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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attatcttctctgaaaagtatcattttaagtgctttattttgtttaatatctattttgttcctcttttaataaaagtgtttattttttggtcacttgtagGGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAATGATGCCCGACATATGTTGCTGTTCTCTTCTGACCAAGAACTTTTTGAA

Basic information

species Vitis vinifera
transcript Vv02s0025g02010.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G25730.1 (Glycine max), 3'ss of exon 4
attatcttctctgaaaagtatcattttaagtgctttattttgtttaatatctat---tttgt-tcctcttttaataaaagtgtttattttttggtcacttgtagGGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAATGATGCCCGACATATGTTGCTGTTCTCTTCTGACCAAGAACTTTTTGAA
 |||   | ||  | |  |  |  | ||   | | |||| | ||||  || | |   | | | |  | || |||| |   | | | | | ||    || |  || |||||||||||||| |||||||| ||||| || |||||||||||||| || |||||    || |||||||||||||| |||||||| |||||  |||||
-ttaaagt-tcaaatacctgcccctctagtggttctattat-tttaccatttgtgcatctatatttttttctaattagtttatatctatcttcaa-acattcagAGATGAAATAGCTGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAAGGATGCTAAGCAAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAA

upper sequence: Vv02s0025g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G08690.1 (Glycine max), 3'ss of exon 4
attatcttctctgaaaagtatcattttaagtgct---ttattttgtttaatatctattt-tgttcctcttttaataaaagtgtttattttttggtcacttgtagGGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAATGATGCCCGACATATGTTGCTGTTCTCTTCTGACCAAGAACTTTTTGAA
  ||   | ||  | |  || |  | ||   | |   ||||||| |    | |  || | ||||| | || |||| |   | | | | | ||    || |  || ||||||||||| || |||||||| ||||| || |||||||||||||| || ||||||   || |||||||||||||| || ||||| |||||  | |||
--taaagt-tcaaatacctacctctctagtggttccattattttatcatttgtgcatctatgttcattttctaattagtttatatctatcttcaa-acattcagAGATGAAATAGCAGGTTGCAGTGAGAAGGCCTATGACTATCTTTCAATTAAGGATGCCAAGCAAATGTTGCTGTTCTCCTCAGACCAGGAACTCCTGGAA

upper sequence: Vv02s0025g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G64520.1 (Arabidopsis thaliana), 3'ss of exon 4
attatcttctctgaaaagtatcattttaagtgctttattttgtttaatatctattttgttcctcttttaataaaagtgtttattttttggtc---acttgtagGGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAATGATGCCCGACATATGTTGCTGTTCTCTTCTGACCAAGAACTTTTTGAA
  || | ||  |||    | || || |       | | || ||| | | |    | |  ||   | |||    |  | |||||| ||  | |   | |   || |||||||||||||| ||||| || || || || || ||| | || ||||  |||||||| || |||||| ||||||||||||| |||||||| ||    
-gtagcatcaatgagtc-tgtccttct------ctgaattagttcagtcttatgtcttctcgcgtgttatctcacctttttattgttatgactgaattcacagAGATGAAATAGCTGGATGCAGCGAGAAAGCTTATGATTATGTCTCTATCAGCGATGCCCGGCAGATGTTGTTGTTCTCTTCTGATCAAGAACTCTTAACC

upper sequence: Vv02s0025g02010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G42040.1 (Arabidopsis thaliana), 3'ss of exon 2
attatcttctctgaaaagtatcattttaagtgctttattttgtttaatatctattttgttcctcttttaataaaagtgtttattttttggtcacttgtagGGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAATGATGCCCGACATATGTTGCTGTTCTCTTCTGACCAAGAACTTTTTGAA
             | | |  ||||||       || |   | | |  | | ||  |  || |  |   | | |||   |       ||| | |  ||||| |||||||||||||| |||||||| || ||||||||  |||| ||||||| ||| |   |  | ||||| || ||||| ||||| ||| |||| ||   |
---------gtaaataggcttcattt--gtcatttgaccctttctcttctttagctcattgccgtg--acttaaaacatca-----ttgtttatctgtagAGATGAAATAGCTGGATGCAGTGAGAAAGCATACGATCATCTCTCAATCAGTGAAGGTTGTAAGATGTTACTCTTCTCGTCTGATCAACAACTGTTAACA

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|349816270|gb|FQ399380.1|FQ399380
EST:     CCCCCTGAAACTTATGTTTATTTCATGGATCTGCTGTCGAAGACCGTCCG                         GGATGAAATACCTGGGTGCAGTGAA
genomic: CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAGgtaaaaactt ... tcacttgtagGGATGAAATAGCTGGGTGCAGTGAA
EST: gi|30298118|gb|CB974912.1|CB974912
EST:     CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAG                         GGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACAATCTTTCAATCAA
genomic: CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAGgtaaaaactt ... tcacttgtagGGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAA
EST: gi|161716840|gb|FC064955.1|FC064955
EST:     CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAG                         GGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCA-
genomic: CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAGgtaaaaactt ... tcacttgtagGGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAA
EST: gi|110718356|gb|EE095093.1|EE095093
EST:     CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAG                         GGATGAAATAGCTGGGTGCAGTNGAAA-GGCATACGACTATCTTTCAATCA
genomic: CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAGgtaaaaactt ... tcacttgtagGGATGAAATAGCTGGGTGCAGT-GAAAAGGCATACGACTATCTTTCAATCA
EST: gi|110731735|gb|EE106407.1|EE106407
EST:     CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAG                         GGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAA
genomic: CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAGgtaaaaactt ... tcacttgtagGGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAA
EST: gi|110707571|gb|EE084124.1|EE084124
EST:     CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAG                         GGATTGAA-TAGCTGGGTGCAGTGAAAAGGCATACNACTATCTTTCAATCA
genomic: CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAGgtaaaaactt ... tcacttgtagGGAT-GAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCA
EST: gi|110374493|gb|EC939283.1|EC939283
EST:     CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAG                         GGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAA
genomic: CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAGgtaaaaactt ... tcacttgtagGGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAA
EST: gi|351044575|gb|FQ443106.1|FQ443106
EST:     CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAG                         GGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTNCA-TCA
genomic: CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAGgtaaaaactt ... tcacttgtagGGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTT-CAATCA
EST: gi|351033177|gb|FQ461949.1|FQ461949
EST:     CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAG                         GGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAA
genomic: CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAGgtaaaaactt ... tcacttgtagGGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAA
EST: gi|110410923|gb|EC976617.1|EC976617
EST:     CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAG                         GGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAA
genomic: CCCCATGAAACTTATGTTTATTTCATGGATCTGCTGGCGAAGACAGTCAGgtaaaaactt ... tcacttgtagGGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatctattttgttcctcttttaataaaagtgtttattttttggtcacttgtagGGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAATGATGCCCGACATATGTTGCTGTTCTCTTCTGACCAAGAACTTTTTGAA
                   ttttaat  putative branch site (score: 3)
                 tcttttaataaaagtg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attatcttctctgaaaagtatcattttaagtgctttattttgtttaatatctattttgttcctcttttaataaaagtgtttattttttggtcacttgtagGGATGAAATAGCTGGGTGCAGTGAAAAGGCATACGACTATCTTTCAATCAATGATGCCCGACATATGTTGCTGTTCTCTTCTGACCAAGAACTTTTTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - -aaaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa