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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcatggttgggccatttttagggcttaagagatcatatgctgttttcaatttctaagataaggcatcttattgtttgatttgtatgtgcatgcatgcagTGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGTGTTGGTCGGCGGAATACTGGAACATGATTTGGGCAGTTATCCTTTCACC

Basic information

species Vitis vinifera
transcript Vv06s0004g08180.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g08180.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA14G38600.1 (Glycine max), 3'ss of exon 9
gtcatggttgggccatttttagggcttaa----gagatcatatgctgttttcaatttctaagataaggcatcttattgtttgatttgtatgtgcatgcatgcagTGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGTGTTGGTCGGCGGAATACTGGAACATGATTTGGGCAGTTATCC-TTTCACC
 || |      |  |    ||| ||  ||     |  |  || |    ||  |  ||||    | |   ||| |||  | |  ||| | | ||| | ||    ||| || || ||  ||||||||||||||||||||||||||||||| ||||||||||| ||  |||| || || ||||  |        | ||   | | |  
atcgtatacttggtaacagtagtgcaaaatgtgaatgtgttagggacattctacattctgtctttaaaaatcctataatgttttttttttttgctttca----gTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGTGTTGGCCGAAGGAACACAGGGACATAGTCCTACTTTTGATTTATGTTAT-

upper sequence: Vv06s0004g08180.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G40310.1 (Glycine max), 3'ss of exon 9
-gtcatggttgggccatttttagggcttaagagatcatatgctgttttcaatttctaagataaggcatcttattgtttgatttgtatgtgcatgcatgcagTGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGTGTTGGTCGGCGGAATACTGGAACATGATTTGGGCAGTTA-TCCTTTCACC
  || ||||     || |   |    | ||    |  |  ||  | | |  | | | |   ||       || |  |   ||| | | |   ||| | ||||| || || ||  ||||||||||||||||||||||||||||||| ||||||||||| ||  |||| || || ||||  |     |  ||| |   |  |  
tatc-tggtaacagcactgccaaacgtgaatgtgttgtgggcactctgcgttctgtcattaaaaatcctataatactgtttttttttttttttgctttcagTGTGGATCAGGAAGATCAGTTGCTCCAATCAAGGCTGGTTTTGTTGCTCGTGTTGGCCGAAGGAACACAGGGACATAGTCCCTACTTTTAATAAATGTAA-
















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|22008615|gb|BQ793649.1|BQ793649
EST:     ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAG                         TGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT
genomic: ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAGgtaatttatg ... atgcatgcagTGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT
EST: gi|26258607|gb|CA809670.1|CA809670
EST:     ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAG                         TGCGGCTCTGGGCGATCAGTTGCTC
genomic: ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAGgtaatttatg ... atgcatgcagTGCGGCTCTGGGCGATCAGTTGCTC
EST: gi|34548729|gb|CF516961.1|CF516961
EST:     ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAG                         TGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT
genomic: ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAGgtaatttatg ... atgcatgcagTGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT
EST: gi|26257846|gb|CA808909.1|CA808909
EST:     ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAG                         TGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT
genomic: ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAGgtaatttatg ... atgcatgcagTGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT
EST: gi|110412214|gb|EC977955.1|EC977955
EST:     ACACAATTCTTTCAAAGGAGAATCGTTTCTTCTTTTTCAGATGCGAGCAG                         TGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT
genomic: ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAGgtaatttatg ... atgcatgcagTGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT
EST: gi|34548647|gb|CF516879.1|CF516879
EST:     ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAG                         TGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT
genomic: ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAGgtaatttatg ... atgcatgcagTGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT
EST: gi|352785931|gb|FQ475934.1|FQ475934
EST:     ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTCCTCAGATGCGAGCAG                         TGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT
genomic: ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAGgtaatttatg ... atgcatgcagTGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT
EST: gi|110363156|gb|EC926727.1|EC926727
EST:     ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAACAG                         TGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT
genomic: ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAGgtaatttatg ... atgcatgcagTGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT
EST: gi|32458044|gb|CD799218.1|CD799218
EST:     ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAG                         TGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT
genomic: ACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAGgtaatttatg ... atgcatgcagTGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaatttctaagataaggcatcttattgtttgatttgtatgtgcatgcatgcagTGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGTGTTGGTCGGCGGAATACTGGAACATGATTTGGGCAGTTATCCTTTCACC
                            gtttgat  putative branch site (score: 5)
                       ttattgtttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatggttgggccatttttagggcttaagagatcatatgctgttttcaatttctaagataaggcatcttattgtttgatttgtatgtgcatgcatgcagTGCGGCTCTGGGCGATCAGTTGCTCCAATCAAGGCTGGTTTTGTGGCTCGTGTTGGTCGGCGGAATACTGGAACATGATTTGGGCAGTTATCCTTTCACC

- - -ggttggg
- - - - - - ccatttt
- - - - - - - - - - - - - taagaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aagataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtgc