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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgctcttttaacagaattttgattgcatgatgatttttgtcttcaacttttaaaatttcatctgatgtgatgctatgttgtgtttctcactttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATGGTTGGTGGAATTGAAGAAGTTATTGCCAAGGCCGAGAAAATTGCCAAGG

Basic information

species Vitis vinifera
transcript Vv17s0000g02900.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g02900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os01g49190.1 (Oryza sativa), 3'ss of exon 8
------gttgctcttttaacagaattttgattgcatgatgatttttgtcttcaacttttaaaatttcatctgatgtgatgctatgttgtgtttctcactttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATGGTTGGTGGAATTGAAGAAGTTATTGCCAAGGCCGAGAAAATTGCCAAGG
        | |||||||     |    | ||   || |||| | || ||||   || |    |||||  | || || |||      | |  |   ||  | || ||||||| ||||| || || || ||||| ||| ||||||| || |||||||||||||| ||||| || || || ||||||||||| ||||| ||||||||||
ccaatgtctactctttttttccaccagtcatatgatcatgactcttatcttgtgctgtctgcatttctaccga-gtaatg----aattttctcaacatgtcac-agGGTGTATTGGACGGGAAGTATGATGACCTTCCTGAGCAGTCATTCTACATGGTTGGAGGAATCGATGAGGTCATTGCCAAGGCAGAGAAGATTGCCAAGG

upper sequence: Vv17s0000g02900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G113408_T01 (Zea mays), 3'ss of exon 8
--gttgctcttttaacagaat-tttgattgcatgatgatttttgtcttcaacttttaaaatttcatctgatgtgatgctatgttgtgtttctcactttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATGGTTGGTGGAATTGAAGAAGTTATTGCCAAGGCCGAGAAAATTGCCAAGG
   ||  | || | | | ||   | |        ||   | |||   |    | ||    |||||   ||| || |  | | | |  | |   | | | | ||||||| |||||||| || || ||||| ||  ||||||| || ||||||||||||||||| ||||| ||||| ||||| ||||| ||||||||||||||||
tgtttagttttgtcagacaacactcgtgcattctatacatgttgcagtatgatgtttctgtttcac--gatctgcttttctatggaatcttatattgtgc-agGGTGTTTTGGATGGGAAGTATGATGACCTCCCTGAGCAGTCATTCTACATGGTTGGTGGCATTGAGGAAGTCATTGCTAAGGCTGAGAAAATTGCCAAGG

upper sequence: Vv17s0000g02900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G021331_T01 (Zea mays), 3'ss of exon 8
gttgctcttttaacagaattttgattgcatgatgatttttgtcttcaacttttaaaatttcatctga-tgtgatgctatgttgtg---tttctcactttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATGGTTGGTGGAATTGAAGAAGTTATTGCCAAGGCCGAGAAAATTGCCAAGG
    || |       | ||  ||||      ||   |    |  |    |  |||  | | | || | | || |||| |  | ||   ||| ||  ||   |||||||| |||||||| || || ||||| ||  ||||||| || |||||||||||||| || ||||| ||||| ||||| |||||||||||||| |||||||
----ctatccatgttgcatcatgatgtttctatttctccaattgttggttagtaatgtatgacctcactatggtgcttttgtatgaattttttctattgtgcagGGTGTTTTGGATGGCAAGTATGATGACCTCCCTGAGCAGTCATTCTACATGGTTGGAGGCATTGAGGAAGTCATTGCTAAGGCCGAGAAAATCGCCAAGG

upper sequence: Vv17s0000g02900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G041275_T01 (Zea mays), 3'ss of exon 8
gttgctcttttaacagaattttgat-tgcatgatgatttttgtcttcaacttttaaaatttcatc--tgatgtgatgctatgttgtgtttctcactttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATGGTTGGTGGAATTGAAGAAGTTATTGCCAAGGCCGAGAAAATTGCCAAGG
  |  | || |  ||  | |   ||    ||||| | |    | ||      || |   || | |  ||||    |  |  |      ||   ||  ||  |||| || |||||||| || || ||||| ||| | || || || |||||||||||||| ||||| || || || || |||||||| ||||| ||||||||||
--tatttttgtctcattactgaaatgcaaatgataactcccatttttgtgcctttaggctttaccagtgattaactatttggaccatctttgtaccgtat-agGGCGTTTTGGATGGCAAGTATGATGACCTTCCAGAACAGTCATTCTACATGGTTGGAGGAATAGAGGAGGTCATCGCCAAGGCAGAGAAGATTGCCAAGG

upper sequence: Vv17s0000g02900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA10G41330.1 (Glycine max), 3'ss of exon 8
-gttgct-cttttaacagaattttgattgcatgatgatttttgtcttcaacttttaaaatttcatctgatgtgatgctatgttgtgtttctcactttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATGGTTGGTGGAATTGAAGAAGTTATTGCCAAGGCCGAGAAAATTGCCAAGG
  | ||| |  ||  || | ||  | ||      ||  |    |  |   ||||    | |   ||| |||    | |   |  |   | |   | |  |||||||| |||||||||||||||||||| ||| | ||||| || || ||||||||||| || ||||| || || ||||| ||||||||||||||||| ||||
tatagctacaattgtcatacttgagtttatgaactgtctacgttgattttctttgtggact--gtctaatgcatggtttaatgattcctttgtatctgacagGGTGTGTTGGATGGAAAATACGATGACCTTCCAGAGCAGTCGTTTTACATGGTTGGCGGTATTGAGGAGGTCATTGCAAAGGCCGAGAAAATTGCTAAGG

upper sequence: Vv17s0000g02900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA10G41330.2 (Glycine max), 3'ss of exon 8
gttgctcttttaacagaattttgattgcatgatgatttttgtcttcaacttttaaaatttcatctgatgtgatgctatgttgtgtttctcactttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATGGTTGGTGGAATTGAAGAAGTTATTGCCAAGGCCGAGAAAATTGCCAAGG----------------------------------
                     ||  | | |  |||||||  |  |  ||| |  ||        || | | ||| |   || ||| ||| ||      ||||||| |||||||||||||||||||| ||| | ||||| || || ||||||||||| || ||||| || || ||||| ||||||||||||||||| ||||                                  
---------------------tgtctacgt--tgattttctttgtggactgtctaa----tgcatggtttaatgattcctt-tgtatctgac------agggtgtgttggatggaaaatacgatgaccttccagAGCAGTCGTTTTACATGGTTGGCGGTATTGAGGAGGTCATTGCAAAGGCCGAGAAAATTGCTAAGGAATCTGCAGCGTCTTAATCACACACAGCCCTGTT

upper sequence: Vv17s0000g02900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA20G25920.1 (Glycine max), 3'ss of exon 8
--gttgctctttta-acagaattttgattgcatgatgatttttgtcttcaacttttaaaatttcatctgatgtgatgctatgttgtgtttctcactttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATGGTTGGTGGAATTGAAGAAGTTATTGCCAAGGCCGAGAAAATTGCCAAGG
   |||   | | | ||     ||  ||||  | | ||  || || |||   || |  | |      || |       |   |||| ||| |   | |  |||||||| |||||||| ||||||||||| ||  | ||||| || || ||||||||||| || |||||||| || ||||| ||||| ||||||||||| ||||
caattgtcatgtcatacttgtgttctattgtct-acgacgttggttttc--tttgtggactaatgcatggttaatgattcctttgtttttgtgtatctgacagGGTGTGTTGGATGGCAAATACGATGACCTCCCAGAGCAGTCGTTTTACATGGTTGGCGGTATTGAAGAGGTCATTGCTAAGGCTGAGAAAATTGCTAAGG

upper sequence: Vv17s0000g02900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G08670.1 (Arabidopsis thaliana), 3'ss of exon 8
gttgctcttttaacagaattttgattgcatgatgatttttgtcttcaacttttaaaatttcatctgatg--tgatgctatgttgtgtttctcactttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATGGTTGGTGGAATTGAAGAAGTTATTGCCAAGGCCGAGAAAATTGCCAAGG
     | |  |  |   || | | |  |||  | |  |||||  | | |       |||   |    |   |||  |||  |  |  || |   | |  |||||| | |||||||| || |||||||||||||| || ||||| || ||||||||||| || || || || ||  |||| ||||| ||||| || || || |
tcctttgtgatgtctatatctagttgccatagttagatttgttgttatcaaaatggattatgtagagtaactgac-ctaaatcat-cttgtgtttgtttcagGGTTTGTTGGATGGCAAGTACGATGATCTTTCCGAACAATCGTTTTACATGGTTGGAGGTATCGATGAGGTGGTTGCAAAGGCAGAGAAGATCGCTAAAG

upper sequence: Vv17s0000g02900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G08680.1 (Arabidopsis thaliana), 3'ss of exon 8
-gttgctct---tttaacagaattttgattgcatgatgatttttgtcttcaacttttaaaatttcatctgatg--tgatgctatgttgtgtttctcactttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATGGTTGGTGGAATTGAAGAAGTTATTGCCAAGGCCGAGAAAATTGCCAAGG
 | ||  ||   ||||        | ||| |  |  | ||| |    |  ||  |||| | |   |     ||    |    || |||||||| |        |||||| | |||||||| || |||||||||||||| || ||||| || ||||||||||| || || || || ||  |||| ||||| ||||| || || || |
agatggactaaatttactctggcgtagatagatttgttattatcaaatagaatatttagagtaagagtaagtgaccaaaatcatcttgtgtttgtt------tcagGGTTTGTTGGATGGCAAGTACGATGATCTTTCCGAACAATCGTTTTACATGGTTGGAGGTATCGATGAGGTGGTTGCAAAGGCAGAGAAGATCGCTAAAG

upper sequence: Vv17s0000g02900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S154_69V6.1 (Physcomitrella patens), 3'ss of exon 4
gttgctcttttaa-cagaattttgattg-catgatgatttttgtcttcaacttttaaaatttcatctgatgtgatgctatgttgtgtttctcactttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATGGTTGGTGGAATTGAAGAAGTTATTGCCAAGGCCGAGAAAATTGCCAAGG
  || |     |      ||| |  |||    |  || |   |   |    ||||    |||    || || ||| |    |      || |   |   |||||||| |||||||| || ||||||||| |  |||||||| |||||||||||||||| || ||||| || |||      ||||| |||||  | |||||||
--tgtttgccgaggttagattgtacttgatgcgtagagtaacgaagtagggtttttgggtttttgatggtgcgattcctgatgagacatcgccgatgtgcagGGTGTGTTGGATGGTAAGTACGATGATTTGCCTGAGCAAGCTTTCTACATGGTTGGCGGTATTGAGGAGGTTTCGCAGAAGGCTGAGAAGCTGGCCAAGG

upper sequence: Vv17s0000g02900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ31624 (Selaginella moellendorffii), 3'ss of exon 8
gttgctcttttaacagaattttgattgcatgatgatttttgtcttcaacttttaaaatttcatctgatgtgatgctatgttgtgtttctcactttac-cagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATGGTTGGTGGAATTGAAGAAGTTATTGCCAAGGCCGAGAAAATTGCCAAGG
                              |    |     ||   | || ||   || |  ||  |             ||   ||   | | |   |||||||| |||||||| || ||||||||| |  | ||||||||||||||||||||||| ||||| || |||||  | || ||||| |  ||  | || ||||
------------------------------gtcagtaaacatcaaaagctcttctcatattttcctagcaagcaaaggactgaagtttggattctttgcagGGTGTTTTGGATGGCAAGTACGATGATTTGCCAGAGCAATCTTTCTACATGGTTGGAGGAATCGATGAAGTGGTCGCAAAGGCTGCTAACTTGGCTAAGG

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|30328286|gb|CD011548.1|CD011548
EST:     GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAA                         GGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAGTCTTTCTACATG
genomic: GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAAgtgagtgtca ... actttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATG
EST: gi|30328075|gb|CD011337.1|CD011337
EST:     GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAA                         GGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAGTCTTTCTACATG
genomic: GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAAgtgagtgtca ... actttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATG
EST: gi|32247472|gb|CD713291.1|CD713291
EST:     GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAA                         GGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAGTCTTTCTACATG
genomic: GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAAgtgagtgtca ... actttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATG
EST: gi|30133973|gb|CB919312.1|CB919312
EST:     GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAA                         GGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAGTCTTTCTACATG
genomic: GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAAgtgagtgtca ... actttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATG
EST: gi|32269428|gb|CD718587.1|CD718587
EST:     GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAA                         GGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAGTCTTTCTACATG
genomic: GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAAgtgagtgtca ... actttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATG
EST: gi|156738949|gb|EV243062.1|EV243062
EST:     GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAA                         GGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAGTCTTTCTACATG
genomic: GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAAgtgagtgtca ... actttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATG
EST: gi|30323044|gb|CD006306.1|CD006306
EST:     GAGCCCCTGGAAAATACGTAGAACTAANAGAGAGCATTACCAGTTTCCAA                         GGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAGTCTTTCTACATG
genomic: GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAAgtgagtgtca ... actttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATG
EST: gi|30129011|gb|CB914350.1|CB914350
EST:     GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAA                         GGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAGTCTTTCTACATG
genomic: GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAAgtgagtgtca ... actttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATG
EST: gi|18459809|gb|BM438087.1|BM438087
EST:     GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAA                         GGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAGTCTTTCTACATG
genomic: GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAAgtgagtgtca ... actttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATG
EST: gi|110381762|gb|EC935319.1|EC935319
EST:     GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAA                         GGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAGTCTTTCTACATG
genomic: GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAAgtgagtgtca ... actttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATG
EST: gi|27586507|gb|CB009202.1|CB009202
EST:     GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAA                         GGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAGTCTTTCTACATG
genomic: GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAAgtgagtgtca ... actttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATG
EST: gi|32267434|gb|CD716397.1|CD716397
EST:     GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAA                         GGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAGTCTTTCTACATG
genomic: GAGCCCCTGGAAAATACGTAGAACTAAAAGAGAGCATTACCAGTTTCCAAgtgagtgtca ... actttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacttttaaaatttcatctgatgtgatgctatgttgtgtttctcactttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATGGTTGGTGGAATTGAAGAAGTTATTGCCAAGGCCGAGAAAATTGCCAAGG
                                        ttctcac  putative branch site (score: 2)
                                       tttctcactttacc  CT-rich tract
     tttaaaatttcatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgctcttttaacagaattttgattgcatgatgatttttgtcttcaacttttaaaatttcatctgatgtgatgctatgttgtgtttctcactttaccagGGTGTCTTGGATGGAAAATACGATGATCTTTCTGAGCAATCTTTCTACATGGTTGGTGGAATTGAAGAAGTTATTGCCAAGGCCGAGAAAATTGCCAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - -aacagaa
- - - - - - - - - - - - - gcatgat
- - - - - - - - - - - - - - - - - - - - - cttcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtg