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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtatatgtgttttggtcactttctggaaaagaatatccactatggattatgtttgttgggagttatttgttttgagtcactaattgggttaatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA

Basic information

species Vitis vinifera
transcript Vv08s0007g04210.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g59990.1 (Oryza sativa), 3'ss of exon 4
--tgtatatgtgttttggtcactttctggaaa-----agaatatccactatggattatgtttgttgggagttatttgttttgagtcactaattgggttaatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA
  |||  |  | |    ||    | | | ||       ||||  |  |  |  || |||    |  |  | ||||| || ||| |  | |     |||       |||| |||  |   || ||||| ||||||||||||||  ||||||| ||||| |||||  |||| ||||| ||||||||| |||| |||||||| ||||  |
catgtgcagttatccgagttttctgcagcaactggctggaattgctgccttatatcatgccctt--gctgctattt-ttctgaatttcaac----gttgcactgtagGACATTCATGCTGAAGCTGTCAAGAAGAGGCGTCGCACCACCAAGAAGCCATACTCACGGTCAATTGTTGGTGCTACACTGGAAGTTATCCAAAAGAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 4
tgtatatgtgttttggtcactttctggaaaagaatatccactatggattatgtttgttgggagttatttgttttgagtcactaattgggttaatgc---tcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA
   ||      ||   |   | | || | |   |      ||||| |||   |  | |  ||   |||   |||    |  |       ||  ||    | |||||||   |   || ||||| ||||||||||| ||  ||||||| ||||| ||||||||||| ||||| |||||| | ||||| || ||||| ||||  |
---atgctcaattccttgtatatatgtacagttagtcatgctatgtattgcttccgatcagataaattctgtttacaccctttcccaattttctgttttttagGATATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCACCACCAAGAAGCCATACTCTAGGTCAATTGTTGGTGCTTCGTTGGAAGTCATCCAAAAGAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G074898_T03 (Zea mays), 3'ss of exon 4
-tgtatatgtgttttggtcactttctggaaaaga-atatccactatggattatgtttgttgggagttatttgttttgagtcactaattgg-gttaatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA
     ||   | ||    ||     ||     |  ||    || |||| |  |    ||   |||    |  | || | |   || |||   ||  |    |||| ||   |   || ||||| ||||||||||| || |||||||| ||||| ||||| |||||||||||||||||| | ||||| || ||||||||||  |
ccaactagacgattgcaacaacaattgtttctgccatgctaacaatgg-tgctagaagtctagagcctctgatcttaaatg--tatttgtcatttgtctgtagGACATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCGCCACCAAGAAGCCATACTCGAGGTCCATTGTGGGTGCTTCCTTGGAAGTGATCCAGAAGAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G110328_T03 (Zea mays), 3'ss of exon 4
tgtatatgtgttttggtcactttctggaaaagaatatccactatg--gattatgtttgttgggagtt---atttgttttgagtcactaattgggttaatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA
     || ||  |   ||  |      | ||  |    | | |     ||||||   | |   |||    |    |||  |   | ||      |   |    |||||||   |   |||||||| ||||||||||| || |||||||| ||||| ||||| |||||||||||||||||| |  | ||||| ||||||||||  |
----catctgaataaatctttgcaacaacaattactctcgccacacttattatggc-gctaaaagtctagaaccttttacatgtattagccatttctgtctgtagGATATCCATGCTGAGGCTGTCAAGAAGAGGCGCCGCGCCACCAAGAAGCCATACTCGAGGTCCATTGTGGGTGCTTCCCTAGAGGTGATCCAGAAGAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G142640_T02 (Zea mays), 3'ss of exon 5
---tgtatatgtgttttggtcactttctggaaaagaatatccactatggattatgtt--tgttgggagttatttgttttgagtcactaattgggttaatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA
     |  || || |   ||||   | || |||  | | ||  | |||  ||||  |  || |   |||   | | ||  |  |  |  ||   ||  |    |||||||   |   || || |||||||||||||| || |||||||| ||||| ||||| ||||| |||||||||||| | ||||| || ||||||||||  |
atcgatccatttgatcatgtcatcgtttgcaaattatt-tctgccatgc-ttataatagtgctataagtctatagcttacatgcttttttt---tttgtctgtagGATATCCATGCTGAAGCGGTAAAGAAGAGGCGCCGCGCCACCAAGAAGCCATACTCCAGGTCAATTGTGGGTGCTTCCTTGGAAGTAATCCAGAAGAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G21520.1 (Glycine max), 3'ss of exon 3
-tgtatatgtgttttggtcactttctggaaaagaatatccactatggattatgtttgttgggagttatttgttttgagtcactaattgggt-taatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA
   |   | |   |     |    || ||      |||  | ||   ||     | ||||   |   |||  ||||| |   |   ||  | | |||   |||||||||||||||| ||||| ||||||||  | ||||| |||||||| || ||||||||||| ||||| |||||||| || || ||||||||||| |  |
acttggttattcctcacataaacacttgactgtgctata-agtaaatatc-caatggttgcatgcattttaatttgattgtttgtgtgcatgtgatgtatagGATATTGCTCAAGAAGCTGTGAAGAAGAGAAGACGTGCTACCAAAAAACCTTACTCTAGGTCTATTGTTGGTGCTACTTTAGAAGTTATCCAGAAAAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G37370.2 (Glycine max), 3'ss of exon 3
----------------------------------------------------------tgt-atatgtgttttggtcactttctggaaaagaatatc----cactatg-gattatgt--ttgttgggagttatttgttttgagtcactaattgggt-taatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA
                                                          |||    | |   ||||| | | |    | ||  |  |       ||| |  ||| ||   | ||||   | | |   |||||| |   |   ||  | | ||    |||| ||||||||||| ||||| | ||||||| | |||||  |||||||||| ||||||||||||||||| ||||| || ||||| || |||||||| |  |
gtgattatttaattgtattattttaaagatgaaacaataaaccaatgagtgaaaatattgttgcctttaacttggttattctacatataaacaggttatggtgctaagtaattctgcaatggttgcatgatttgaattttgattgtttgtgtgcatgtgatatctagGACATTGCTCAAGAAGCTGTGAGGAAGAGGAGACGTGCTGCCAAAAAGCCTTACTCTAGGTCCATTGTTGGTGCGACCTTGGAAGTAATCCAGAAAAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G34700.1 (Glycine max), 3'ss of exon 3
tgtatatgtgttttggtcactttctggaaaagaatatccactatggattatgtt-tgttgggagttatttgttttgagtcactaattgggt-taatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA
    |   |||||  ||   | ||  |   || | ||    ||   ||  ||   || | | |   |||||  |||| |   |   ||  | | |||   |||| ||||||||||| ||||| ||||||||| | || ||  |||||||||| ||||||||||||||||| ||||| ||  |||| ||||||||||| |  |
--attggttgtttgtgtgcatgtcatgtgtaggacattgcttagtaatactgcaatggttgcatgcatttgaattgattgtttgtgtgcatgtcatgtgtagGACATTGCTCAAGAAGCTGTGAAGAAGAGGAGACGCGCTGCCAAAAAGCCTTACTCTAGGTCCATTGTTGGTGCCACTCTGGAAGTTATCCAGAAAAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G07680.1 (Glycine max), 3'ss of exon 3
tgtatatgtgttttggtcactttctggaaaagaatatccactatggattatgtt-tgttgggagttatttgttttgagtcactaattgggttaatgctc-----agGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA
    ||  || ||   ||    | |  | | |    |   |||    | ||  |   |||   | | |   |||| | | | |  ||| ||| |||        |||| ||||||||||| ||||| ||||| ||  | |||||  |||||||||| ||||| ||||||||||| ||||| || ||||| ||||||||||| |  |
----tacttggtt-attcctcatataaacaggtgactttgctacaagtaattctgcattgtttgct-tgcattttaattgattgtttgtgttcatgtgttgtgtagGACATTGCTCAAGAAGCTGTGAAGAAAAGAAGACGTGCTGCCAAAAAGCCTTACTCCAGGTCCATTGTCGGTGCCACTTTGGAAGTTATCCAGAAAAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G53020.1 (Arabidopsis thaliana), 3'ss of exon 3
-tgtatatgtgttttggtcactt---tctggaaaagaatatccactatggattatgtttgttgggagttatttgttttgagtcactaattgggttaatgct-cagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA
 |  | |      |  || | ||   ||||        | |  ||| ||  || | ||  |||    | |||||||   | ||   || |  |||  |  |  |||||   || ||||||||||| ||||  ||| | ||||||||||| ||||| ||||| ||||||||||| |||||||| ||||| || || |||||||  |
gtaaaaaaaaaactcagtaatttggatctgttttgttgtttgtactttgtttttt-ttcattgatcctgatttgttaacattctaaaactctgtttcttttatagGATGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCCACCAAGAAGCCATACTCAAGGTCCATTGTTGGTGCTACCTTGGAAGTAATTCAGAAGAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G36620.1 (Arabidopsis thaliana), 3'ss of exon 3
----tgtatatgtgttttggtcactttctggaaaagaatatccactatggattatgtttgttgggagttatttgttttgagtcactaattgggttaatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA
    ||| | | | |||| ||  |||  ||         ||  | ||    | |  | ||||| ||  | ||||||||   || ||  ||           |||||    || ||||||||||| ||||  ||| | ||||| || || ||||| ||||| ||||| ||||| |||||||| ||||||||||| |||||||   
gtaatgtttcttt-ttttagttgcttcttgttttcatg-atttagtactattgaattctgttgtga--tctttgttttc--tctcttctta----------cagGACGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCAACTAAGAAGCCTTACTCAAGGTCGATTGTCGGTGCTACTTTGGAGGTTATTCAGAAGAAGC

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|33408532|gb|CF214159.1|CF214159
EST:     AGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAAAG                         GATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC
genomic: AGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAAAGgtagcacttg ... taatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC
EST: gi|110404057|gb|EC970014.1|EC970014
EST:     AGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAAAG                         GATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC
genomic: AGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAAAGgtagcacttg ... taatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC
EST: gi|26262650|gb|CA813713.1|CA813713
EST:     AGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAAAG                         GATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC
genomic: AGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAAAGgtagcacttg ... taatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC
EST: gi|26261571|gb|CA812634.1|CA812634
EST:     AGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAAAG                         GATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC
genomic: AGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAAAGgtagcacttg ... taatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC
EST: gi|110398469|gb|EC964851.1|EC964851
EST:     AGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAAAG                         GATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC
genomic: AGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAAAGgtagcacttg ... taatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC
EST: gi|26261679|gb|CA812742.1|CA812742
EST:     AGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAAAG                         GATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC
genomic: AGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAAAGgtagcacttg ... taatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC
EST: gi|294966178|gb|GW839401.1|GW839401
EST:     AGCCATCAAAGCTTACCTGGACAGCCATGTGCAGGAAGCAACATAAAAAG                         GATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC
genomic: AGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAAAGgtagcacttg ... taatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC
EST: gi|71867860|gb|DT016915.1|DT016915
EST:     AGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAAAG                         GATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC
genomic: AGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAAAGgtagcacttg ... taatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattatgtttgttgggagttatttgttttgagtcactaattgggttaatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA
                  ttatttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtatatgtgttttggtcactttctggaaaagaatatccactatggattatgtttgttgggagttatttgttttgagtcactaattgggttaatgctcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - tttctgg
- - - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - tccacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgttggg