaatggggcaatgtttgtgtatctagGAATATTGTGTCTACAGTCAACTTAGATTGCAAATTGGATCTCAAGGCCATTGCATTGCAAGCTCGAAATGCAGAATACAATCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - -tcatgtc
- - - - - - - - - - - cagaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtt