Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattatggcatcaagtcactcacccatatgacttgatccatcttttattctgattgaattggagttagatttaggtgttgatgaccttccatatttgcagGCAATGAATGGTCAGTATCTCTGCAACCGGCAGATAACTGTGTCCTATGCATACAAGAAAGACACTAAAGGGGAGCGGCATGGTACCCCAGCAG

Basic information

species Vitis vinifera
transcript Vv04s0023g01470.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G170699_T01 (Zea mays), 3'ss of exon 7
cattatggcatcaagtcactcac-ccatatgacttgatccatcttttattctgattgaattggagttagatttaggtgttgatgaccttccatatttg-cagGCAATGAATGGTCAGTATCTCTGCAACCGGCAGATAACTGTGTCCTATGCATACAAGAAAGACACTAAAGGGGAGCGGCATGGTACCCCAGCAG
|| ||        |   | |  | | | | |       || |   | ||| || |||   |||  || | || | |  ||  |    | |  |||||  ||||| |||||    ||  || | ||||||||||  || ||||| || ||||| |||||||||||||| ||||| ||||| ||||| || |||||||
cactacaatccacatggagtggcactacaaggaacaggcccttagtgattttggttgt-ctggcttttgtttcatgc-ttctttctgtgctgtatttttcagGCCATGAACAACCAACATTTGTGCAACCGGCCAATCACTGTCTCTTATGCTTACAAGAAAGACACAAAAGGAGAGCGCCATGGCACACCAGCAG

upper sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA09G00310.1 (Glycine max), 3'ss of exon 7
cattatggcatcaagtcactcacccatatgacttgatccatcttttattctgattgaattggagtt----agatttaggtgttgatgaccttccatattt-gcagGCAATGAATGGTCAGTATCTCTGCAACCGGCAGATAACTGTGTCCTATGCATACAAGAAAGACACTAAAGGGGAGCGGCATGGTACCCCAGCAG
       |  |||| |   |   |   ||  |   |||   |         ||||  |   |  ||     |    |  | ||||     ||| |||||| | ||||||||||||| || ||||| ||||| || || || || ||||| ||||| ||||||||||||||||| ||||| |||||||||||||| || |
----tctgtttcaattttgttgtctggatatccaaatcatacggaacaatagattataaaagcattcccacgccacatatattga-atttttctatattttgtagGCAATGAATGGACAATATCTTTGCAATCGTCAAATTACAGTGTCATATGCTTACAAGAAAGACACTAAGGGGGAACGGCATGGTACCCCGGCTG

upper sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G36950.1 (Glycine max), 3'ss of exon 7
cattatggcatcaagtcactcacccatatgacttgatccatc-ttttattctgattgaattggagttagatttaggtgttgatga--ccttccatattt-gcagGCAATGAATGGTCAGTATCTCTGCAACCGGCAGATAACTGTGTCCTATGCATACAAGAAAGACACTAAAGGGGAGCGGCATGGTACCCCAGCAG
       |  |||| |   |   |    |      |||  || |  || |   ||  ||  | | |   |      || |  |||    ||| |||||| | ||||||||||||| || ||||| ||||| || || || || ||||| ||||| || |||||||||||||| || || |||||||||||||||||||
----tctgtttcaattttgttgtctgggtattcaaatcattcgtaatagtagaatataaaagcattcccacgccactgatattgaatttttctatattttgtagGCAATGAATGGACAATATCTTTGCAATCGTCAAATTACAGTGTCATATGCTTATAAGAAAGACACTAAGGGTGAACGGCATGGTACCCCAGCAG

upper sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------------------------------cattatggcatcaagtcactcacc-catatgacttgatccatcttttattctgattgaattggagttagatttaggtgttgatgaccttcc-atatttgcagGCAATGAATGGTCAGTATCTCTGCAACCGGCAGATAACTGTGTCCTATGCATACAAGAAAGACACTAAAGGGGAGCGGCATGGTACCCCAGCAG
                                       | |  |  |   |||   | ||    || | ||    |  |  | |     |   | |      | |||  |       ||||     ||  |   |||||| |||||| ||| || |||||| | || || || || || || || || ||||||||||||||||| ||||| ||||| |||||||| |||||||
gtaattatctgcttctttcataactctcagttctatgaacttgcttacgaaaaggagcccaatatatttcacacatttaacttctccgattacctaatccaatggtagtatattcctctgatctttgtctgactattgcagTCAATGACTGGACAATATCTCAGTAATCGTCAAATCACAGTCTCTTACGCATACAAGAAAGACACCAAAGGAGAGCGCCATGGTACTCCAGCAG

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|71877269|gb|DT026324.1|DT026324
EST:     TTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAG                         GCAATGAATGGTCAATATCTCTGCAACCGGCAGATAACAGTGTCCTATGCA
genomic: TTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAGgtatatatct ... atatttgcagGCAATGAATGGTCAGTATCTCTGCAACCGGCAGATAACTGTGTCCTATGCA
EST: gi|110729959|gb|EE106491.1|EE106491
EST:     TTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAG                         GCAATGAATGGTCAGTATCTCTGCAACCGGCAGATAACAGTGTCCTATGCA
genomic: TTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAGgtatatatct ... atatttgcagGCAATGAATGGTCAGTATCTCTGCAACCGGCAGATAACTGTGTCCTATGCA
EST: gi|161719366|gb|FC068974.1|FC068974
EST:     TTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAG                         GCAATGAATGGTCAATATCTCTGCA
genomic: TTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAGgtatatatct ... atatttgcagGCAATGAATGGTCAGTATCTCTGCA
EST: gi|110387686|gb|EC952373.1|EC952373
EST:     TTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAG                         GCAATGAATGGTCAATATCTCTGCAACCGGCAGATAACAGTGTCCTATGCA
genomic: TTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAGgtatatatct ... atatttgcagGCAATGAATGGTCAGTATCTCTGCAACCGGCAGATAACTGTGTCCTATGCA
EST: gi|37186306|gb|CF605659.1|CF605659
EST:     TTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAG                         GCAATGAATGGTCAATATCTCTGCAACCGGCAGATAACAGTGTCCTATGCA
genomic: TTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAGgtatatatct ... atatttgcagGCAATGAATGGTCAGTATCTCTGCAACCGGCAGATAACTGTGTCCTATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctgattgaattggagttagatttaggtgttgatgaccttccatatttgcagGCAATGAATGGTCAGTATCTCTGCAACCGGCAGATAACTGTGTCCTATGCATACAAGAAAGACACTAAAGGGGAGCGGCATGGTACCCCAGCAG
                                       ccttccat  CT-rich tract
                   ttagattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattatggcatcaagtcactcacccatatgacttgatccatcttttattctgattgaattggagttagatttaggtgttgatgaccttccatatttgcagGCAATGAATGGTCAGTATCTCTGCAACCGGCAGATAACTGTGTCCTATGCATACAAGAAAGACACTAAAGGGGAGCGGCATGGTACCCCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - -gcatcaa
- - - - - - - - - ctcaccc
- - - - - - - - - - - - - - tgacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgttg