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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgattcagaatccaaaatgttgtttgagtttgtgggattgattggatttggagaatacccagttgcttatttctttgattctttctgaaatttcagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTGGGTAGACCTCGACACACTGGAGTGATGGTTGGGATGGGACAGAAAGATG

Basic information

species Vitis vinifera
transcript Vv08s0007g06520.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g06520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G29160.2 (Glycine max), 3'ss of exon 2
---gtattgattcagaatccaaaatgttgtttgagtttgtgggattgattggatttggagaatacccagttgcttatttctttgattctttctgaaattt-cagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTGGGTAGACCTCGACACACTGGAGTGATGGTTGGGATGGGACAGAAAGATG
     |   |  |  ||  || ||||    | |  | |  |   |   |||| ||| ||  ||      |  |||      ||||||  |  | || ||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||| | || || |||||||| ||||||||||| ||||| || || || |
tggagaacaacacctaaaacagaatggaact-gtatctaagttgtcctttggtttttgatgatttt---tctctttcggtgttgatttgtgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCTGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGACG

upper sequence: Vv08s0007g06520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G32990.2 (Glycine max), 3'ss of exon 1
------gtattgattcagaatccaaaatgttgtttgagtttgtgggattgattggatttggagaatacccagttgcttatttctttgattctttctgaaatttcagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTGGGTAGACCTCGACACACTGGAGTGATGGTTGGGATGGGACAGAAAGATG
      |    |  |  | ||  |  ||  ||||  | |  ||   |||  |   | ||    | ||   |  || | || |  |||  | | | ||| ||   ||||||| ||||||||||||||||| |||||||||||||| ||||||||||||||  | || || |||||||| ||||||||||||||||| ||||| ||||
ggggggggggggtgttggcatttaggat-ctgttacaat--gtaaaattattcttaattcttaattaataaaatgttaatgttgttgggtttgtgtgatat---agGCTGGTTTTGCTGGAGATGATGCACCGAGGGCTGTGTTCCCTAGCATTGTGGGGCGTCCACGTCACACTGGGGTGATGGTTGGGATGGGGCAGAAGGATG

upper sequence: Vv08s0007g06520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G17040.1 (Glycine max), 3'ss of exon 1
-gtattgattcagaatccaaaatgttgtttgagtttgtgggattgattggatttggagaa-tacccagttgcttatttctttgattctttctgaaatttcagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTGGGTAGACCTCGACACACTGGAGTGATGGTTGGGATGGGACAGAAAGATG
 || |||  |     |     ||| |  | || ||||     | |  |  |    ||||| ||    | ||  || |||    ||| | |   |  || ||||||||||||||||||||||||||||| ||||| ||||| ||||||||||||||| | || || |||||||| ||||||||||| ||||| || || ||||
agttttgtcttttggtttttgatgatactagattttgacccgtgggatacaaagagagaactaattgggtgagtacttca--aattatgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCCGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGATG

upper sequence: Vv08s0007g06520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G30110.1 (Glycine max), 3'ss of exon 2
--gtattgatt-cagaatccaaaatgttgtttgagtttgtgggattgattggatttggagaatacccagttgcttatttctttgattctttctgaaatttcagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTGGGTAGACCTCGACACACTGGAGTGATGGTTGGGATGGGACAGAAAGATG
  | |  |||    ||||     || || |      ||      |  |      ||  |     |  | | |  | ||  | |  ||     |    |   ||||||| ||||| ||||||||||| |||||||| ||||| || |||||||||||  | || || ||||| |||||||||||||||||||| ||||| ||||
tagcagagataatcgaatttgcgatcttttcc---cttaatcattcaacccaccttatatcccccttaatagtgtgttaatgttgttgggatttgtgtgatagGCTGGTTTTGCCGGAGATGATGCGCCGAGGGCGGTGTTCCCCAGCATTGTGGGGCGTCCACGTCACACGGGAGTGATGGTTGGGATGGGGCAGAAGGATG

upper sequence: Vv08s0007g06520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 3
--gtattgattcagaatccaaaatgttgtttgagtttgtgggattgattggatttggagaatacccagttgcttatttctttgattctttctga--aatttcagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTGGGTAGACCTCGACACACTGGAGTGATGGTTGGGATGGGACAGAAAGATG
   | |||  ||   ||  | ||||  |   ||  ||| |   | || |  ||||       | ||  | |    | | ||| ||| |     |   |   |||||||| || |||||||| ||||||||  | ||||| || || |||||||| ||  | ||  | ||||||||||||||||| || ||||||||||| || |
ctcttttgcatctttatttataatg--ggcagacattg-gatgtagacta-atttatgatcaatcctctcgaaactgtgtttaattttggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: Vv08s0007g06520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 2
gtattgattcagaatccaaaatgttgtttgagtttgtgggattgattggatttggagaatac---ccagttgcttatttctttgattctttctgaaat---ttcagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTGGGTAGACCTCGACACACTGGAGTGATGGTTGGGATGGGACAGAAAGATG
      |||||    | | ||||  |||   | |  |   ||| |   || ||      | |   ||||      |     || | |  |  |||| |     |||||||| || |||||||| ||||||||  | ||||| || || |||||||| ||  | ||  | ||||||||||||||||| || ||||||||||| || |
----caattcatg--ctataatggcgttcatgataatactattcaagtgacttcagttgtgctgtccagaacgaaaccgtgtttaattgtggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: Vv08s0007g06520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 1
gtattgattcagaatccaaaatgttgtttgagtttgtgggattgattggatttggagaatacccagttgcttattt-ctttgattctt----tctgaaatttcagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTGGGTAGACCTCGACACACTGGAGTGATGGTTGGGATGGGACAGAAAGATG
                                                  |  |       | | ||| ||| |    |||||| |      | ||   || |||||||||||||| ||||| |||||||| ||||| |||||||| |||||||||||  | ||    ||||| || || |||||||| ||||| ||||| ||||
-------------------------------------------------gtgcgctcctggcgcggtttcttgtggattttgatccggggggtgtgttcttgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG

upper sequence: Vv08s0007g06520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ35077 (Selaginella moellendorffii), 3'ss of exon 1
gtattgattcagaatccaaaatgttgtttgagtttgtgggattgattggatttggagaatacccagttgcttatttctttgattctttctgaaatttcagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTGGGTAGACCTCGACACACTGGAGTGATGGTTGGGATGGGACAGAAAGATG
                            || | |  |||    ||||   | ||||   |   | |  |  | | | ||||                |||||||||||||| ||||| |||||||| ||||| |||||||| |||||||||||  | ||    ||||| || || |||||||| ||||| ||||| ||||
---------------------------gtgcgctcctggcgc-gatttcttgtggattttgatccggggggtgtgtttttg----------------cagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG

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|161709872|gb|FC058058.1|FC058058
EST:     CTGAGGATATTCAGCCTCTTGTCTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGATTTGCTGGACATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTG
genomic: CTGAGGATATTCAGCCTCTTGTCTGCGATAATGGAACCGGAATGGTCAAGgtattgattc ... gaaatttcagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTG
EST: gi|161719596|gb|FC067042.1|FC067042
EST:     CTGAGGATATTCAGCCTCTTGTCTGCGATAATGGAACCGGAATGGTCAAG                         GCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTG
genomic: CTGAGGATATTCAGCCTCTTGTCTGCGATAATGGAACCGGAATGGTCAAGgtattgattc ... gaaatttcagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggatttggagaatacccagttgcttatttctttgattctttctgaaatttcagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTGGGTAGACCTCGACACACTGGAGTGATGGTTGGGATGGGACAGAAAGATG
                               ctttgat  putative branch site (score: 5)
                                     ttctttctg  CT-rich tract
                         ttatttctttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgattcagaatccaaaatgttgtttgagtttgtgggattgattggatttggagaatacccagttgcttatttctttgattctttctgaaatttcagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTGGGTAGACCTCGACACACTGGAGTGATGGTTGGGATGGGACAGAAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG