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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatctatttgtgcaggattctttatggtttactataactatgtttaatttttttccatttgttgcaatgctaaattttatgcatgtgatgactttcagGATATTGGCTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAG

Basic information

species Vitis vinifera
transcript Vv00s0207g00090.t01
intron # 7
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 7
lower sequence: GRMZM2G100913_T02 (Zea mays), 3'ss of exon 7
----agaatctatttgtgcaggattctttatggtttactataactatgtttaatttttttccatttgttgcaatgctaaattttatgcatgtgatga--ctttcagGATATTGGCTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAG
    |     || ||||| | | || | | |  ||   | |  | |  |  ||||   |   |    ||   |||      ||||||| |||| | |   |||||||||| |||||||||| ||||| ||||||||||| || |||||||| || |||||||| || || |||||||| |||||||| || || |||||||| || 
atttaactgataattgtgaatgtttttattttattccttgtggc-acttcaaattgcatgaaaaggtttattatgta----tttatgc-tgtgttcatcttttcagGATACTGGCTAATTCTAAGCCCTGTCCAAAGTGCAAACGGCCAATAGAGAAAAACCAGGGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAA

upper sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G006428_T02 (Zea mays), 3'ss of exon 7
agaatctatttgtgcaggattctttatggtttactataactatgtttaattttttt---ccatttgttgcaatgctaaatttta---tgcatgtgatgactttcagGATATTGGCTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAG
      |  |  | |     |||| |||   || |  |  ||| |      | |||   | |     | ||||  | | ||  |   ||  | |      |||||||||| |||||||||| ||||||||||| || || |||||||| || |||||||| || || || ||||| ||||||||||| || ||||| |||||||||
------tggtctttcctctctcttaatgcaataatgcacatatttcctgcgtgtttgagcaaaaatatccaatattgacttcgaaactgtctattcatggtttcagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAGCGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG

upper sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM5G876621_T01 (Zea mays), 3'ss of exon 7
------agaatctatttgtgcaggattctttatggtttactataactatgtttaattt-ttttccatttgttgcaatgctaaattttatgcatgtgatgactttcagGATATTGGCTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAG
          ||| ||  ||||    |    | | | | || |   | ||   ||     | |||| |  |  |  |||||   | ||| ||||       |||||||||| |||||||||| ||||||||||| || || || ||||| || |||||||| || || || ||||| ||||||||||| || ||||| |||||||||
ttcctctctctctcttaatgcaaccatgcaca-gatctcctgtgtttttgagaaaaaaactgtccagtgttgactttgctactgtctattcatgg------tttcagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG

upper sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 7
agaatctatttgtgcaggattctttatggtttactataactatgtttaatttttttccatttgttgcaatgctaaattttatgcatgtgatgactttcagGATATTGGCTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAG
  || | ||||  |     |||| |    | | |||  | || | |  ||  |  | ||  | |||   || |     | |      |  ||| ||||||||| ||||| ||||||||||| |||||||| || || |||||||| || |||||||| |||||||||||||| || ||||| || |||||||||||||||
gaaaaccattttcggtttcttctcttccatctcctagcattagggtgcatcatgcttcacattttgttttgttgctgctaagttccatattgaatttcagGATTTTGGCAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAG

upper sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S156_28V6.1 (Physcomitrella patens), 3'ss of exon 7
agaatctatttgtgcaggattctttatggtttactataactatgtttaatttttttccatttgttgcaatgctaaattttatgcat-gtgatgacttt----cagGATATTGGCTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAG
    | |  |    |   | ||| |||    |   | || |    || |   | ||    ||   | |   |  | | |||| |||  |      |||    ||||||  | || ||   ||| || || || || |||||  ||||||| || ||||||||||| |||||||| || || |||||||| || || |||||||||
--gctattctaaccctctaatctctata---tgtaagaagtgaacttgaagatatttgtcttagagaatgacctattcttattcattatcgctgttttaaaacagGATTCTTGCAAACAGCAAACCCTGCCCCAAATGTAAAAGGCCAATTGAGAAAAACCAAGGGTGTATGCACATTACTTGCACACCTCCTTGCAAATTTGAG

upper sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 3'ss of exon 7
----agaatctatttgtgcaggattctttatggtttactataactatgtttaatttttttccatttgttgcaatgctaaattttatgcatgtgatgactttcagGATATTGGCTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAG
      || | | |  |     ||   || | |   | | | |  | |||   |   |||  ||||   ||| |  |    | |     |    |||    ||||||  | || ||   ||| ||||| || ||||||||| ||||||| || ||||||||||| || ||||||||||| ||||| || || || |||  ||||
ggaccaaaccaactcttaagtcatagatt-taggacaatgtgatgaagttccttgcctttatatttaacgcattagtgttatctcctttttctttga---gcagGATTCTTGCAAACAGCAAACCTTGCCCCAAGTGTAAGAGGCCAATTGAGAAAAACCAAGGCTGCATGCATATCACTTGCACTCCACCTTGCAAACATGAG

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|110378373|gb|EC943503.1|EC943503
EST:     GTGGCCAAGTGGATTTTGAAGAATAGTGCTGAGTCTGAGAACATGAATTG                         GATATTGGCTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGNNNN
genomic: GTGGCCAAGTGGATTTTGAAGAATAGTGCTGAGTCTGAGAACATGAATTGgttgaacaca ... tgactttcagGATATTGGCTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAA
EST: gi|110383372|gb|EC947743.1|EC947743
EST:     GTGGCCAAGTGGATTTTGAAGAATAGTGCTGAGTCTGAGAACATGAATTG                         GATATTGGCTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGNNNN
genomic: GTGGCCAAGTGGATTTTGAAGAATAGTGCTGAGTCTGAGAACATGAATTGgttgaacaca ... tgactttcagGATATTGGCTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatttttttccatttgttgcaatgctaaattttatgcatgtgatgactttcagGATATTGGCTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAG
                        tgctaaa  putative branch site (score: 2)
                                                ctttc  putative PPT
                      aatgctaaattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaatctatttgtgcaggattctttatggtttactataactatgtttaatttttttccatttgttgcaatgctaaattttatgcatgtgatgactttcagGATATTGGCTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAG

- - - - tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtga