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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccatatttcacttctagttaggattctggggtaaccaatagacggtatcaaaccaagaagggtgttaaagcttttcatcctatagGATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCATTTATACCGAATGGACTATATGGACTTTGTTCAG

Basic information

species Vitis vinifera
transcript Vv05s0020g02880.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 4
---gtacccatatttcacttctagttaggattctggggtaaccaatagacggtatcaaac--caagaagggtgttaaagc------ttttcatcctatagGATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCATTTATACCGAATGGACTATATGGACTTTGTTCAG
    |  | ||  | |  |  || ||     |        ||  | | ||   ||||  |  |    |   | |||| ||       | || |  | ||||||   | |  ||| || || || |||||||||||||| ||||| |||||| | ||||| |||||||| |||||||||||||||
aacttttcaattatcccttgttatttgatcgtactattctactgaaaaacctcatcatgctccttacataattttaatgcatcgtgctatcgttttgtagGATGCCAAAGCTAAAGACATCGATGATGTGCTGATTCTTTCTGGTGATCATCTCTACCGCATGGACTACATGGACTTTGTTCAG

upper sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G391936_T02 (Zea mays), 3'ss of exon 4
-------gtacccatatttcacttctagttaggattctggggtaaccaatagacggta---tcaaaccaagaaggg-tgttaaagcttttcatcctatagGATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCATTTATACCGAATGGACTATATGGACTTTGTTCAG
       | ||    | ||| ||  |  ||    || |    | |  |  | ||   |        ||  ||||   |  |||  | |    |  | ||||||  || |  ||| || ||||| |||||||||||||| ||||| || ||| | ||||| |||||||| |||||||||||||||
ttcaaagggactgccagttccctattgctttactttgtaatattattataataccacaaagctgttccttgaagaaattgtaatacataatgttttgtagGATGCAAAATCTAAAGACATTGAAGATGTGCTGATTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG

upper sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 4
------gtacccatatttcacttctagttaggattctggggtaaccaa----tagacgg-tatcaaaccaagaagggtgttaaagcttttcatcctatagGATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCATTTATACCGAATGGACTATATGGACTTTGTTCAG
       ||    | |     |  |||  | |     |  | | | ||    |||  || | | |||    | |  ||   | |   ||  ||  | ||||||| |||||||||||| |||||||||||  ||||||| |||||||||||  | ||||||||||||||||||||||||||||| 
cttttgttatttctttcctcatcatagcaaaggccaagaagaatctaaatgctagttggatgttaaatgtggtaatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCTGGAGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA

upper sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G38820.1 (Glycine max), 3'ss of exon 4
------gtacccatatttcacttctagttaggattctggggtaaccaa----tagacgg-tatcaaaccaagaagggtgttaaagcttttcatcctatagGATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCATTTATACCGAATGGACTATATGGACTTTGTTCAG
       ||    | |     |  ||   | |     |  | | | ||    |||  || | | |||      |  ||   | |   ||  ||  | ||||||| |||||||||||| |||||||||||  ||||||| || || |||||  | ||||||||||||||||||||||||||||| 
cttttgctatttctttcctcatcataaaaaaggccaagaagaatctaaatgctagttgggtgttaaatgcgataatgtagaatatgcttctatgttgtagGATCCAAGAAGTAAGGATATTGAGGATGTCTTGATTCTTTCCGGGGATCACCTCTACCGAATGGACTATATGGACTTTGTTCAA

upper sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S175_26V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------------gtacccatatttcacttctagttaggattctgggg--taaccaatagacggtatca--aaccaagaagggtgttaaagcttt--tcatcctat----------agGATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCATTTATACCGAATGGACTATATGGACTTTGTTCAG
                                                          | ||     |||   |  |  |   ||| || ||  ||  | |     | ||| |   |    || | ||  |||   | |  ||||||| |          |||||   |  | |||| || ||||| ||||||| ||||| ||||||||||| || || || |||||||||||||| ||  |||||
gtatgtatgtactacactaccttccgtgtgttttagttgtctatgcattttatgatatttcctggggttcg--tggaactcaaattttgagggatattcgaatagagctattattgattcggatgagtaataagcttgtattcatcctgttgttgagagcagGATGCTAAGAATAAGCAAGTTGAGCATGTGCTTATTCTTTCTGGAGATCACTTGTATCGCATGGACTATATGGATTTCATTCAG

upper sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S389_5V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------gtacccatatttca---cttctagttaggattctggggtaacc--aatagacggtatcaaaccaagaagggtgttaaagcttttcatcctatagGATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCATTTATACCGAATGGACTATATGGACTTTGTTCAG
                      ||  |   |||||   | |  | ||      || ||  | ||  |||  |  |  |  |   |        | |      ||  ||  |  |||||   |  | |||||   | || || ||  | ||| | || ||||| ||||| ||||| |||||||| |||||||||||||||
gtatcacccagcattttaatcttaatctagtttcaaaacgttcacttcatgcacttggaaagcctgaatttatcgcttgtacgtatcttacaggctcgtctgttgaatgtttcagGATGCCAAGAATAAGGTTGTGGAAGACGTAGTAATTTTATCCGGAGACCATTTGTACCGTATGGACTACATGGACTTTGTTCAG

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|110379176|gb|EC944355.1|EC944355
EST:     GGTTCCAGGGCACTGCAGATGCTGTGCGGCAGTTCCATTGGCTCTTTGAG                         GATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCAC
genomic: GGTTCCAGGGCACTGCAGATGCTGTGCGGCAGTTCCATTGGCTCTTTGAGgtacccatat ... catcctatagGATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCAT
EST: gi|110379174|gb|EC944353.1|EC944353
EST:     GGTTCCAGGGCACTGCAGATGCTGTGCGGCAGTTCCATTGGCTCTTTGAG                         GATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCAC
genomic: GGTTCCAGGGCACTGCAGATGCTGTGCGGCAGTTCCATTGGCTCTTTGAGgtacccatat ... catcctatagGATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCAT
EST: gi|110373811|gb|EC938181.1|EC938181
EST:     GGTTCCAGGGCACTGCAGATGCTGTGCGGCAGTTCCATTGGCTCTTTGAG                         GATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCAT
genomic: GGTTCCAGGGCACTGCAGATGCTGTGCGGCAGTTCCATTGGCTCTTTGAGgtacccatat ... catcctatagGATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaccaatagacggtatcaaaccaagaagggtgttaaagcttttcatcctatagGATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCATTTATACCGAATGGACTATATGGACTTTGTTCAG
 gggtaac  putative branch site (score: 3)
                                        cttttcatcct  putative PPT
               tatcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacccatatttcacttctagttaggattctggggtaaccaatagacggtatcaaaccaagaagggtgttaaagcttttcatcctatagGATCAAAGAAGTAAGGAAATTGAGGATGTGCTGATTCTGTCTGGAGATCATTTATACCGAATGGACTATATGGACTTTGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA