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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttatttttttttcaaattttaattcatatttagctttggagttctaaaaatgaacactttgtttcttcatgtatgctcttcgataatgtatgcttgcagGCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTATGCATGTAACCGTTATGAGACAGCAAAGCAAGAGGGAGTG

Basic information

species Vitis vinifera
transcript Vv00s0207g00090.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 8
gttatttttttttcaaattttaattcatatttagctttggagttctaaaaatgaacactttgtttcttcatgtatgctcttcgataatgtatgcttgcagGCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTATGCATGTAACCGTTATGAGACAGCAAAGCAAGAGGGAGTG
          | |  |||  ||||   | | |   | ||   |||  |  |    || | |  |    | ||||||  |||     || ||     ||||||| ||||||||| ||||||| || ||||| ||  |||| ||||| |||||||| ||||||||||||||| |||||| ||| || |||| |
---------gtatgtaatcataatc--tctctgtttatgctcttcatagcacttgcagtctcatatggcttgtatgtacttgttctatataa---cgcagGCTGTGTCTTGGTCCATGGTCGGAGCATGGAGAACGGACTGGTGGATTTTATGCCTGTAACCGTTATGAGGCAGCAAGGCAGGAAGGAGCG

upper sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os09g33876.1 (Oryza sativa), 3'ss of exon 8
gttatttttttttcaaattttaattcatatttagctttggagttctaaaaatgaacactttgtttcttcatgtatgctcttcgataatgtatgcttgcagGCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTATGCATGTAACCGTTATGAGACAGCAAAGCAAGAGGGAGTG
|| |  ||   |          ||   | ||| | |   || |    | | |   || |    || || || | || |||  |||  |  ||| ||||||| | || || |||||||||||||||||||| ||  |||| ||||| |||||||| || || |||||| |  ||||||||   |  ||  ||
gtaagcttccctctcggc----atatttgttttgatggtgattgtgtacattttgcattgaaattgtttatctttggtct--gattttccatggttgcagGTTATGCCTAGGTGCATGGTCAGATCATGGAGATGGGACTGGTGGCTTTTATGCTTGCAATCGTTATCAATCAGCAAAGATGGGAGGCATG

upper sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G100913_T02 (Zea mays), 3'ss of exon 8
gttatttttttttcaaattttaattcatatttagctttggagttctaaaaatgaacactttgtttcttcatgtatgctcttcgataatgtatgc-ttgcagGCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTATGCATGTAACCGTTATGAGACAGCAAAGCAAGAGGGAGTG
                  | |  ||||  |   ||||   ||   |  |        |  ||||| |     | ||   |  | |  | |   | || |||| | ||||| ||||||||||||||||| || ||||| |||||||| |||||||| || || ||||||||  |||||||| |||||||||| 
-----------------gtattgttcacttactgcttgaaagaattgcagtattctgccatgtttatcttcttttgtcttgaggttctttgcacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTATGCTTGCAATCGTTATGAATCAGCAAAGAAAGAGGGAGTT

upper sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 8
gttatttttttttcaaattttaattcatatttagctttg-gagttctaaaaatgaacactttgtttcttcatgtatgctcttcgataatgtatgcttgcagGCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTATGCATGTAACCGTTATGAGACAGCAAAGCAAGAGGGAGTG
  ||| || |  ||  ||  | ||    || | | | ||  || |       ||  |||  ||     |||| |||         |  ||| |   || |||||||| ||||| || ||| |||| |||||||||| ||||||||| |||||||| ||||||||||||||  ||||||||||||| ||  | 
tgtatcttgtaatctgatcgtcatatgaatctggttgtgtaagattcttggttgctcacaatgaaatctcat-tataaatagttgtgttgtttaaatgtagGCTTTGCCTTGGGGCGTGGACAGAGCATGGTGAGAAGACAGGTGGCTTTTATGCTTGTAACCGTTATGAAGCAGCAAAGCAAGATGGCATT

upper sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------------------------------------------------------gttatttttttttcaaattttaattcatatttagctttggagttctaaaaatgaacactttgtttcttcatgtatgctcttcgataatgtatgcttgcagGCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTATGCATGTAACCGTTATGAGACAGCAAAGCAAGAGGGAGTG
                                                                                                         |    |          ||  || |  || || |   || ||||        || | |   |||  ||| |     | ||   |||| | ||      ||||||||||||||| |||||| | ||||| || || ||||| || ||||| |||||||| |||||||| || || || || ||||| || |||
gtaaacaatttaatgtaattttaaaaaaatagttttttattttcccttattgaagttaagcttgttaacgaatgaaattcggtcttgctcattaagctcatcagtgcagctgcggcagtccatgctattgtattttaacgctttgagtgtctggtttggaaatagtgtcactt-acaagagttcactgatactata-----acagGCTTTGTCTTGGAGCATGGACTGATCACGGGGAAAGGACCGGAGGTTTCTATGCATGCAACCGTTACGAAACTGCGAAACAAGAAGGCGTG

upper sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S178_72V6.3 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------------------------gttatttttttttcaaattt-taattcatatttagctttggagtt--ctaaaaatgaacactttgtttc---ttcatgtat-gctcttcgataatgtatgctt--gcagGCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTATGCATGTAACCGTTATGAGACAGCAAAGCAAGAGGGAGTG
                                                             ||||  | | | ||| |    || | |||   |   |  | |   ||         ||  |||  ||    ||| || | ||| ||  |   ||  | |||  ||||||| |||||||| |||||| | ||||| |||||  | || || ||||| |||||||||||||||||||| || || |||||||| || |||
gtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcagGCTGTGTCTTGGAGCATGGACTGATCACGGTGAACGAACTGGAGGTTTCTATGCATGTAACCGTTATGAAACTGCCAAGCAAGAAGGCGTG

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|37183601|gb|CF602955.1|CF602955
EST:     CCGCCATGTAAATTTGAGTTTTGCTG                         GCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTA
genomic: CCGCCATGTAAATTTGAGTTTTGCTGgtaagtttat ... atgcttgcagGCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTA
EST: gi|110378373|gb|EC943503.1|EC943503
EST:     GGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAGTTTTGCTG                         GCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGA
genomic: GGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAGTTTTGCTGgtaagtttat ... atgcttgcagGCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGA
EST: gi|110383372|gb|EC947743.1|EC947743
EST:     GGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAGTTTTGCTG                         GCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTA
genomic: GGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAGTTTTGCTGgtaagtttat ... atgcttgcagGCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaatgaacactttgtttcttcatgtatgctcttcgataatgtatgcttgcagGCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTATGCATGTAACCGTTATGAGACAGCAAAGCAAGAGGGAGTG
 ttctaaa  putative branch site (score: 2)
                                      ataatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatttttttttcaaattttaattcatatttagctttggagttctaaaaatgaacactttgtttcttcatgtatgctcttcgataatgtatgcttgcagGCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTATGCATGTAACCGTTATGAGACAGCAAAGCAAGAGGGAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - -taaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtatgct