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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcaccctcttctatatttcaccatttatggtggctcatgcagctctgcaaacctagatcttgagcttatttgcttattgtttgatctgcttttgtttaaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT

Basic information

species Vitis vinifera
transcript Vv17s0000g00500.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os01g70360.1 (Oryza sativa), 3'ss of exon 9
gttcaccctcttctatatttcaccatttatggtggctcatgcagctctgcaaacctagatcttgagcttatttgctt------attgtttgatctgcttttgtttaaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT
                         | |||    |||     |  |     ||  |   || | |  |    || ||      | |   ||||    | |||||  ||    ||||||  ||||  | || |  ||  | || ||||| || || ||| | ||||| || ||||| ||||||||||||||||||||||||||||| || |||||
------------------------gtatatatctgcttccaaaatttgaacaaattgactcataatttctcctgttttgaggaaattcatgatgcaatgttgttgtaaa--cagGGGCCAAGAAGATTGCTCAGATTAGAGATAACAGCAATTTCTTCCGTTCAGAGCTTCAGAAAATGGGCTTTGAGGTTCTTGGAGATAATGACTCACCTGT

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 9
--gttcaccctcttctatatttcaccatttatggtggctcatgcagctctgcaaacctagatcttgagcttatttgcttattgtttgatctgcttttgtttaaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT
    |  || | |  | |  |||  |  ||    ||     |||||  ||    |  ||  | ||       ||   || || |||  | || ||||| |    |   ||| || |||||| | ||||| || ||||||||||| || || || || ||||| ||  |||||||||| ||||||||||| ||||| ||||| ||||| ||
gtactagccttttcttctgcttcgaccctttcaatgcgc--tgcagg-ctatccatgtaagtttta----ctttcaattcttatttattttggttttgatgtcttgc-agGTGCCCAGAAACTTGCACGCATCCGTGAGAACAGCAATTTCTTTAGGTCAGAGCTCAAGAAGATGGGTTTTGAGGTTCTCGGAGACAATGACTCTCCAGT

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G030862_T01 (Zea mays), 3'ss of exon 8
gttcaccctcttct-atatttcaccatttatggtggctcatgcagctctgcaaacctagatcttgagcttatttgcttattgtttgatctgcttt---tgtttaaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT
|| |  || ||| |  |     || || ||||    |   |  |    ||     ||  ||  |   ||| |||  || || |||    |||||    ||| |   |   ||| || |||||| |||| || || ||||||||||| ||||| ||||| ||||| ||  ||||||||||||||||||||||||| || || || ||||||||
gtccctccccttttcgttcgcgactatatatgtgtccaactagaataatgttgtactgaataatc--cttttttttttgtttttttgcttgcttgggatgtgttgcttgcagGTGCCCAGAAACTGGCGCGCATCCGTGAGAACAGCAACTTCTTCAGGTCAGAGCTCAAGAAGATGGGCTTTGAGGTTCTTGGTGACAACGACTCTCCTGT

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G142030_T01 (Zea mays), 3'ss of exon 9
--gttcaccctcttctatatttcaccatttatggtggctcatgcagctctgcaaacctagatcttgagcttatttgcttattgtttgatctgcttttgtttaaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT
    | | ||   | | | |  |||  ||  | ||| |   | |   | ||||    |     | | | | | ||    | |||||  | | ||| || | | ||   ||| || || ||| | ||||| || ||||||||| |||| || ||||| || |||||  |||||||||| |||||||||||||| || ||||||||||||||
gtactaaaccagctttttttaacacttttatttgtgcccttttcg--tttgcagctgtg---ttagtgttcaatta---aatgtttttttttcttgtgat-atattgaagGTGCCCAAAAACTTGCACGCATCCGTGAGAACGGTAATTTCTTCAGGTCCGAACTCAAGAAGATGGGTTTTGAGGTTCTTGGCGACAATGATTCTCCTGT

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G010202_T02 (Zea mays), 3'ss of exon 8
gttcaccctcttctatatttcaccatttatggtgg-ctcatgcagctctgcaaacctagatcttgagcttatttgcttattgt-ttgatctg-cttttgtttaaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT
               ||   ||  |   ||       || | || ||   ||       ||  |   ||   ||| | | ||| || || |  |  |||||  |||  |||||||  ||||  | || | ||| || |||||||| || || ||| | || || || ||||| ||||| |||||||||||||||||||||||||| |||||
--------------gtacaacataaagaattccaaattcttacaccttaccagtttcttatacttc-ctgccttgttgaatgtcttaatgtaacaattgttctaat--tagGGGCCAAGAAGCTCGCTCAAATTCGAGAGAACAGCAATTTCTTCCGCTCGGAGCTTCAGAAAATGGGTTTTGAGGTTCTTGGAGATAATGATTCACCTGT

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G055854_T01 (Zea mays), 3'ss of exon 7
--------------------------------------------------gttcaccctc--ttctatatttcaccatttatggtggctca-tgcagctctgcaaacctagatcttgagcttatttgctt--attgtttgatctgcttttgtttaaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT
                                                  ||| |   ||  ||  ||| |||    ||  | |||    | || || |   ||||       || | |  | || | ||  ||  ||   | | | ||    |  |    ||| || || ||| | || || || || ||||| ||||| || ||||| ||||| ||  |||||||||| |||||||||||||| || ||||| ||||||||
gtactaaaccagtttctttaacactttttgcccttttcatttgcagctgtgttaatgttcgattaaataattcttttttccttgtgatgtactgaagGTGCCCAAAAACTTG-CTCGCGGATGTTCGATTAAATAATTCTTTTTTCCTTGTGATGTACTGAAGGTGCCCAAAAACTTGCTCGCATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGGTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G357734_T03 (Zea mays), 3'ss of exon 14
gttcaccctcttctatatttcaccatttatggtggctcatgcagctctgcaaacctagatct-tgagcttatttgcttat-tgtttgatctgcttttgtttaaatatt--agGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT
               || |  |||| ||    |  | | |   || ||    |  |  | || ||    | || | |||  |  ||  | |  |  |  | |  || |  ||| || || ||| | || || || || ||||| ||||| || ||||| ||||| ||  |||||||||| |||||||||||||| || ||||| ||||||||
------------aggtactaaaccagtttctttaacactttttgcccttttcatttgcagctatgttaatgttcgattaaataattctttttttccttgtgatgtactgaagGTGCCCAAAAACTTGCTCGCATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGGTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G067257_T01 (Zea mays), 3'ss of exon 10
gttcaccctcttctatatttcaccatttatggtggctcatgcagctctgcaaacctagatct-tgagcttatttgcttat-tgtttgatctgcttttgtttaaatatt--agGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT
               || |  |||| ||    |  | | |   || ||    |  |  | || ||    | || | |||  |  ||  | |  |  |  | |  || |  ||| || || ||| | || || || || ||||| ||||| || ||||| ||||| ||  |||||||||| |||||||||||||| || ||||| ||||||||
------------aggtactaaaccagtttctttaacactttttgcccttttcatttgcagctgtgttaatgttcgattaaataattctttttttccttgtgatgtactgaagGTGCCCAAAAACTTGCTCGCATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGGTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM5G891276_T01 (Zea mays), 3'ss of exon 6
gttcaccctcttctatatttcaccatttatggtggctcatgcagctctgcaaacctaga-tcttgagcttatttgcttattgtttgatctgcttttgtttaaatatt--agGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT
               || |  |||| ||    |  | | |   || ||    |  |  | |  ||    | |||| |||     | || |  |  |  | |  || |  ||| || || ||| | || || ||  | ||||| ||||| || ||||| ||||| ||  |||||||||| |||||||||||||| |||||||| |||| |||
--------------gtactaaaccagtttctttaacactttttgcccttttcatttgcagttgtgttaatgtttgattaaataattattttttccttgtgatgtactgaagGTGCCCAAAAACTTGCTCGCATCTGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGGTTTTGAGGTTCTTGGTGATAATGACTCTCATGT

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G370377_T01 (Zea mays), 3'ss of exon 11
--------------------------------------------------gttcaccctc--ttctatatttcaccatttatggtggctca-tgcagctctgcaaacctagatcttgagcttatttgctt--attgtttgatctgcttttgtttaaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT------------------------------------
                                                  ||| |   ||  ||  ||| |||    ||  | |||    | |  || |   ||||       || | |  | || | ||  ||  ||   | | | ||    |  |    ||| || || ||| | || || || ||      |    | || ||||| ||||| ||  |||||||||| |||||||||||||| || ||||| ||||||||                                    
gtactaaaccagtttctttaacactttttgcccttttcatttgcagctgtgttaatgttcgattaaataattcttttttccttgtgatgtactaaaggtgcccaaaaacttg-ctcgcggatgttcgattaaataattcttttttccttgtgatgtactgaaggtgcccaaaaacttgctcgcatccg-----gctaagATTTCTTCAGGTCAGAGCTCAAGAAGATGGGTTTTGAGGTTCTTGGTGACAATGACTCTCCTGTCATGCCCATAATGCTCTACAATCCGGCTAAGATTCC

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 9
gttcaccctcttctatatttcaccatttatggtggctcatgcagctctgcaaacctagatcttgagcttatttgcttattgtttgatctgcttttgttt---aaatatt--agGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT
               || |  ||||  |    |  | | |   || ||    |  |  | || | ||| || | |  |||   | ||    ||||  ||   |  || |  ||| || || ||| | || || || || ||||| ||||| || || || ||||| ||  |||||||||| |||||||||||||| || ||||| ||||||||
--------------gtactaaaccagcttctttaacactttttgcccttttcatttgcagct-gtgctaatgttcg-attaaataattcttttttccttgtgatgtactgaagGTGCCCAAAAACTTGCTCGCATCCGCGAGAATAGTAATTTCTTTAGGTCAGAGCTCAAGAAGATGGGTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G137556_T01 (Zea mays), 3'ss of exon 5
gttcaccctcttctatatttcaccatttatggtggctcatgcagctctgcaaacctagatct-tgagcttatttgcttat-tgtttgatctgcttttgtttaaatatt--agGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT
               || |  |||| ||    |  | | |   || ||    |  |  |  | ||    | || | |||  |  ||  | |  |  |  | |  || |  ||| || || ||| | || |  || || ||||| ||||| || ||||| ||||| ||  |||||||||  |||||||||||||| || ||||| ||||||||
------------aggtactaaaccagtttctttaacactttttgcccttttcatttgtagttgtgttaatgttcgattaaataattctttttttccttgtgatgtactgaagGTGCCCAAAAACTTGCTCACATCCGCGAGAATAGTAATTTCTTCAGGTCAGAGCTCAAGAAGATGGTTTTTGAGGTTCTTGGTGACAATGACTCTCCTGT

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G23670.1 (Arabidopsis thaliana), 3'ss of exon 9
---gttcaccctcttctatatttcaccatttatggtggctcatgcagctctgcaaacctagatct--tgagcttatttgcttattgtttga----tctgcttttgtttaaatatt----agGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT
    |  |   | ||    |      |||| || | | |||||   | ||    | |  | ||||  | || | ||   || ||    | |    ||   || |  | ||||| |    |||||| || ||  | ||| |||||||||||||||| ||||||||| |  | || |||||||||||||| |||||||| |||||||| |||||||| || ||
gtactcgattttttttctcaccgtgtcattaattg-gcctcatttgggtcactgagcaca-atctaatcaggtcatg-actcataacctaaaaactcccattcttctcaaatactgaacagGGGCACAAAAGCTAGCAAGAATACGTGAGAACAGCAACTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGT

upper sequence: Vv17s0000g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G48780.1 (Arabidopsis thaliana), 3'ss of exon 9
gttcaccctcttctatatttcacca-tttatggtggctcatgcagctctgcaaacctagatct-tgagcttatttgcttattgtttgatctgcttttgtttaaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT
               ||| |    |  ||||  | |||| | ||||| |       | | ||| |||||||  |    |     ||    |    |    |    |   ||||| || || || ||| ||||| | |||||||| |||||||||||  | ||  ||||||||||||| ||||| ||||||||||| |||||||| || ||
--------------gtatcttgatagcttatttttgctctttcagctgtaactcttttgctctatgagcttcgtaatctcaaactt---ttataatcacctgggca---gGGGCACAAAAGTTAGCAAGAATAAGGGAGAACAGCAACTTTTTCAGGGCTGAGTTGCAGAAGATGGGGTTTGAAGTTCTTGGAGACAATGATTCACCAGT

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|71872282|gb|DT021337.1|DT021337
EST:     GATTATATCTTCCATCAAGGTTATTCTTGGAGAAGATGGCTCTAGTAGAG                         GGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAG
genomic: GATTATATCTTCCATCAAGGTTATTCTTGGAGAAGATGGCTCTAGTAGAGgttcaccctc ... taaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAG
EST: gi|71866164|gb|DT015219.1|DT015219
EST:     GATTATATCTTCCATCAAGGTTATTCTTGGAGAAGATGGCTCTAGTAGAG                         GGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAG
genomic: GATTATATCTTCCATCAAGGTTATTCTTGGAGAAGATGGCTCTAGTAGAGgttcaccctc ... taaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAG
EST: gi|110360549|gb|EC923744.1|EC923744
EST:     GATTATATCTTCCATCAAGGTTATTCTTGGAGAAGATGGCTCTAGTAGAG                         GGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAG
genomic: GATTATATCTTCCATCAAGGTTATTCTTGGAGAAGATGGCTCTAGTAGAGgttcaccctc ... taaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAG
EST: gi|34542727|gb|CF510959.1|CF510959
EST:     TGGAGAAGATGGCTCTAGTAGAG                         GGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAG
genomic: TGGAGAAGATGGCTCTAGTAGAGgttcaccctc ... taaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAG
EST: gi|110385601|gb|EC950143.1|EC950143
EST:     GATTATATCTTCCATCAAGGTTATTCTTGGAGAAGATGGCTCTAGTAGAG                         GGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAG
genomic: GATTATATCTTCCATCAAGGTTATTCTTGGAGAAGATGGCTCTAGTAGAGgttcaccctc ... taaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAG
EST: gi|110366510|gb|EC930420.1|EC930420
EST:     GATTATATCTTCCATCAAGGTTATTCTTGGAGAAGATGGCTCTAGTAGAG                         GGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAG
genomic: GATTATATCTTCCATCAAGGTTATTCTTGGAGAAGATGGCTCTAGTAGAGgttcaccctc ... taaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAG
EST: gi|110697624|gb|EE074785.1|EE074785
EST:     GATTATATCTTCCATCAAGGTTATTCTTGGAGAAGATGGCTCTAGTAGAG                         GGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAG
genomic: GATTATATCTTCCATCAAGGTTATTCTTGGAGAAGATGGCTCTAGTAGAGgttcaccctc ... taaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctagatcttgagcttatttgcttattgtttgatctgcttttgtttaaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT
                           gtttgat  putative branch site (score: 5)
                                     cttttgttt  putative PPT
                                      ttttgtttaaatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcaccctcttctatatttcaccatttatggtggctcatgcagctctgcaaacctagatcttgagcttatttgcttattgtttgatctgcttttgtttaaatattagGGGCTCAGAAATTGGCACGAATACGTGAGAACAGTAACTTTTTCAGATCAGAACTGCAGAAGATGGGCTTTGAGGTTCTTGGAGATAATGATTCTCCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT