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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgctttatggccttcttttttcagtttgaatttagcttcatggaataattgcatttgaaatgatatttgttgaatttaaagttacattatatgtgcagGATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAGTTTGATTATGATCTAAAACAG

Basic information

species Vitis vinifera
transcript Vv12s0035g01870.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g66350.1 (Oryza sativa), 3'ss of exon 3
tttgctttatggccttcttttttcagtttgaatttagcttcatggaa--taattgcatttgaaatgatatttgttg-aatttaaagttacattatatgtgcagGATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAGTTTGATTATGATCTAAAACAG
 || | |  ||    | |||| |    ||    |||||  ||  | |   | ||  || |    ||  || |  |   | ||   ||||   |||   | ||||||||||| |||||||| || ||||||||||||||||| ||||| ||||||||||| ||||| ||||| |||
-tttcctgttgattatattttctt--cttatccttagcaacaaagtaggcattttaatctaccttgtaatataatatgagttcttgttatgctattgcttcagGATGGTGCAGGTCGTGTCGGAAAAATGCTTTTTGCACGTCAAGGAAAGAAGTTTGACTATGACCTAAAGCAG

upper sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g34650.1 (Oryza sativa), 3'ss of exon 3
tttgctttatggccttcttttttcagtttgaatttagcttcatggaataattgcatttgaaatg-atatttgt-tgaatttaaagttacattatatgtgcagGATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAGTTTGATTATGATCTAAAACAG
  | |    || ||| ||   |    |||   ||     |  ||   |  |   |||     |   |  ||||   | | |    |    | ||   | |||||||| ||||| || ||||| |||||||||||||| || ||||||||||| ||||| || || ||||| |||
-atacca-gtgacctactcagtatgatttagtttctaagtgctgatgtgttcatattaaccttttgtgattgtgctattctctgatagtttcattcctacagGATGGAGCTGGCCGAGTTGGAAAAATGCTTTTTGCCCGCCAAGGGAAGAAATTTGACTACGACCTAAAGCAG

upper sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G081188_T01 (Zea mays), 3'ss of exon 3
---tttgctttatgg--ccttcttttttcagtttgaatttagcttcatggaataattgcatttgaaatgatatttgttgaatttaaagttacattatatgtgcagGATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAGTTTGATTATGATCTAAAACAG
   | || | | | |  || |  |||     || | | | |  |  |||  ||||      ||| ||||  || || |     ||   |  || |       |||||||||||||| ||||| |||||||||||||||||||| ||||| ||||||||||| ||||| ||||| |||
tactctgttctgttgtgccatgctttaatgcttaggaatcatgtagatgtcataacctggcttgtaatgtaatatggt-----tatcatcgcacttgtaccacagGATGGTGCTGGGCGTGTCGGGAAAATGCTTTTTGCACGTCAAGGAAAGAAGTTTGACTATGACCTAAAGCAG

upper sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G833124_T01 (Zea mays), 3'ss of exon 3
---tttgctttatggccttcttttttcagtttgaatttagcttcatggaataattgcatttgaaatgatatttgttgaatttaaagttacattatatgtgcagGATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAGTTTGATTATGATCTAAAACAG
   | ||   | || | || |||    || |  | | |       | | | ||    |    || |  | |||| ||  |  |  |||    ||    | |||||||| ||||| |||||||| || ||||||||||| || ||||||||||| ||||||||||| || || |||
acttgtgaactgtgactttttttcactagatccactatgtgcagttagcaaaaaaaaaaaaaaactactgtttgatgtctgcattgttttgctac---tacagGATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG

upper sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AC218035.3_FGT004 (Zea mays), 3'ss of exon 3
tttgctttatggccttcttttttcagtttgaatttagcttcatggaataattgcatttg-----aaatgatatttgttgaatttaaagttacatta-tatgtgcagGATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAGTTTGATTATGATCTAAAACAG
    | |     ||  |        |  |||     | |  |  |||||  |||  ||      || |  |  |   |||  |     ||   ||  ||  | |||||||| ||||| |||||||| || ||| ||||||| || ||||||||||| ||||||||||| || || |||
----catctgaaccgccccagagaggagtgacccggggt--agagaatatgtgctgttagcaaaaagtactgctgtctgatatctgtattgttttgctacatacagGATGGGGCTGGGCGTGTTGGAAAGATGTTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG

upper sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 3
--tttgctttatggccttcttttttcagtttgaatttagcttcatggaataattgcatttgaaatga--tatttgttgaatttaaagttacattata---tgtgcagGATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAGTTTGATTATGATCTAAAACAG
  ||| |||| | |  |  |  |||||   || ||   || |  |  || |||    |   | |||   || |   | | | |  | |  || | ||     || ||||||||||||| |||||||||||||||||||||||  |||| || ||||| |||||||||||| | ||||||
gttttcctttctcgtata-tcctttca---tgcatcatgcat-gtataacaatcctttaaaacatggcttactcactcattgttgaatatcaatgtaattcttgtagGATGGTGCTGGGCGTGTTGGGAAAATGCTTTTTGCGAGGCAGGGAAAGAAATTTGATTATGATTTGAAACAG

upper sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ32878 (Selaginella moellendorffii), 3'ss of exon 3
tttgctttatggccttcttttttcagtttgaatttagcttcatggaataattgcatttgaaatgatatttgttgaatttaaagttacattatatgtgcagGATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAGTTTGATTATGATCTAAAACAG
                                 |  |     ||  ||       |||||  |  |  |     ||       | || | || | | |||||||||||||| ||  |||| |||||| ||||||| ||||| || |||||||| |||| | | || || |||
--------------------------------gtcggtgctgtgttatgcaaaactttgacgtagttct----aaaacgggcttcacttcatttct-cagGATGGTGCTGGCCGAATTGGAAAAATGATTTTTGCTCGGCATGGAAAGAAGTTCGATTGTCACCTTAAGCAG

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|352777603|gb|FQ466656.1|FQ466656
EST:     CTAGAAACCGATCTGCTCCTGGGGCTGTTGCTATCAACTGGATTCTCAAG                         GATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAG
genomic: CTAGAAACCGATCTGCTCCTGGGGCTGTTGCTATCAACTGGATTCTCAAGgtgcacatgg ... atatgtgcagGATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataattgcatttgaaatgatatttgttgaatttaaagttacattatatgtgcagGATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAGTTTGATTATGATCTAAAACAG
              aaatgatatttgttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgctttatggccttcttttttcagtttgaatttagcttcatggaataattgcatttgaaatgatatttgttgaatttaaagttacattatatgtgcagGATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAGTTTGATTATGATCTAAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - ggccttc
- - - - - - - - - - - - - - - - - - - - - -ggaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - gcatttg