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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcacatattttttactatattttccttttaacaaatttactctttagatttatggatcaatttattaagatagttgaatctatctttttgttctttagGTTGGCTCGATAGAGGGAAGGGTTGGCGTACATCATCTTGATGATGCACAACAAAGTAAAAACTTTACTTTTAAATGCCACAGGGAAGGCAATGAGATAT

Basic information

species Vitis vinifera
transcript Vv12s0055g00900.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g44394.1 (Oryza sativa), 3'ss of exon 6
----tctcacatattttttactatattttccttttaacaaatttactctttagatttatggatcaatttattaagatagttgaatctatctttttgttctttagGTTGGCTCGATAGAGGGAAGGGTTGGCGTACATCATCTTGATGATGCACAACAAAGTAAAAACTTTACTTTTAAATGCCACAGGGAAGGCAATGAGATAT
    |    |||| || |   |   | | |||| ||| |  |  ||| |||    | ||        |||      || || || |||| ||||   | |  ||||||| |||||||| ||| | ||||| || |||||| |||||||||  |||||| | ||||||||||| |||||||| ||| | || |||||||| ||||
actttactgcataattgtgtttg-gtgtaccttataaaaggtcaactgtttctgatcatttgagcgcttaaatgcttaatt-aacctatgtttta--tttgaagGTTGGATCGATAGAAGGACGAGTTGGTGTTCATCATGTTGATGATGGTCAACAAGGGAAAAACTTTACATTTAAATGTCACCGTGATGGCAATGACATAT

upper sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os08g07960.2 (Oryza sativa), 3'ss of exon 7
tctcacatattttttactatattttccttttaacaaatttactctttagatt-tatg-gatcaatttattaagatagttgaatctatcttt---ttgttctttagGTTGGCTCGATAGAGGGAAGGGTTGGCGTACATCATCTTGATGATGCACAACAAAGTAAAAACTTTACTTTTAAATGCCACAGGGAAGGCAATGAGATAT
     |  ||    | ||     || | |   |  |||||     | | ||| ||   ||   || | |  |  |   ||| |||  |  |   ||  | |  |||| || || ||||| ||||| ||||| || |||||| |||||||  |||| ||||| ||||| || || || ||||| ||||||||||| ||||| || |
-----cggatagagtgctcagcgttacctaagaataatttctatctgacattatacaagaggtatatttccatgtgtctgactctgaccctaattttgtttcaagGTGGGTTCCATAGAAGGAAGAGTTGGTGTGCATCATATTGATGACTCACAGCAAAGCAAAAATTTCACGTTCAAATGTCACAGGGAAGGGAATGATATTT

upper sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 7
tctcacatattttttactatattttccttttaacaaatttactcttta-----gatttatggatcaattta----ttaagatagttgaatctatctttttgttctttagGTTGGCTCGATAGAGGGAAGGGTTGGCGTACATCATCTTGATGATGCACAACAAAGTAAAAACTTTACTTTTAAATGCCACAGGGAAGGCAATGAGATAT
       ||  |  ||  ||||||||  |||||  | |||||  ||||     || ||   || ||| |||    || |  |  ||||  |  | || |  || |  ||||||| || ||||| ||||| |||||||| |||||| | ||||| ||||| ||||| |||||||| || || ||||||||||||||||| ||||| ||||
------gtacctgatagcatattttc--tttaaatactttacaatttacatatgactttgagaacaaattagattttcatgtgattgacccactgttctcatt-taaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAGCAAAGCAAAAACTTCACATTCAAATGCCACAGGGAAGGAAATGATATAT

upper sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G19260.1 (Glycine max), 3'ss of exon 6
-tctcacatattttttactatattttccttttaacaaatttactctttagatttatggatcaatttattaaga-tagttgaatctatctttttgttcttt--agGTTGGCTCGATAGAGGGAAGGGTTGGCGTACATCATCTTGATGATGCACAACAAAGTAAAAACTTTACTTTTAAATGCCACAGGGAAGGCAATGAGATAT
 |||  || ||| || | |  | | |  || | | || | ||   | ||  | ||  |||  ||| |||  ||   |||||| ||     | |  | |||  |||| || || ||||| ||||||||||| || |||||| | ||||||   || ||  |||||||||| |||||||||||||| || || |||||||| ||||
gtcttccagattctt-atttcagtgtaattatca-aattgtaagttgtaagtcta--gattgattaattttgagctgttgaaactgatgatatactttttgtagGTCGGATCAATAGAAGGAAGGGTTGGGGTGCATCATTTGGATGATAGTCAGCAGGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATAT

upper sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA15G05740.1 (Glycine max), 3'ss of exon 6
tctcacatattttttactatattttccttttaacaaatt-tactctttagatttatggatcaatttatta-agatagttgaatctatctttttgtt--ctttagGTTGGCTCGATAGAGGGAAGGGTTGGCGTACATCATCTTGATGATGCACAACAAAGTAAAAACTTTACTTTTAAATGCCACAGGGAAGGCAATGAGATAT
    |  | ||    | | |  |||    ||| |||||| ||   | ||  | ||  |||  ||| |||   |   |||||| ||     | |  |  || |||||||| || ||||| ||||| ||||| || |||||| | || |||   || ||  |||||||||| |||||||||||||| || || |||||||| ||||
--atatgtcttccagattcttgtttgtaattatcaaattgtaagttgtaagtcta--gattgattaattttgggctgttgaaactgatgatatacttgctgtagGTTGGATCAATAGAAGGAAGAGTTGGGGTGCATCATTTGGACGATAGTCAGCATGGTAAAAACTTCACTTTTAAATGCCATAGAGAGGGCAATGAAATAT

upper sequence: Vv12s0055g00900.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G80670.1 (Arabidopsis thaliana), 3'ss of exon 7
tctcacatattttttactatattttccttttaacaaattta----ctctttagatttatggatcaatttattaagatagttgaatctatctttttgt-tctttagGTTGGCTCGATAGAGGGAAGGGTTGGCGTACATCATCTTGATGATGCACAACAAAGTAAAAACTTTACTTTTAAATGCCACAGGGAAGGCAATGAGATAT
       ||| |   |   | |||| ||  | |||  |  |    || | || ||           |  ||    | | || |    |||   |  | ||| |||||||| || || |||||  ||||||| || |||||||| |||||| | ||||| || |||||||| || || ||||||||||| || || ||||| ||||
-----tttatatgggagattgttttgctagtcacatctccagatcctatctaaatcacaatggtgttgaatatgaaaaattaaccagatccaatgatctctatagGTTGGTTCAATTGAGGGGCGGGTTGGTGTTCATCATCTGGATGATTCTCAACAGAGCAAAAACTTCACATTCAAATGCCACAGAGATGGAAATGATATAT

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|110386126|gb|EC950701.1|EC950701
EST:     AGTATCAGACAAGATGTGTTGCTGCCTTTCCGGATCAGCAAGGATTCTTG                         GTTGGCTCGATAGAGGGAAGGGTTGGCGTACATCATCTTGATGATGCACAA
genomic: AGTATCAGACAAGATGTGTTGCTGCCTTTCCGGATCAGCAAGGATTCTTGgtatgtgttt ... tgttctttagGTTGGCTCGATAGAGGGAAGGGTTGGCGTACATCATCTTGATGATGCACAA
EST: gi|351043163|gb|FQ451336.1|FQ451336
EST:     AGTATCAGACAAGATGTGTTGCTGCCTTTCCGGATCAGCAAGGATTCTTG                         GTTGGCTCGATAGAGGGAAGGGTTGGCGTACATCATCTTGATGATGCACAA
genomic: AGTATCAGACAAGATGTGTTGCTGCCTTTCCGGATCAGCAAGGATTCTTGgtatgtgttt ... tgttctttagGTTGGCTCGATAGAGGGAAGGGTTGGCGTACATCATCTTGATGATGCACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagatttatggatcaatttattaagatagttgaatctatctttttgttctttagGTTGGCTCGATAGAGGGAAGGGTTGGCGTACATCATCTTGATGATGCACAACAAAGTAAAAACTTTACTTTTAAATGCCACAGGGAAGGCAATGAGATAT
                                   tctatctttttgttct  CT-rich tract
               aatttattaagatagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcacatattttttactatattttccttttaacaaatttactctttagatttatggatcaatttattaagatagttgaatctatctttttgttctttagGTTGGCTCGATAGAGGGAAGGGTTGGCGTACATCATCTTGATGATGCACAACAAAGTAAAAACTTTACTTTTAAATGCCACAGGGAAGGCAATGAGATAT

-ctcacat
- - - - - - - - - - - - - - - -aacaaat