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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtctttttagaaccagatcttaagccatatctcttacctaaatgtctttttccttaacttttttattttttttttctgagtaattctcattaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA

Basic information

species Vitis vinifera
transcript Vv19s0135g00100.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G13270.1 (Glycine max), 3'ss of exon 3
--tgtctttttagaaccagatcttaagccatatctcttacctaaatgtctttttccttaacttttttattttttttttctgagtaattctcattaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA-
   |  |   | ||  |   | ||   || | | | |  | | |   |  |   |   ||   ||  |     |  |    | |  ||     | | || ||||||||||||| ||||| |||||||| || || |||||||||||| |||||||||||||||||||||| |||||||||||||||||||||||||| || | 
taggagtacctggagacgatttttttcccctgtttttagcttcagcattctaggctccaa---ttgcagacagtgatgtataattctttatgcttattgtagaTTTTTGAGAAAAATCCTACCAAGATCAAGAATTATGGAATTTGGCTGCGATATCAGAGCCGAACTGGTTATCACAACATGTACAAGGAATATCGCGATAC

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G03380.1 (Glycine max), 3'ss of exon 3
tgtctttttagaaccagat-cttaagccatatctcttacctaaatgtctttttccttaacttttttattttttttttctgagt---aattctc--attaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA
      ||  |||  | || ||| | | |    |  ||  | |   ||   || ||    | ||  |   |     |    ||   | || |   | | | |||||||||||||||||||||| |||||||| || || |||||||||||| |||| ||||||||||| ||||| |||||||| |||||||||||||| || || |
------ttaggaaagaaatacttgaacaaatatttgtattttagcttccaattgctgtcttattggacaatggacatggaggtttgagtttttgtactgattgcagATTTTTGAGAAGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGTTATCAGAGCCGCACTGGTTATCACAATATGTACAAGGAATACCGAGATA

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G45430.1 (Glycine max), 3'ss of exon 3
tgtctttttagaaccagatcttaagccatatctcttacctaaatgtctttttccttaacttttttattttttttttctgag---taattctc---attaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA
      ||  |||  | ||  ||   || || | |    |  | ||     |      ||| ||      |       |||   | ||| |      | | ||||||||||||||| |||||| |||||||| || || |||||||||||| |||| |||||||| || ||||| |||||||| |||||||||||||| || || |
------ttaggaaagaaatactagaacaaatatttgtattctaggttccaattgcagtcttattggacaatgaacatggaggtttgattttttgtgctgattgcagATTTTTGAGAGGAATCCTACCAAGATTAAGAATTATGGAATTTGGCTGCGGTATCAGAGTCGTACTGGGTATCACAATATGTACAAGGAATACCGAGATA

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G10220.1 (Glycine max), 3'ss of exon 3
-tgtctttttaga--accagatcttaagccatatctcttacctaaatgtctttttccttaacttttttattttttttttctgagtaattctcattaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA
 ||  |||   ||  |    | || |      |   |     ||  | ||| ||  || |   |   |  | | || |  ||| | ||| |  ||   | ||||||||||||||||| || ||||| || || |||||||| || |||||||| ||||||||  | ||||| || ||||||||||||||||| || || ||||
ctggatttgcggattatttcaactcagtttgaaatacaatgttagttttctgttggctaattgtgggtgctctgttctgttgaattattttattt---tccagATTTTTGAGAAGAACCCAACCAAAATTAAGAACTATGGTATATGGTTGCGGTATCAGAGTAGGACTGGTTACCACAACATGTACAAGGAGTACCGTGACA

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S74_193V6.2 (Physcomitrella patens), 3'ss of exon 3
tgtctttttagaaccagatcttaagccatat-ctcttacctaaatgtctttttccttaacttttttat-----tttttttttctgagta--attctcattaa------ctgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA
  ||  ||| ||||| | ||| |    |||  |||||      ||  |  | ||   || || |            || |   ||| ||  | ||| |  |       |||||||||||||||||| | || ||||  || || |||||||| || ||| |||| |||||||| || || || || ||||||||||||||||            
-ttcaatttcgaacc-gttctcagtgtatacgctcttgaaaccatcccaatgtcgggaaattataagcagagacaattgtcgttgaatatgaatctgaccagACGTTCCTGCAGATTTTTGAGAAGTACCCTACCACTATCAAGAACTATGGTATCTGGGTGCGTTATCAGAGTCGGACCGGGTACCACAACATGTACAAGG------------

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S44_13V6.1 (Physcomitrella patens), 3'ss of exon 3
tgtctttttagaaccagatcttaagccatatctcttacctaaa-----tgtctttttccttaacttttttatttttttttt-ctgagtaattct--cattaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA
         | || | |    |    | | ||  | |||||||       |   || ||  |  ||    ||   | | |  ||||  | | ||       | | ||||||||||||||| | || ||||  || || ||||| || |||||| || | ||||| || || || ||||| |||||||||||||||||||| || ||  
--------gacaaacgggcaatgccacgtttcgttaacctaaagagagcattggttaccgaaggttgcacatcggtgtgtcactgaacactcctgttgcccattccagATTTTTGAGAAGTACCCTACCACCATCAAGAACTACGGTATTTGGGTGAGGTATCAAAGTCGTACCGGATACCACAACATGTACAAGGAATACCGTGATC

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S56_243V6.3 (Physcomitrella patens), 3'ss of exon 3
---tgtctttttagaaccagatcttaagccatatctcttacctaaatgtctttttccttaacttttttattttttttttctgagtaattctcattaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA
   |   || || ||    ||  ||| |  |    | |||   |  ||   ||     | || ||   | || | ||      ||| || |    | || ||||||||||||||| |||||||||  || || |||||||| || ||| |||| ||||||||||| ||||| || ||||||||||||||||| || || ||| 
agatacattgtttgagggcgaaattatgttaacaatgttaatca--tgggcttgaaagtgacgttacgaattctattactaatgtagtttttga-accttcagATTTTTGAGAAGTATCCCACCACCATCAAGAACTATGGTATCTGGGTGCGTTATCAGAGCCGGACTGGCTACCACAACATGTACAAGGAGTACCGTGACC

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S74_193V6.1 (Physcomitrella patens), 3'ss of exon 3
-tgtctttttagaaccagatcttaagccatatctcttacctaaatgtctttttccttaacttttttattttttttttctgagtaattctcattaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA
  ||  |    | |   | |||| |  |    |   |  |   |  |  |   |    ||  || |   ||   | |     | |       |  |||||||||||||||||| | || ||||  || || |||||||| || ||| |||| |||||||| || || || || ||||||||||||||||| ||||| ||| 
ccgttctcagtgtatacgctcttgaaaccatcccaatgtcgggaaattataagcagagacaattgt-cgttgaatatgaatctgaccagacgttcctgcagATTTTTGAGAAGTACCCTACCACTATCAAGAACTATGGTATCTGGGTGCGTTATCAGAGTCGGACCGGGTACCACAACATGTACAAGGAGTATCGTGACC

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S5_178V6.1 (Physcomitrella patens), 3'ss of exon 3
tgtctttttagaaccagatcttaagccata-tctcttacc--taaatgtctttttccttaacttttttatttttttt--ttctgagtaattc--tcattaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA
       | |  | || || ||| |  | | ||  | | |   ||| |  | |      ||         |  |  |  | |||| | |  |  || ||   | ||||||||||||||| | || ||||  || || || ||||| || ||| |||| |||||||| |||||||| || ||||||||||||||||| || || ||| 
------atcactagcatattttatgggagactcattcagcgacaaacggatgtagaggaaatgagccagataatcatgatactgaatgacccaatcgttgttt-cagATTTTTGAGAAGTACCCTACCACTATCAAGAATTATGGTATCTGGGTGCGTTATCAGAGTCGAACTGGCTACCACAACATGTACAAGGAGTACCGTGACC

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S184_111V6.1 (Physcomitrella patens), 3'ss of exon 3
--tgtctttttagaaccagatcttaagccatatctcttacctaaatgtctttttccttaacttttttattttttttttctg-agtaattctcattaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA
  ||    || || |  |  |   || ||| |  | ||    |   |  |   |   |   || |  | |||  || |    | |  || |     |   ||||| || |||||| |||| || |  || || ||||| || || ||| |||| || ||||||||||| || || |||||||||||||||||||| || ||  
agtgggcgttaaggat-atgtgggaatccagagattttgg--agtcggttcacttgatggtttatccaatttcattgttgacaatgcttgttgcgcatgccagATCTTCGAGAAGTATCCAACTACCATCAAGAACTACGGTATATGGGTGCGGTACCAGAGCCGAACCGGCTACCACAACATGTACAAGGAATACCGTGATC

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S101_218V6.1 (Physcomitrella patens), 3'ss of exon 3
tgtctttttagaaccagatcttaagccatatctcttacctaaatgtctttttccttaacttttttattttttttttctgagtaattctcattaactg--cagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA
 |   | | ||    | ||   ||  || || | ||     |   |  ||       | | |   ||||    | | | || |  |||  ||  | |  ||||| ||||||||| |||| ||||  || || ||||| || || ||| |||||||||| |||||||| || || ||||| ||||||||||| || || ||  
cggtctctgagggt-atatagcaatgcagatattttgatacagcctacttcaggcggagtgtccaatttcgaatat-taaggatgtctgtttcgcggttcagATCTTTGAGAAGTATCCAACCACCATCAAGAACTACGGGATCTGGGTGCGATATCAAAGCCGAACCGGCTACCACAATATGTACAAGGAGTACCGTGATC

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ38689 (Selaginella moellendorffii), 3'ss of exon 3
tgtctttttagaaccagatcttaagccatatctcttacctaaatgtctttttccttaacttttttattttttttttctgagtaattctcattaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA
                           | |  |||| | |     |  |||||   | | ||   | |      ||  ||      ||   | ||  |||||||| |||||||| || |||| ||| || |||||||| || ||| || | || |||||||| || || || ||||||||||||||||| || || ||||
-------------------------gtaaagttctttctttttctttcttttctcgagccttacaagtgagaactttggaa-----cttcgtgac-acagATTTTCGAGAAGAACCCGACCACGATCAAGAACTATGGCATCTGGGTGAGGTACCAGAGCCGGACGGGGTACCACAACATGTACAAGGAGTACCGCGACA

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ31458 (Selaginella moellendorffii), 3'ss of exon 3
tgtctttttagaaccagatcttaagccatatctcttacctaaatgtctttttccttaacttttttattttttttttctgagtaattctcattaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA
                    | |||   | ||| || | |   |  ||   | ||  |   ||  |  |      | ||    |   || | |    |||||||| |||||||| || |||| ||| || |||||||| || ||| || | || |||||||| || || || ||||||||||||||||| || || ||||
-------------------gtaaagttctttctttttctttctttcctcgatgctctagccttacaagtgagaactttgg---aacttcgtga--cacagATTTTCGAGAAGAACCCGACCACGATCAAGAACTATGGCATCTGGGTGAGGTACCAGAGCCGGACGGGGTACCACAACATGTACAAGGAGTACCGCGACA

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|30135992|gb|CB921330.1|CB921330
EST:     AGCTCAAGAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAG                         ATTTTTGAGAAGAATCCTACCAAGATAAAAAACTATGGAATTTGGTTGCGA
genomic: AGCTCAAGAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAGgtacctgtta ... ttaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGA
EST: gi|51990043|gb|CV179498.1|CV179498
EST:     AGCTCAAGAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAG                         ATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGA
genomic: AGCTCAAGAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAGgtacctgtta ... ttaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGA
EST: gi|294966449|gb|GW839556.1|GW839556
EST:     AGCTCAAGAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAG                         ATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGA
genomic: AGCTCAAGAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAGgtacctgtta ... ttaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGA
EST: gi|71875043|gb|DT024098.1|DT024098
EST:     AGCTCAAGAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAG                         ATTTTTGAGAAGAATCCCACTAAGATAAAAAACTATGGAATTTGGTTGCGA
genomic: AGCTCAAGAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAGgtacctgtta ... ttaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGA
EST: gi|71869765|gb|DT018820.1|DT018820
EST:     AGCTCAAGAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAG                         ATTTTTGAGAAGAATCCCACTAAGATAAAAAACTATGGAATTTGGTTGCGA
genomic: AGCTCAAGAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAGgtacctgtta ... ttaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGA
EST: gi|27586002|gb|CB008697.1|CB008697
EST:     GAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAG                         ATTTTTGAGAAGAATCCTACCAAGATAAAAAACTATGGAATTTGGTTGCGA
genomic: GAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAGgtacctgtta ... ttaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGA
EST: gi|71875150|gb|DT024205.1|DT024205
EST:     AGCTCAAGAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAG                         ATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGA
genomic: AGCTCAAGAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAGgtacctgtta ... ttaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGA
EST: gi|87585836|gb|DY474390.1|DY474390
EST:     AGCTCAAGAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAG                         ATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGA
genomic: AGCTCAAGAAAGTTAAGAAGAGCAATGGTCAAGTTTTGGCAATTAATGAGgtacctgtta ... ttaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttccttaacttttttattttttttttctgagtaattctcattaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA
                                           cattaac  putative branch site (score: 2)
                                       ttctcatt  CT-rich tract
              ttttttattttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtctttttagaaccagatcttaagccatatctcttacctaaatgtctttttccttaacttttttattttttttttctgagtaattctcattaactgcagATTTTTGAGAAGAATCCCACCAAGATAAAAAACTATGGAATTTGGTTGCGATATCAGAGCCGAACTGGATATCACAACATGTACAAGGAATATCGGGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - -agaacca
- - - - - - - - - - -taagcca
- - - - - - - - - - - - - - - - - - acctaaa