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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaatgtgggcatggttctaatatctttttgttgaatttctgtggtatggtgcttatttttattattttaagtctaatttatattgatgtacttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT

Basic information

species Vitis vinifera
transcript Vv13s0067g01290.t01
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 27
---ttaatgtgggcatggttctaatatctt-tttgttgaatttctgtggtatggtgcttatttttattattttaagtctaatttatattgatgtacttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT
   || | |||      |       | ||  ||| ||  |||  |  || ||  |   ||||   ||| |  | |||   || |||| |  ||||   |||||||||||||||||||||||||| ||||| |||||| | || || ||||| || ||| | ||  |||||||||| ||||| ||||| ||||| ||||| ||||
caattgaagtgaaacaagcaagctcacctgattttttttattatttaggcataatctgtattgc-attctgatgagtaacatctataattgtgta---ttgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 27
-------ttaatgtgggcatggttctaatatctttttgttgaatttctgtggtatggtgcttatttttattattttaagtctaatttatattgatgtacttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT
        | |     |||  | ||   |   ||||| ||  |||  |  || ||  |   ||||   ||| |  | |||   || |||| |  ||||   |||||||||||||||||||||||||| ||||| |||||| | || || ||||| || ||| | ||  |||||||||| ||||| ||||| ||||| ||||| ||||
aattgaagtgaaacaagca-agctcacctgattttttatt--attatttaggcataatctgtattgc-attctgatgagtaacatctataattgtgta---ttgcagGGAAAGAAAGAATGCTTTGCTTCTTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 25
---------------ttaatgtgggc--atggttc--taatatctttttgttgaatttctgtggtatggtgcttatttttattattttaagtctaatttatattgatgtacttt---tgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT
                |  | | |||  ||| |     | || ||  ||    | | | |   | |    ||||||  ||   ||| | | |   |   | ||  |   |  |    || |||| ||||||||||| ||||| |||||||||||  | ||||||||| | || || |||||  | |||||||| ||||| ||||| ||||| ||||| ||||
gtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaagcttatgcttgc-attctgattagtaaacacatccaatcatatgtaatgtagGGTAAGAAAGAATGTTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCAGATGTGGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 7
----------------------ttaatgtgggcatggttctaatatctttttgttgaatttctgtggtatggtgcttatttttattattttaagtcta-atttatattgatgtacttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT
                      |   ||  |  ||||   ||   |  ||   |   || |       | || |  |  ||  ||| |  | |||  | |  |  | | || |  |  ||||||| ||||||||||| ||||| |||||||||||  | ||||||||| | || || || ||  | |||||||| ||||| ||||| ||||| ||||| ||||
gtttggttcgaacccattgtattggctgatgatatgggagtagc-taattcaatactatatacagcaaaaggcgtatgcttgcattctgattagtaaacacatccaatcatatg-taatgcagGGTAAGAAAGAATGTTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 12
---------------ttaatgtgggc--atggttc--taatatctttttgttgaatttctgtggtatggtgcttatttttattattttaagt--ctaatttatattgatgtac-ttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT
                |  | | |||  ||| |     | || ||  ||    | | | |   | |    || |||  ||   ||| | | |    ||   ||       ||  |  ||||||| ||||||||||| ||||| |||||||||||  | ||||||||| | || || || ||  | |||||||| ||||| ||||| ||||| ||||| ||||
gtttggttcgaacccattgtattggctgatgatatgggagtagctaattcaatactatatacagcaaaaggcgtatgcttgc-attctgattagtaaacgcatccaatcatatgtaatgcagGGTAAGAAAGAATGTTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 4
----------------------------ttaatgtgggcatggttctaatatctttttgttgaatttctgtggtatggtgcttatttttattattttaagtctaatttatattgatgtacttt-tgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT
                             |||| || |  | |   |||   ||  ||  | |  | ||    | |  | |||    ||   ||| | | |   |  |  ||  ||  |  |    ||||| ||||||||||||||||| |||||||||||  | ||||||||| | || || || ||  | |||||||| ||||| ||||| ||||| ||| | ||||
gtttggttgaaacccattctattgactgataatatgagactagcgataag--ctaattcataaggtcctagtctgtc-tacttggcattgc-attctgattagcaaatccatccattcatgtaacacagGGTAAGAAAGAATGCTTTGCTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCGTGGATGAACAACATGTTGGACT

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 12
ttaatgtgggcatggttctaatatctttttgttgaatttctgtggtatggtgcttatttttattattttaagt--ctaatttatattgatgtacttt-tgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT
        | ||   |   | || ||  ||    | | | |   | |    || |||  ||   ||| | | |    ||   ||       ||  |  ||||||| ||||||||||| ||||  |||||||||||  | ||||||||| | || || || ||  | |||||||| ||||| ||||| ||||| ||||| ||||
--gtccccgacaatatgggagtagctaattcaatactatatacagcaaaaggcgtatgcttgc-attctgattagtaaacgcatccaatcatatgtaatgcagGGTAAGAAAGAATGTTTTGTTTCTTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACT

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 26
-ttaatgtgggcatg-gttctaatat-ctttttgttgaatttctgtggtatggtgcttatttttattattttaagtctaatttatattgatgtacttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT-
  | |      ||||  || |||| | ||| ||  | |||     |   || | |     |     |||| |||     |||| | |  |  |  || ||||||||||||||||||||||||| || || || ||||| ||||| || || || ||  ||||||||||||||||| | |||||||| ||||||||| |||||| 
tcttacagtcccatgtattttaattttcttatttgttaatgcgcatacaattgagtagggtcaatatattctaat----atttctttccacatggttatgcaggGAAAGAAAGAATGCTTTGCCTCGTGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAATTGGCCTGGATGAACAATATGATTGACTT

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 26
--ttaatgtgg-gcatggttctaatatctttttgttgaatttctgtggtatggtgcttatttttattattttaagtctaatttatattgatgtacttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT
  |||  ||      | |||  | | |||| ||  | ||| |   |  ||| |  || |  |  | ||| ||        ||| | |  |  |  || ||||||||||||||||||||||||| || || || ||||| ||||| || || || ||  ||||||||||||||||  | |||||||| ||||||||| ||||||
tcttacagtcccatgtagtttaattttcttatttgttaatgtgcatactattg-actaaggtcaaatatattctaat--gtttctttccacatgtttatgcagGGAAAGAAAGAATGCTTTGCCTCGTGTCTATTTGTTTGCTATGATTTGATCCGGGCAGACATTGCTCTTGAGTTGGCCTGGATGAACAATATGATTGACT

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 27
--------ttaatgtgggcatggttctaatatctttttgttgaatttctgtggtatggtgcttatttttattattttaagtctaatttatattgatgtacttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT
        ||  | ||  |  ||   | |||   |||     ||||| | |  |||  ||| |||  ||   ||||  |    | ||| | || || | ||| ||||||||||||| ||||||||||| || || || ||||| ||||| || || || ||  ||||||||| ||||||||| || |||||  |||||||| ||||||
caatcttttttgtttgtcctcgggagtgatagtatttc----aatttatttattata-tgcatataattgagatttctaa---attttcttttcatatgcttatgcagGGAAAGAAGGAATGCTTTGCCTCATGTCTATTTGTTTGCTATGATTTGATACGGGCAGACATTGTTCTTGAACTAGCTTGGATGCACAATATGATTGACT

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 27
-ttaa--tgtgggcatggttctaatatctttttgttgaatttctgtggtatggtgcttatttttattattttaagtctaatttatattgatgtacttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT
 | ||  | |     | || |||||    |  |  |   |   | |  |   |||| |||  ||   ||||  |    | ||| | || || | ||| ||||||||||||| ||||||||||| || || || ||||| ||||| ||  | || ||  ||||||||| ||||||||| || |||||  |||||||| ||||||
ttcaagctttttagtttgtcctaatggagtgatagtatttcaatttatttatgtgcatataattgagatttctaa---attttcttttcatatgcttatgcagGGAAAGAAGGAATGCTTTGCCTCATGTCTATTTGTTTGCTATGATCTCATACGGGCAGACATTGTTCTTGAACTAGCTTGGATGCACAATATGATTGACT

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 27
-----------------------------ttaatgtgggcatggttctaatatctttttgttgaat-ttctgtggtatggtgcttatttttatt--------attttaagtc-----taatttatattgatgtacttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT
                               || |     |   |  |   | ||||||   | || |  |     |    |  ||||  || |        | ||||  ||     |  | ||| |||   |  |||| ||||| || || |||||||||||  | || |||||||| || || |||||||| || |||||| ||||||| |||||||| ||||| ||||||||| | ||||
gtatggataggtttcaggcaggattacatcgaaagccattagtctattttcaactttttaccgtatatggtaaaacagaaagactattggtactgaagatgaaatttacatccccgttgttgtatgttgtgctggttttacagGGGAAAAAGGAATGCTTTGCTACATGTCTCTTTGTCTGTTATGACTTAATCCGACCAGACGTTGCTCTAGAACTTGCTTGGATCAACAATATGATCGACT

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 27
-------------ttaatgtgggcatggttctaatatctttttgttgaatttctgtggt--atggtgcttatttttattattttaagtc-taatttatat-tgatgtacttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT
             | ||  |   |  | | ||| |  ||     || | |||   | ||  |      ||  |       ||  | ||  ||     | | |  ||   || | ||||| || || |||||||||||  | || |||||||| || || |||||||| || |||||| | ||||| |||||||||||||| ||||||||| | ||||
gtatgatgatggttaaacatttacgagatgctagtg-ctagccattcagtttggttagttgaaaagaattggtccagacgttgaacgtagtatcccgtgtcttctgctgttatacagGGCAAAAAGGAATGCTTTGCTACATGTCTCTTTGTATGTTATGACTTAATCCGACCAGACGTGGCTCTAGAACTTGCCTGGATCAACAATATGATGGACT

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|71858842|gb|DT007897.1|DT007897
EST:     CTGGTGACCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGAAG                         GGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATT
genomic: CTGGTGACCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGAAGgtacccagaa ... acttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATT
EST: gi|161720108|gb|FC066740.1|FC066740
EST:     CTGGTGACCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGAAG                         GGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATT
genomic: CTGGTGACCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGAAGgtacccagaa ... acttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATT
EST: gi|71888995|gb|DT038050.1|DT038050
EST:     CTGGTGACCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGAAG                         GGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTA
genomic: CTGGTGACCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGAAGgtacccagaa ... acttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTA
EST: gi|294964474|gb|GW838277.1|GW838277
EST:     CTGGTGACCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGAAG                         GGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATT
genomic: CTGGTGACCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGAAGgtacccagaa ... acttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATT
EST: gi|33402568|gb|CF208195.1|CF208195
EST:     CTGGTGACCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGAAG                         GGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATT
genomic: CTGGTGACCGTGAACTTGCAGAGGAGTTGCTTGTTTATTTCATTGAGAAGgtacccagaa ... acttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggtgcttatttttattattttaagtctaatttatattgatgtacttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT
                                    tattgat  putative branch site (score: 3)
                                            tactttt  CT-rich tract
        ttatttttattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaatgtgggcatggttctaatatctttttgttgaatttctgtggtatggtgcttatttttattattttaagtctaatttatattgatgtacttttgcagGGAAAGAAAGAATGCTTTGCATCTTGCCTCTTTGTGTGCTACGACTTAATTCGTCCAGACATTGCTCTTGAACTTGCCTGGATTAACAATATGGTTGACT

- - - - -gcatggt