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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattagttttgatggagaattacaatgcatgggtttagagattattccatattaatgtattattcctttatttatttatttattatttacattttatcagGGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAAGTATAAAGAGATGATGGAAGCCTATAGGGTGATGTTGACCTATATTAAA

Basic information

species Vitis vinifera
transcript Vv08s0040g00430.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g17180.2 (Oryza sativa), 3'ss of exon 3
aattagttttga-tggagaattacaatgcatgggtttagagattattccatattaatgtattattcctttatttatttatttattatttacattttatcagGGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAAGTATAAAGAGATGATGGAAGCCTATAGGGTGATGTTGACCTATATTAAA
|||  ||| | | | |  | | | |     ||  | |  |    |   |  | | || | |||    | |         | | | | |    | ||   ||||| || |||||||| ||||||||||| ||||| ||||||  | | |||||||| ||||| |||||||| |||||||||| ||||||||| || || |||
aatgtgttataagttgtcagtgaaatcaagtgtatctgtatccaacagc-cactcatattttagagatctgacgtcagttctgtaactcttttctttatagGGGTTTCAAAGCTCTGAAACAAACAGTGAAGCTGTATTATAAGCTTGGGAAGTACAAAGAAATGATGGATGCCTATAGGGAGATGTTGACATACATCAAA

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 3
aattagttttgatggagaattacaatgcatgggtttagagattatt-ccatattaatgtatt-attcctttatttatttatttattatttacattttatcagGGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAAGTATAAAGAGATGATGGAAGCCTATAGGGTGATGTTGACCTATATTAAA
    | ||||  ||   ||| |  ||| ||   ||   |  |||    ||  |   | | ||    | | |  |  |||| |   || |   || ||   ||||||||||||||||| |||||||| ||||||||||| |||  | | || || || ||||| |||||||| |||||||| | |||||| || || || |||
-gccactttttttgtgaaatca-gatgtattatttattattttaccatcacttcgttatctttgcacttctgatgctttactctgtaatgttatctttatagGGGATTTAAAGCTCTTAAACAAACTGTCAAGCTTTACTATAAGCTGGGAAAATACAAAGAAATGATGGATGCCTATAGAGAGATGTTAACATACATAAAA

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 3
-aattagttttgatggagaattacaatgcatgggtttagagattattccatattaatgtattattcctttatttatttatttattatttacattttatcagGGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAAGTATAAAGAGATGATGGAAGCCTATAGGGTGATGTTGACCTATATTAAA
 | | | ||||  || |     |      ||   ||    ||| ||    | || |  | |    | | |  |  |||| |   || ||  || ||   ||||||||||||||||| |||||||| ||||||||||| |||  | | ||||| || ||||| |||||||| || ||||| | |||||| || || || |||
gagtcactttttctgaaatcaaatgtattatttattatttgatcatcatttttttacctgt-gcgcttctgatgctttactctctaattttatctttatagGGGATTTAAAGCTCTTAAACAAACTGTCAAGCTTTACTATAAGCTGGGGAAATACAAAGAAATGATGGATGCATATAGAGAGATGTTAACATACATAAAA

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 3
aattagttttgatggagaattacaatgcatgggtttagagattattcca---tattaatgtattattcctttatttatttatttattatt-tacattttatcagGGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAAGTATAAAGAGATGATGGAAGCCTATAGGGTGATGTTGACCTATATTAAA
       ||| ||| |  |         ||  || |    ||  ||| |   |  |||   | || | | || |  | ||| || | ||| |  ||| ||||||||||||||||||||||||||| || |||||||| ||||||||  | || | ||||||||||||||||||||||||||||| ||||||||| |||||||| 
----ctctttcatgtaccacatagtaatatttgtctgagaatctttctactgtgataagaaactactgcattttgcacttaattttcattctgtattctatcagGGGATTTAAAGCTCTAAAACAGACTGTCAAGCTATATTATCGACTGGGAAGGTATAAAGAGATGATGGAAGCCTATAGGGAGATGTTGACATATATTAAG

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 3
aattagttttgatggagaattacaatgcatgggtttagagattattccatattaatgtattattcctttatttatt-tatttattatt-----tacattttatcagGGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAAGTATAAAGAGATGATGGAAGCCTATAGGGTGATGTTGACCTATATTAAA
     ||  ||      |||   |||     |  ||||| || |||||  |      || ||  || |||| ||||  ||||  ||||     ||||||||| ||||||||||||||||||||||||||| || |||||||||||| |  | || | ||||||||||||||||||||||||  ||| ||||||||| || ||||||
-----gtagtgcatagtaatagtaatattatgtcttaga-atcattcctcacagtgataataaaccattatgtattgcatttcatatttatcttacattttaccagGGGATTTAAAGCTCTAAAACAAACTGTGAAGCTTTATTATAGACTTGGAAGGTATAAAGAGATGATGGAAGCCTACCGGGAGATGTTGACTTACATTAAA

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G17660.2 (Glycine max), 3'ss of exon 3
aattagttttgatggagaattacaatgcatgggtttagagattattccatattaatgtattattcctttatttatttatttattatt-tacattttatcagGGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAAGTATAAAGAGATGATGGAAGCCTATAGGGTGATGTTGACCTATATTAAA
   || | |  ||  |  |         |   ||||    ||  | | |   |||   | |||| | || |  | ||| || | ||| |  ||||||||||||||||||||||||||||||| || ||||||||  |||||||  | || | | |||||||||||||| |||||||||||| |||| |||| |||||||| 
-tgtactctacatataccacatagtaatacttgtttgagaatcttactagtgtaagaaactattacattttgcacttaattttcattctgtattttatcagGGGATTTAAAGCTCTAAAACAGACTGTCAAGCTACATTATCGACTGGGAAGGCATAAAGAGATGATGAAAGCCTATAGGGAGATGCTGACATATATTAAG

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 3
aattagttttgatggagaattacaatgcatgggtttagagattattccatattaatg------tattattcctttatttatttatttattatttacattttatcagGGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAAGTATAAAGAGATGATGGAAGCCTATAGGGTGATGTTGACCTATATTAAA
  ||   | |  || | | | | | |       | |  | || |||||| | | ||        ||||    ||  |||   |||||||   ||||||||||  |||||||||||||||||||| ||||| || ||||| |||||| |  | || | |||||||||||||||||||||||| |||| ||||||||| || ||||| 
--ttg--tgtagtgcatagtaatagtaatattatgttaaaatcattccacagtgataaaaatccattacgtattgcttttcatatttatc--ttacattttactagGGGATTTAAAGCTCTAAAGCAAACTGTGAAGCTCTATTATAGACTTGGAAGGTATAAAGAGATGATGGAAGCCTACAGGGAGATGTTGACTTACATTAAG

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 3'ss of exon 3
-----aattagttttgatggagaattacaatgcatgggtttagagattattccatattaatgtattattcctttatttatttatttattatttacattttatcagGGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAAGTATAAAGAGATGATGGAAGCCTATAGGGTGATGTTGACCTATATTAAA
      |  |  |||| |  |  |   |  ||| |   |      | | || | | |    |||   ||   ||    |  |  |||||  |||| ||   |||||||||| || || || || ||||||||||||||| |||||||| | || || || ||  |||||||||| || ||||| |  ||||||||||| || || 
tctacgaaaacctttgctccattaaatcgttgcttcactgctactactcttacgtgtg---gtagattttggttgcaaagctgattatttgttacgttc--tcagGGGATTCAAGGCGCTGAAGCAAACAGTCAAGCTTCATTATCGGGTCGGTAATTACAAGCAGATGATGGATGCGTATAGAGAAATGTTGACCTACATCAAG

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|71855965|gb|DT005020.1|DT005020
EST:     CTTGCTGGCTTTGCTGAAGTAGTTCGCATGGAACCAGAGAAGGCAGAGTG                         GGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAA
genomic: CTTGCTGGCTTTGCTGAAGTAGTTCGCATGGAACCAGAGAAGGCAGAGTGgtgagcagat ... attttatcagGGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAA
EST: gi|110724456|gb|EE100301.1|EE100301
EST:     CTTGCTGGCTTTGCTGAAGTAGTTCGCATGGAACCAGAGAAGGCAGAGTG                         GGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAA
genomic: CTTGCTGGCTTTGCTGAAGTAGTTCGCATGGAACCAGAGAAGGCAGAGTGgtgagcagat ... attttatcagGGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAA
EST: gi|161718082|gb|FC068585.1|FC068585
EST:     CTTGCTGGCTTTGCTGAAGTAGTTCGCATGGAACCAGAGAAGGCAGAGTG                         GGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAA
genomic: CTTGCTGGCTTTGCTGAAGTAGTTCGCATGGAACCAGAGAAGGCAGAGTGgtgagcagat ... attttatcagGGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatattaatgtattattcctttatttatttatttattatttacattttatcagGGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAAGTATAAAGAGATGATGGAAGCCTATAGGGTGATGTTGACCTATATTAAA
    tattaat  putative branch site (score: 2)
                                              ttttatc  putative PPT
     attaatgtattattcc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattagttttgatggagaattacaatgcatgggtttagagattattccatattaatgtattattcctttatttatttatttattatttacattttatcagGGGATTTAAAGCTCTAAAACAAACAGTCAAGCTTTATTATCGGTTAGGGAAGTATAAAGAGATGATGGAAGCCTATAGGGTGATGTTGACCTATATTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - -tgatgga
- - - - - - - - - - - caatgca