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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctttgaagatatggatggaaagatgttgaattcttttctttgttacttatgagatgtcattcctggagtcaagtctgtatttattgtttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG

Basic information

species Vitis vinifera
transcript Vv02s0012g00530.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g03540.1 (Oryza sativa), 3'ss of exon 5
agctttgaaga-tatggatggaaagatgttgaattcttttctttgttacttatgagatgtcattcctggagtcaagtctgtatt-tattgtttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG
   |  || || | |  ||    | |||||| || ||| | |   ||  | |||   ||| |          | |   | |||  | ||  ||   |||||||| |||||||| ||||| ||||| | ||||||||| || || ||| ||||||| ||||||||||| ||||
-tttcagacgagtctatatcactacatgttgcatacttgtttaaatt-ttcatgctttgtgagattaaaccactacagtttatcatgttcatttttttacagGTAATGAATCTTATTGGAGATGTTAGAGGAAAAGTGGCTGTTATGATGGATGATATGATTGATACAGCTG

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G038791_T01 (Zea mays), 3'ss of exon 5
--agctttga--agatatgga-----tggaaagatgttgaattcttttctttgttacttatgagatgtcattcctggagtcaagtctgtatttattgtttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG
  ||||||      |||   |     || |   ||| ||||| | | | | | ||| || | ||    |||        |    | || |||||||         ||||||||||||||| ||||| || || | ||||||||| || || ||| ||||||| ||||| || || || |
acagctttagctgaatacaaaccatctgcagctatgctgaatacatgtttatcttaattttcaggctgcatgttcatcttgtcatgtgcatttatt---------acagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G06110.1 (Glycine max), 3'ss of exon 5
------agctttgaagatatggatggaaagatgttgaattcttttctttgttacttatgagatgtcattcctggagtcaagtctgtatttattgtttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG
      || ||||||  |    ||||     |    | || | |  | |  || ||||     | ||  | |    ||     | | | |  |||||    | ||||||||||| |||||||||||||| |||||||||||||| || ||||||||||| |||||||| |||||||
attgttagttttgaatgtgctcatggtt---tagctagttttatggtatactaattatcctcgggcaaactta---tctgtcttctgtcttatgtttgtgatgcagGTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTGGATGATATGATTGACACTGCTG

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G16400.4 (Glycine max), 3'ss of exon 5
agctttgaag-atatggatggaaagatgttgaattcttttctttgt--tacttatgagatgtcattcctggagtcaagtctgtatttattgtttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG------------------------------
| ||| |  | ||    ||    || | ||||||    |   | ||  || ||||        | |     |  |   | |||  |||| ||||  |    |||||||||| |||||||||||||| |||||||||||||| || ||||| ||||| ||||| || |||||||                              
aacttagttgcattcttatttttagtt-ttgaatgtactagctagtagtaattatcct-cacgactaacttaaacgtatatgtggttat-gtttgaccggtagGTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTAGATGATATGATCGACACTGCTGGTATGCCATCGTCATTGTCCAATTTGAACT

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G16400.3 (Glycine max), 3'ss of exon 5
agctttgaag-atatggatggaaagatgttgaattcttttctttgt--tacttatgagatgtcattcctggagtcaagtctgtatttattgtttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG
| ||| |  | ||    ||    || | ||||||    |   | ||  || ||||        | |     |  |   | |||  |||| ||||  |    |||||||||| |||||||||||||| |||||||||||||| || ||||| ||||| ||||| || |||||||
aacttagttgcattcttatttttagtt-ttgaatgtactagctagtagtaattatcct-cacgactaacttaaacgtatatgtggttat-gtttgaccggtagGTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTAGATGATATGATCGACACTGCTG

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G35390.3 (Arabidopsis thaliana), 3'ss of exon 4
agctttgaagatatggatggaaagatgttgaattcttttctttgttacttatgagatgtcattcctggagtcaagtctgtatttattgt--ttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG
              | ||       | |   | ||     ||  | ||  |       |  ||||     | ||||    |||| || |  || |||| ||||| ||||| || ||||||||||| | ||| || || ||| | ||||||||||| ||||||||||||||||
--------------gtatccctttctttcagagtcagagtttgctcaccaacaccgcttgcttcccc---ttaagttcacatttgttatactttcctttcagGTCATGAACCTAATTGGTGATGTAAGAGGGAAGGTGGCAATAATGGTGGATGATATGATTGATACTGCTG

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 5
agctttgaagatatggatggaaagatgttgaatt-cttttctttgttacttatgagatgtcattcctggagtcaagtctgtatttattgtttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG
                  | ||| || |  | || | ||  |||  | |||   | | |  | | ||   ||   ||   ||   ||  | |  |  |||||| ||||| || || |||||||| ||||| || || ||||| ||||||||||| || |||||||| ||||
------------------gtaaaaatttaaatttaccttcattttatcctttctacacgcaagttctcatgt---gttgata---atactctttcccacagGTCATGAACCTAATCGGTGATGTTAAAGGGAAGGTGGCAGTAATGGTGGATGATATTATTGATACAGCTG

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S152_123V6.1 (Physcomitrella patens), 3'ss of exon 5
agctttgaagatatggatggaaagatgtt---gaattcttttctttgttactta-tgagatgtcattcctgg--agtcaagtctgtatttattgtttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG
      ||    ||     || | || ||   | ||   |     ||  |   | | || || |||    |   | ||    |  |   ||| | | |  | |||||| |||||| ||||||| || |||||||||||||| || ||||||||||| |||||||| || ||||| |
-----cgagataatacgctgacatatctttgaggatagatgaaactggaatgaactcagttgacatggacgactattcgcagccctgagtatggatgatgt-acagGTCATGAATTTGATTGGAGACGTCAAAGGAAAAGTGGCTGTCATGGTGGACGACATGATAGACACTGCCG

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S123_105V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------------------agctttgaagatatggat-ggaaagatgttgaattcttt-tctttgttacttatgagatgtcattcctgg--agtcaagtctgtatttattgtttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG
                                                                                                 |  | |  ||| |   | || |  || | ||  |   | | ||| ||       | || |  |  |        |||     |||||  |   |   |  ||||||||||| ||||| || |||||||| ||||| || ||||| ||| | ||||| |||||||| |||||||
gtgaattggcatcagcatccgcaccatctctaatgcactttgttttgtggatacaccctgcatgaccacttactcttccatggtgtaatttcctactgtatagttgatgtcatttggcatcatttagagctaagtatgtttcttgacggaaaaatcttgtatcaaactgaccaaagaaatatttgattcatgtttggcagGTGATGAACCTGATCGGAGATGTCAAGGGAAAGGTAGCAGTTATGCTTGATGATATGATTGACACTGCTG

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S212_43V6.1 (Physcomitrella patens), 3'ss of exon 3
agctttgaagatatggatggaaagatgttgaattctt-ttctttgttactta--tgagatgtcattcctggagtcaagtctgtatttattgtt---taccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG
          |  |  ||  | | |  || || | || || | |  |    |  | | ||    ||        ||  |  | |  |  | ||   ||   | ||||| ||||||||||| ||||||||  | || ||||| || || ||||| || || ||||||||||||||||
------atgtactttcataaagaaaatttaaactattattatctaatgtggaacttaaattcggtttggatcaccattttggaagctgattttggataatgtgcagGTTATGAATCTGATAGGTGATGTGCACGGGAAAGTGGCCGTGATGGTAGACGATATGATTGATACTGCTG

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ12994 (Selaginella moellendorffii), 3'ss of exon 4
agctttgaagatatggatggaaagatgttgaattcttttctttgttacttatgagatgtcattcctggagtcaagtctgtatttattgtttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG
                         ||  || || |||||||  ||  ||        || |||        |||  | | ||| |  ||| | || |||||||||||||| || ||||||||||| || ||| | |||||| |||| ||||| |||||||| |||||||
------------------------gtgc-gatttgttttcttctttggtt--------tctttca-------aagattttctttttctttttcttttcagGTGATGAATCTTATCGGTGATGTCAATGGCAAAATCGCAGTCGTGGTAGATGATATGATTGACACTGCTG

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ14005 (Selaginella moellendorffii), 3'ss of exon 4
agctttgaagatatggatggaaagatgttgaattcttttctttgttacttatgagatgtcattcctggagtcaagtctgtatttattgtttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG
                          ||   |||  |||| || ||            |  || ||    ||||   | | ||| |  ||| | || |||||||||||||| || ||||||||||| || ||| | |||||| |||| ||||| |||||||| |||||||
--------------------------gtgcgatttgtttccttctt------------tggtttctc---tcaaagatttctttttctttttcttttcagGTGATGAATCTTATCGGTGATGTCAATGGCAAAATCGCAGTCGTGGTAGATGATATGATTGACACTGCTG

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|45368105|gb|CK906464.1|CK906464
EST:     CGCCTTTAGCCATAGTGGATAAAAGGCGTCAAGGACATAATGTTGCTGAG                         GTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGAT
genomic: CGCCTTTAGCCATAGTGGATAAAAGGCGTCAAGGACATAATGTTGCTGAGgtaatttcca ... taccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGAT
EST: gi|30253361|gb|CB970912.1|CB970912
EST:     GCCTTTAGCCGTAGTGGATAAAAGGCGTCAAGGGACATAATGANGCTGAG                         GTGATGAATCTGATTGGTGATGTCAAAGGAAAAGANGCAGTCATGGTNGAT
genomic: GCCTTTAGCCATAGTGGATAAAAGGCGTCAAGG-ACATAATGTTGCTGAGgtaatttcca ... taccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGAT
EST: gi|30253440|gb|CB970991.1|CB970991
EST:     CGCCTTTACCCGTAGTGGATAAAAGGCGTCAAGGACATAATGTTGCTGAG                         GTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGAT
genomic: CGCCTTTAGCCATAGTGGATAAAAGGCGTCAAGGACATAATGTTGCTGAGgtaatttcca ... taccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGAT
EST: gi|30129654|gb|CB914993.1|CB914993
EST:     CGCCTTTAGCCATAGTGGATAAAAGGCGTCAAGGACATAATGTTGCTGAG                         GTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGAT
genomic: CGCCTTTAGCCATAGTGGATAAAAGGCGTCAAGGACATAATGTTGCTGAGgtaatttcca ... taccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGAT
EST: gi|161721761|gb|FC071122.1|FC071122
EST:     CGCCTTTAGCCATAGTGGATAAAAGGCGTCAAGGACATAATGTTGCTGAG                         GTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGAT
genomic: CGCCTTTAGCCATAGTGGATAAAAGGCGTCAAGGACATAATGTTGCTGAGgtaatttcca ... taccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttatgagatgtcattcctggagtcaagtctgtatttattgtttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG
                                           tttacctt  CT-rich tract
                                tgtatttattgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctttgaagatatggatggaaagatgttgaattcttttctttgttacttatgagatgtcattcctggagtcaagtctgtatttattgtttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - ggaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaagtc