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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagaaaataaccctatatatatatactccattctatttggatctcgctattttattttatttttttgtgattttatttttatgtgattgggcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTTGGCCCACACACAAGGGAAGAGGCATCAGACGAATTTGGCCAAGAGAGCT

Basic information

species Vitis vinifera
transcript Vv08s0007g04710.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g04710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g15700.1 (Oryza sativa), 3'ss of exon 1
cagaaaataaccctatatatatatactccattctatttggatctcgctattttattttatttttttgtgattttatttttatgtgattgggcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTTGGCCCACACACAAGGGAAGAGGCATCAGACGAATTTGGCCAAGAGAGCT
  | |      || |       | || | |   |  ||    |||| |   |   |||  |   | | |    || |       ||||  |    | |||||| ||||| ||||| ||||||||  |||||||||||||||| || ||  |||| ||||| || |||||| |||| ||||| ||  | |||||| | || 
--gtactgcctcccacccgctaaaaccctagctttcttcttcctcgat---tcggtttgctccctcgcg---ctaatcccgctcgatttcgtg--tccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCTGGCTCACACGCAGGGGAAGCGGCACCAGACCAACCTCGCCAAGCGTGCC

upper sequence: Vv08s0007g04710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G100620_T01 (Zea mays), 3'ss of exon 1
cagaaaataaccctatatatatatactccattctatttggatctcgctattttattttatttttttgtgattttatttttatgtgattgggcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTTGGCCCACACACAAGGGAAGAGGCATCAGACGAATTTGGCCAAGAGAGCT
       ||||||    || |       | | || || | | |||||       | |   ||   |  ||| |      |   |   ||     ||  ||||||||||| ||||| ||||||||  |||||||||||||||| || ||  | |||||||| |||||||||||||| ||||| ||  | |||||| | || 
------gtaacccgccctaaaccc-tagcgtactcttcgaa-ctcgcc--cccgtctcgattcgcttcgatctatgcgctgatt--ctgattgtttgtagCTATGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCTAGCCCACACGCAAGGGAAGAGGCACCAGACCAACCTCGCCAAGCGCGCC

upper sequence: Vv08s0007g04710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G32600.1 (Arabidopsis thaliana), 3'ss of exon 1
cagaaaataaccctatatatatatactccattctatttggatctcgctattttattttatttttttg----tgattttattttta-tgtgattgggcaat-tacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTTGGCCCACACACAAGGGAAGAGGCATCAGACGAATTTGGCCAAGAGAGCT
       | |   | | |   | |  |   |   ||| || |||   | ||| |||||    |  ||    | |||| ||||||  |||| ||      | | ||||||||||||||| || || || ||| |||| ||||| || || || || ||||| || || ||||| |||||||||||||| || ||||| |||||||||
-----cttgagtttgtttggctgttgtttctagaattaggttcttttt-tttaattttcccctcatgccactaatttgatttttggtgtgtttttatgttgtgcagCTATGAGTGTAAACTATGTCTAACACTGCATAACAATGAAGGAAACTACTTGGCACATACTCAAGGTAAGAGGCATCAGACAAACTTGGCAAAGAGAGCT

upper sequence: Vv08s0007g04710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S318_71V6.1 (Physcomitrella patens), 3'ss of exon 1
cagaaaataaccctatatatatata---ctccattctatttggatctcgctattttattttatttttttgtgattttatttttatgtgattgggcaat-tacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTTGGCCCACACACAAGGGAAGAGGCATCAGACGAATTTGGCCAAGAGAGCT
  ||   |    || ||| | | ||    |    |  | | | |  |   |    ||  |      | |    ||  ||||| |   | ||| |   | | ||| ||||| |||||||||||  ||||  | |||||||||||||| |||||| |||| ||||| || |||||  |||||||||| || ||||| ||  | || 
--gatttttctgctgtatgtgtgtagatttgtgatggaatggaaattgattgcgctaagtcgaaaatct--tgttgaattttgagcggtttgtgttgtgtgcagTTATGAATGTAAGCTTTGTTTGACGCTCCACAACAACGAGGGTAATTATCTGGCTCACACTCAGGGGAAACGGCATCAGACCAACTTGGCGAAACGTGCA

upper sequence: Vv08s0007g04710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S29_139V6.1 (Physcomitrella patens), 3'ss of exon 1
-------cagaaaataaccctatatatatatactccattctatttggatctcgctattttattttatttttttgtgattttatttttatgtgattgggcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTTGGCCCACACACAAGGGAAGAGGCATCAGACGAATTTGGCCAAGAGAGCT
       | || | |  |||| | | | | |||| |||   |  |  || || ||       || || || |||  || |  |   ||| |  ||||     | ||| ||||| |||||||||||| ||||| | || ||||||||||| ||||||||||| || || ||||| ||| |||||||||| |||||||| ||  | || 
atgtgtacggatattgtccctttctctttgtactgcatggaaggtc-atttcactggaacgatt-atcttattgaaatatagtgggtatttccttgg-----tgcagTTATGAATGTAAGCTTTGCTTGACACTTCATAACAACGAGGGTAATTATTTGGCTCATACCCAAGGCAAGCGGCATCAGACAAATTTGGCAAAACGTGCA

upper sequence: Vv08s0007g04710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ15163 (Selaginella moellendorffii), 3'ss of exon 1
cagaaaataaccctatatatatatactccattctatttggatctc-gctattttattttatttt---tttgtgattttatttttatgtgattgggcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTTGGCCCACACACAAGGGAAGAGGCATCAGACGAATTTGGCCAAGAGAGCT
       |  | || | |   | |  ||  ||  |   | || || ||| ||||  |  |  ||      |||||   |||   || |  || ||   |  |||||| ||||||||||||||| ||||  |||||||||| ||||| || || ||||| ||||| ||||| ||| | || |||||||||||||||||| | || 
----gtctgtctctctttcatttttttctcttggaggagaatgtccgctgtttttctcgagattgggcgagtgatggcattgaaat-tcctttggttttggcagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGAAACTACTTGGCACACACGCAAGGCAAGCGCCACCAGACGAATTTGGCCAAGCGCGCG

upper sequence: Vv08s0007g04710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ08420 (Selaginella moellendorffii), 3'ss of exon 1
cagaaaataaccctatatatatatactccattctatttggatctc-gctattttattttatttt---tttgtgattttatttttatgtgattgggcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTTGGCCCACACACAAGGGAAGAGGCATCAGACGAATTTGGCCAAGAGAGCT
      ||  | || | |     |  ||  ||  |   | || || ||| ||||  |  |  ||      |||||   |||   || |  || ||   |  |||||| ||||||||||||||| ||||  |||||||||| ||||| || || ||||| ||||| ||||| ||| | || |||||||||||||||||| | || 
----gtatgtctctctttcatgtttttctcttggaggagaatgtccgctgtttttctcgagattgggcgagtgatggcattgaaat-tcctttggttttggcagCTACGAGTGTAAGCTTTGCTTGACGCTGCACAACAATGAGGGGAACTACTTGGCACACACGCAAGGCAAGCGACACCAGACGAATTTGGCCAAGCGCGCG

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|161708910|gb|FC060919.1|FC060919
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|110713132|gb|EE088784.1|EE088784
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|30134998|gb|CB920336.1|CB920336
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|110710951|gb|EE087592.1|EE087592
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|161711277|gb|FC060365.1|FC060365
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|30133297|gb|CB918636.1|CB918636
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|110713768|gb|EE089980.1|EE089980
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAATAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|110686098|gb|EE063396.1|EE063396
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|156739019|gb|EV243140.1|EV243140
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|161707166|gb|FC055570.1|FC055570
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|71872083|gb|DT021138.1|DT021138
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|71869160|gb|DT018215.1|DT018215
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|110698196|gb|EE075475.1|EE075475
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAATAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|161714376|gb|FC063217.1|FC063217
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGGAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|71869133|gb|DT018188.1|DT018188
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|294964013|gb|GW836888.1|GW836888
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|27584644|gb|CB007339.1|CB007339
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
EST: gi|161712620|gb|FC061943.1|FC061943
EST:     ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAG                         CTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT
genomic: ACTATTGATCTCGCCAAAGATCCCTATTTCATGCGTAATCATCTCGGAAGgtacatcctt ... gcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctattttattttatttttttgtgattttatttttatgtgattgggcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTTGGCCCACACACAAGGGAAGAGGCATCAGACGAATTTGGCCAAGAGAGCT
     tttattttattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagaaaataaccctatatatatatactccattctatttggatctcgctattttattttatttttttgtgattttatttttatgtgattgggcaattacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTTGGCCCACACACAAGGGAAGAGGCATCAGACGAATTTGGCCAAGAGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- -aaaataa
- - - - - ccctata
- - - - - - - - - - - - - -ccattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgg