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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgcctgaaattacttctgataaaaaaatttatttaaacagagctcaactgagcctcagttgtcttgacttttccttttactttatttttattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGCAGGAAAAACATCACTTGTAAATGTTATTGCA

Basic information

species Vitis vinifera
transcript Vv03s0091g00970.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0091g00970.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G007188_T01 (Zea mays), 3'ss of exon 1
-cttgcctgaaattactt---ctgataaaaaaatttatttaaacagagctcaactgagcctcagttgtcttgacttttccttttactttatttttattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGCAGGAAAAACATCACTTGTAAATGTTATTGCA
     | || || |   |   |||||  ||   | |  |      ||    |  ||   ||    ||  |  |    |  || | |||| |||  || |||||||||||| ||||| ||||| |||||||| || ||| |||| || || ||||| || |||||||||||||| ||    ||||| 
taacacttgtaaatggatgaactgatgtaatcttctgctcctttcgattcaaggtg---cttgcctgcttgaataactatttctgctttttttacat-ctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT

upper sequence: Vv03s0091g00970.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 1
-cttgcctgaaattacttctgataaaaaaatttat--ttaaacagagctcaactgagcctcagttgtcttgacttttccttttactttatttttattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGCAGGAAAAACATCACTTGTAAATGTTATTGCA
     | || || |   |    | | | ||| ||   || |       ||||  || |||    ||  |  |    |  || ||||||  |||   ||||||||||||| ||||| ||||| |||||||| || |||||||| || || ||||| || ||||| |||||||| ||   |||||| 
gtgcacttgtaaatggatgaactgatataatctaccgttcatttcgattcaaagga-ccttgtctgcttgaataactgtttgtacttt--tttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT

upper sequence: Vv03s0091g00970.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G27070.2 (Glycine max), 3'ss of exon 1
-----cttgcctgaaattacttctgataaaaaaatttatttaaacagagctcaactgagcctcagttgtcttgacttttccttttactttatttttattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGCAGGAAAAACATCACTTGTAAATGTTATTGCA------------------
      |   ||     || |||   | || |   ||| || ||      |||     |  |  ||   | |   | || || ||||| |  |   ||  |  |||||||||||||| |||||||||||| |||||||| | ||||||||| |||| || |||||||||||| ||||||||||||||                  
tgtgtatgttctattgatatttc-attgaacaggattaattgaatgaccttcatagtggaatttgtaaacat--ttgtttctcttactcttgtccaatgat--agCCTCTTTTTCAAGCAAGAAATGGAGTTATCTTTGGTTGGCCTTCAGGATGCTGGGAAAACATCACTTATAAATGTTATTGCAGTATCTTACCAGACCTTC

upper sequence: Vv03s0091g00970.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G49870.1 (Arabidopsis thaliana), 3'ss of exon 1
-cttgcctgaaattacttctgataaaaaaatttatttaaacagagctcaactgagcctcagttgtcttgacttttccttttactttatttttattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGCAGGAAAAACATCACTTGTAAATGTTATTGCA
   |  |     | |  | | || ||| | |   | |     |     || | |   |  | | ||   | |      |||  ||   | | ||| ||||||||||| ||||| |||||||||||||| ||||||||||| ||||| ||||||||||| |||||||||||||||||| |||||
ttctaacaatcgtaaaatttcatgaaagattggttctttttggtatctaatttatgtttcgat-tcggtattcaattgtttgtttccatatgattttgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCTTTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTAAATGTTGTTGCA

upper sequence: Vv03s0091g00970.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G67560.1 (Arabidopsis thaliana), 3'ss of exon 1
cttgcctgaaattacttctgataaaaaaat--ttatttaaacagagctcaactgagcctcagttgtcttgacttttccttttactttatttttattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGCAGGAAAAACATCACTTGTAAATGTTATTGCA
  |   ||||  |  |      || ||  |  ||    ||| | |  |    ||   | || ||| |     | | | |  |     | |    |  ||||||||||| ||||| |||||||||||||| || |||||||| ||||| ||||||||||| ||||||||||| || ||| |||||
agtagatgaagattgtgagagcaagaacttagtttcccaaaaaaaagttgcttgcttcgcatttgcccga--tatgcatagtctcacaatgccttattgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTTAACGTTGTTGCA

upper sequence: Vv03s0091g00970.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S6_409V6.2 (Physcomitrella patens), 3'ss of exon 2
cttgcctgaaattacttctgataaaaaaatttatttaaacagagctcaactgagcctcagttgtcttgacttttccttttactttattt----ttattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGCAGGAAAAACATCACTTGTAAATGTTATTGCA
          ||| |   | ||||  |   | || |  |  ||  |    ||| |  |   |   |   ||  |    ||| ||         || | | ||||||| || ||||| ||||| |||||||| ||  ||||||| || ||||| || || |||||||| ||||| ||||||||||| 
---ataaacgatttcaatttataattactgtgatgttgatgga-ttgggttgatctcctaattcttgagctagtgtgattaattggagagagattgtgcggcagCCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG

upper sequence: Vv03s0091g00970.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S263_59V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------------------------------------cttgcctgaaattacttctgataaaaaaatttatttaaacagagctcaactgagc--ctcagttgtcttgacttt-tccttttactttatttttattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGCAGGAAAAACATCACTTGTAAATGTTATTGCA
                                                                                     ||  |   |   ||||  || | |  |  |      |  |   ||   |  |   |||     |   | || | | ||| |||  |  |  |  | ||||| ||||||||||||||||| |||||||| ||||||||||| || || || || |||||||| || || || ||||| ||||| 
gtagttactgaatttctgtctgtccatgcgattaagattcaattacacaattttataatttttcttgttatgttgttttgtgctgtgagtttgacgccttcgaatcagaggacatgcgggcattggtatcggtttggttgctcgaagatgcaggctctgtacttatacggttctcatcctgtgcagTCTCTTTTTCAAACAAGAGATGGAGCTGTCTTTGATAGGGCTGCATAACGCCGGAAAAACCTCTCTCGTCAATGTCATTGCG

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|10283307|gb|BE846430.1|BE846430
EST:     AATCGTTGCTCAATTGGCTGCGAAG                         CCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGC
genomic: AATCGTTGCTCAATTGGCTGCGAAGgtaaattagg ... tattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGC
EST: gi|351040174|gb|FQ425260.1|FQ425260
EST:     GTTTCGTTTCGAATGGGGTTGTGGGAATCGTTGCTCAATTGGCTGCGAAG                         CCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGC
genomic: GTTTCGTTTCGAATGGGGTTGTGGGAATCGTTGCTCAATTGGCTGCGAAGgtaaattagg ... tattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGC
EST: gi|30300622|gb|CB977416.1|CB977416
EST:     GTTTCGTTTCGAATGGGGTTGTGGGAATCGTTGCTCAATTGGCTGCGAAG                         CCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGC
genomic: GTTTCGTTTCGAATGGGGTTGTGGGAATCGTTGCTCAATTGGCTGCGAAGgtaaattagg ... tattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaactgagcctcagttgtcttgacttttccttttactttatttttattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGCAGGAAAAACATCACTTGTAAATGTTATTGCA
                  tcttgac  putative branch site (score: 3)
                        cttttccttttacttt  CT-rich tract
                         ttttccttttacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgcctgaaattacttctgataaaaaaatttatttaaacagagctcaactgagcctcagttgtcttgacttttccttttactttatttttattctgcagCCTCTTTTTCAAACAAGAAATGGAGCTATCTTTGATAGGCCTTCAGAATGCAGGAAAAACATCACTTGTAAATGTTATTGCA

cttgcct
- - - -gaaatta
- - - - - - - cttctga
- - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - aaacaga
- - - - - - - - - - - - - - - - - - - - - -gctcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - agcctca