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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggagtgatcatatatatagccccataatccttagacttccttttttctttttttttttgtgtagtcataataataaaaaggtatttttttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAAC

Basic information

species Vitis vinifera
transcript Vv14s0030g00700.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0030g00700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os07g19060.2 (Oryza sativa), 3'ss of exon 1
-----agggagtgatcatatatatagccccataatccttagacttccttttttctttttttttttgtgtagtcataataataaaaaggtatttttttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAAC
         | |  |||   | |||    |||  || ||| | ||  ||  ||   |        |||  |  |   |||  |||  || | | ||     | ||||||||||||||| | || || |||||||||||||| || |||||||| ||||||||||| ||||| ||||| ||| | |||||||||||||| ||||| 
acaaatataactactcactgaaatatttgcat--tctttata-ttggttccttacctccaggccagtgctgcaaagttaaccaaa--gtttctgttcaaaatcagATATACTATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAAT

upper sequence: Vv14s0030g00700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os09g06970.3 (Oryza sativa), 3'ss of exon 1
agggagtgatcatatatatagccccat---aatccttagacttccttttttctttttttttttgtgtagtcataataataaaaaggtatttttttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAAC
   |    |   ||  |   | |  |     ||   |  | |   || || | |    |  ||||   |     || | |  |   | | | ||     | |||||||| |||||| | || || |||||||||||||| || |||||||| ||||||||||| ||||| ||||| ||||| ||||||||||| || ||||| 
--agcacaaatgtaactgctgtctgaattgcatatgtgtattgggttcttacctccactccttgtagtgctgcgatta-accataatttctgttcaaaatcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAAT

upper sequence: Vv14s0030g00700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM5G886989_T03 (Zea mays), 3'ss of exon 2
agggagtgatcatatatatagccccataatccttagacttccttttttctttttttttttgtgtagtcataataataaaaaggtat-ttttttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAAC
   ||    |||  | | |       || |  ||    |   |       |    |   |||  |     |     ||  |  | | || ||  | || |||||||| |||||| | || || |||||||||||||| || |||||||||||||||||||| || || ||||| ||||| ||||||||||| || ||||| 
-cagatctgtcagttttctgtgtgattattttttttggtcagtgcaacactccaatgcatgtacatctgcagactcaaccaaatttattgttcatattcagATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAAT

upper sequence: Vv14s0030g00700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G123807_T02 (Zea mays), 3'ss of exon 2
-agggagtgatcatatatatagccccataatccttagacttccttttttctttttttttttgtgtagtcataataataaaaaggtatttttttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAAC
 |        |||  | | |       ||||  ||  | |   |    |  |    |   |||        |  | | ||    | ||| ||  | || |||||||| |||||| | || || |||||||||||||| || |||||||| ||||||||||| ||||||||||| ||||| |||||||| || || ||||| 
caaatctgtctcagttttctgtgtgattaatttttttagtcagtgcaatgctccaatgcatgtacttctgcag-actcaaccattttttgttcatattcagATATACCATGGAGCGTCCACGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTCTGGTCAGAGCTGTTCAAGAAACAGATTGACAAT

upper sequence: Vv14s0030g00700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G42850.1 (Glycine max), 3'ss of exon 1
----agggagtgatcatata-tatagccccataatccttagacttccttttttctttttttttttgtgtagtcataataataaaaaggtatttttttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAAC
    |    || || || || | |||  | | |     |     ||         || |  |    | |  |   | || |||||  ||  ||| || ||   || ||||| |||||| |||| ||||| |  |||||||| ||||| |||||||| ||||||||||| || ||||||||||||||||||||||| || ||||||
gttaactttgtaatgatgtaatgtagttctaca--tgatgactctctaaagggaattatcatgaaatttgattgaattagtaaaattgtggtttgttgtt---agGTATACCATGGAGCGGCCTCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAAC

upper sequence: Vv14s0030g00700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G05000.1 (Arabidopsis thaliana), 3'ss of exon 1
agggagtgatcatatatatagccccata-atccttagacttccttttttctttttttttttgtgtagtcataataataaaaaggtatttttttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAAC
 | |  ||   | ||| | |      || |   ||  |          | |||    ||||   |  |  |    |     ||   ||||| | |  |||| || |||||||| || ||  |||| ||||| ||||||||||||||||||||||||||||| ||||||||||||||| ||||||||||||| || || || 
-gtgtttgcctacataaaaactgttttacagtgttgtatgatggcagatatttagcattttacttgattgtgcataacttcagccttttttatgtcgttagGTACACTATGGAAAGACCAAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAAT

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|30304539|gb|CB981333.1|CB981333
EST:     CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACG                         ATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
genomic: CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACGgtatgctgtc ... ttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
EST: gi|161709339|gb|FC059668.1|FC059668
EST:     CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACG                         ATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
genomic: CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACGgtatgctgtc ... ttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
EST: gi|26262203|gb|CA813266.1|CA813266
EST:     CGTAG-ATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACG                         ATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
genomic: CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACGgtatgctgtc ... ttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
EST: gi|26263640|gb|CA814703.1|CA814703
EST:     CGTAG-ATCGAGGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACG                         ATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
genomic: CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACGgtatgctgtc ... ttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
EST: gi|30132412|gb|CB917751.1|CB917751
EST:     CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACG                         ATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
genomic: CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACGgtatgctgtc ... ttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
EST: gi|28966801|gb|CB345834.1|CB345834
EST:     CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACG                         ATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
genomic: CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACGgtatgctgtc ... ttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
EST: gi|26262474|gb|CA813537.1|CA813537
EST:     CGTAG-ATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACG                         ATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
genomic: CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACGgtatgctgtc ... ttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
EST: gi|26262213|gb|CA813276.1|CA813276
EST:     CGTAG-ATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACG                         ATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
genomic: CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACGgtatgctgtc ... ttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
EST: gi|30135317|gb|CB920655.1|CB920655
EST:     CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACG                         ATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
genomic: CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACGgtatgctgtc ... ttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
EST: gi|110380802|gb|EC946095.1|EC946095
EST:     CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACG                         ATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT
genomic: CGTAGAATCGAAGCCATTGGCTACCAGGTCGGCCACCAGCTCTCCGAACGgtatgctgtc ... ttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttttttttttgtgtagtcataataataaaaaggtatttttttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAAC
                                      tattttttttttttt  CT-rich tract
                tgtagtcataataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggagtgatcatatatatagccccataatccttagacttccttttttctttttttttttgtgtagtcataataataaaaaggtatttttttttttttagATATACTATGGAGAGGCCCCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
-gggagtg
- - - - - - - - - - -ccccata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaaa