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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaattgaaatttctgaggacaggtacagagtgctttgtaatatcatggcagcatgtgaaactgtaaattgacttgctcattatttgtggtggtttgaagGTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCTTCATTCGAGCAAGCGGCAGGGATCGGGTCCGCCAAAACTTACACAGCCC

Basic information

species Vitis vinifera
transcript Vv08s0105g00230.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G35450.1 (Glycine max), 3'ss of exon 3
aaaattgaaatttctgaggacaggtacagagtgctttgtaatatcatggcagcatgtgaaactgtaaattgacttgctcattattt-gtggtggtttgaagGTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCTTCATTCGAGCAAGCGGCAGGGATCGGGTCCGCCAAAACTTACACAGCCC
||  |      || |         || | |  |   |    | |  | |||  || |       | | ||    |   ||| |||| ||   || ||||||||||||||||| ||| ||||||| ||    ||||||||||||||||| || || ||||||||||| || ||||| || || || |  || ||||| || |
aaggtcatgtattatataattttata-atatagtcctactttgtagtagcattattttgtttcttgatttctaatttacatgattttgtttgggattgaagGTGGAGCAAAGGTACAGGCAGTACCACAGCCAGATGCAGATTGTGATATCCTCTTTCGAGCAAGCTGCTGGGATAGGCTCAGCGAGGACGTACACTGCTC

upper sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA19G38690.1 (Glycine max), 3'ss of exon 5
--aaaattgaaatttctgaggacaggtacagagtgctttgtaat-atcatggcagcatgtgaaactgtaaattgacttgctcattatttgtggtggtttgaagGTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCTTCATTCGAGCAAGCGGCAGGGATCGGGTCCGCCAAAACTTACACAGCCC
   |||||| | |   || ||     | |||         || |  | | |      |     |  ||  |||||  || |   ||||| |  |   ||||||||||||||||| ||| ||||||| || || |||||| |||| ||| |||| || || |||||||| || ||||| || || || |  |||||||| ||||
cttaaattgca-tggttgtggttgattgcagttaataaaatatttgtgaagttgaattaatggatagtttattgatgtgatt-ctatttttcttt-cttgaagGTGGAGCAAAGGTACAGGCAGTACCAGCAGCAGATGGAGATAGTGGTTTCATCGTTTGAGCAAGCTGCGGGGATTGGTTCTGCGAGGACTTACACTGCCC

upper sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA03G36070.1 (Glycine max), 3'ss of exon 3
aaaattgaaatttctgaggacaggtacagagtgctttgtaatatcatggcagcatgtgaa---actgtaaattgact--tgctcattatttgtggtggtttgaagGTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCTTCATTCGAGCAAGCGGCAGGGATCGGGTCCGCCAAAACTTACACAGCCC
     | ||||| |   |    |||  |  |   ||  ||| ||  | |    |  ||||   |  | || || | |  ||    || ||| |  |   ||||||||||||||||| ||| ||||||| || || |||||| |||| |||  ||| ||||| |||||||| || ||||| || || || |  |||||||| ||||
-----ttaaattgcatggttgtggttgattgcagttaataaaatatttgtgatagttgaattaatagaaagtttattgatgtagttttttttttctttcttgaagGTGGAGCAAAGGTACAGGCAGTACCACCAGCAGATGGAGATAGTGGGTTCATCATTTGAGCAAGCTGCGGGGATTGGTTCAGCAAGGACTTACACTGCCC

upper sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G10040.1 (Glycine max), 3'ss of exon 3
-----aaaattgaaatttctgaggacaggtacagagtgctttgtaatatcatggcagcatgtgaaactgtaaattgacttgctcattatttgtggtggtttgaagGTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCTTCATTCGAGCAAGCGGCAGGGATCGGGTCCGCCAAAACTTACACAGCCC
      |  || ||   | | |  | |  | |  | |   | |||  || ||    |  | |  |  ||||| ||    |  | ||| | | | | || ||||||||||||||||| ||| ||||||| ||  | |||||| |||| ||||| || ||||| |||||||| || || || || || || | ||| ||||| || |
tatcttatcttaaatactttcataatatattcttactttgtagtagcattatttt-gtttcttgatttgtaattt----tcttaattttcttttggggattgaagGTGGAGCAAAGGTACAGGCAGTACCACAACCAGATGAAGATAGTGATATCCTCATTTGAGCAAGCTGCTGGAATAGGCTCAGCAAGAACGTACACTGCGC

upper sequence: Vv08s0105g00230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G35940.2 (Arabidopsis thaliana), 3'ss of exon 2
aaaattgaaatttctgaggacaggtacagagtgctttgtaatatcatggcagcatgtgaaactgtaaattgacttgctc-attatttgtggtggtttgaagGTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCTTCATTCGAGCAAGCGGCAGGGATCGGGTCCGCCAAAACTTACACAGCCC
    | | ||   || |  ||   || ||| |   ||    ||    |    | | ||    |   | |    || ||   ||  |||      |   ||||||||||| |||||  | ||||| || || ||||||||||| ||||| ||||| |||||||||||||||||||| || || || ||  | |||||  | |
ctcttagtaaagactaacaacttttatagattatatttatgtagaccgtacacttatgttcataagactcacgttactttgttggttgaaa-aatgaaaagGTGGAGCAGAGATATAGACAGTACCACCAGCAGATGCAGATGGTGATCTCTTCGTTCGAGCAAGCGGCAGGGATAGGATCAGCGAAGTCATACACGTCGC

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|161714978|gb|FC063948.1|FC063948
EST:     GGCAAGAGATTCAGATGAAGAAAGCTAAGCTCCTCAACATGCTTGATGAG                         GTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCT
genomic: GGCAAGAGATTCAGATGAAGAAAGCTAAGCTCCTCAACATGCTTGATGAGgtatgacatg ... tggtttgaagGTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCT
EST: gi|161716829|gb|FC068101.1|FC068101
EST:     GGCAAGAGATTCAGATGAAGAAAGCTAAGCTCCTCAACATGCTTGATGAG                         GTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCT
genomic: GGCAAGAGATTCAGATGAAGAAAGCTAAGCTCCTCAACATGCTTGATGAGgtatgacatg ... tggtttgaagGTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCT
EST: gi|29786121|gb|CB343619.2|CB343619
EST:     ATGCTTGATGAG                         GTGGAGCAAAGATACCGG-ATCTATCATCATCAGATGCAGATTGTGATTTC
genomic: ATGCTTGATGAGgtatgacatg ... tggtttgaagGTGGAGCAAAGATACCGGCA-GTATCATCATCAGATGCAGATTGTGATTTC
EST: gi|71861288|gb|DT010343.1|DT010343
EST:     GGCAAGAGATTCAGATGAAGAAAGCTAAGCTCCTCAACATGCTTGATGAG                         GTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCT
genomic: GGCAAGAGATTCAGATGAAGAAAGCTAAGCTCCTCAACATGCTTGATGAGgtatgacatg ... tggtttgaagGTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCT
EST: gi|110712074|gb|EE089283.1|EE089283
EST:     GGCAAGAGATTCAGATGAAGAAAGCTAAGCTCCTCAACATGCTTGATGAG                         GTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCT
genomic: GGCAAGAGATTCAGATGAAGAAAGCTAAGCTCCTCAACATGCTTGATGAGgtatgacatg ... tggtttgaagGTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggcagcatgtgaaactgtaaattgacttgctcattatttgtggtggtttgaagGTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCTTCATTCGAGCAAGCGGCAGGGATCGGGTCCGCCAAAACTTACACAGCCC
                     aattgac  putative branch site (score: 3)
                                tcattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaattgaaatttctgaggacaggtacagagtgctttgtaatatcatggcagcatgtgaaactgtaaattgacttgctcattatttgtggtggtttgaagGTGGAGCAAAGATACCGGCAGTATCATCATCAGATGCAGATTGTGATTTCTTCATTCGAGCAAGCGGCAGGGATCGGGTCCGCCAAAACTTACACAGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
-aaattga
- - - - - - - - - - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - - - - -tcatggc
- - - - - - - - - - - - - - - - - - - - - - - - - - catgtga