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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttcaaatactagtttgatttggacccctgattgagggtggttcaccttcttttcagttacataaattttaaagtaagcaaatctctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA

Basic information

species Vitis vinifera
transcript Vv15s0048g02350.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g62490.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------------------------------aatttcaaatactagt-ttgatttggacccctgattgagggtggttcaccttcttttca---gttacataaattttaaagtaagc-aaatctctctgg----------tgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA
                                                                          | ||| |   || | | || |     | |  ||     |  |  |||  | |  |||||    || |||   | ||   ||  |   | |||  |||           |||||||||||||||||||||||| |||||||| ||| | || |||  |||||| || || ||| || | ||| || | ||||||||| || | || ||  | || |
gtaagcaaagatgcaatggattatttctggtttagatggctttcaccatattccttgataagtttactacctgtagttttagtgacaattgttaagacatatcaatggcactgtttatttcttcattgtttcatatatttcatttttgttggtgtgggttgagtctgactgtgaggcctgcttgaacagGGTGAGGCTAAGAGTGCACAGCTGATTGGTGAGGCGATTAACAACAACCCTGCCTTCCTCGCTCTCCGACAGATTGAAGCTGCCAGGGAGATCTCTCACA

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g60000.1 (Oryza sativa), 3'ss of exon 4
-------aatttcaaatactagtttgatttggacccctgattgagggtggttcaccttcttttcagttacataaattttaaagtaagcaaatctctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA
        || ||||   |    || ||||  | |  || || |   |  ||||   | |||   ||    | | | | |  || ||    |||   |  |||||||||||||||||||||||| |||||||| ||| | || |||  |||||| || || ||| || | ||| || | ||||||||| || | || ||  | || |
gttaagacatatcaatggcactgttcatttc-atcattgttttata-tatttcattgtgtttggtgtgggttgagtctgactgtgag---gtctgctt--tgaacagGGTGAGGCTAAGAGTGCACAGCTGATTGGTGAGGCGATTAACAACAACCCTGCCTTCCTCGCTCTCCGACAGATTGAAGCTGCCAGGGAGATCTCTCACA

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G145964_T01 (Zea mays), 3'ss of exon 1
----aatttcaaatactagt-ttgatttggacccctgattgagggtggttcaccttcttttcagttacataaattttaaagtaagcaaatctctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA
    |  || |    || || ||||  |  |||  |   |||       ||  ||||||| |     |  |||   ||       |   ||| |   |||||||||| ||||||||||||||  ||||||| |||||||| || || ||||| || || ||| |  | || ||  | ||||||||| |  | || ||  | || |
tgctatgttgatgcccttgtgttgagctaaacctttccctgaaacattatctgcttctttcc-----ctgaaacactatctgcttctggtctgtgctgtgaacagGGAGAGGCTAAGAGTGCGGAGCTGATTGGTCAAGCCATAGCGAACAACCCTGCCTTCCTTGCCCTGAGGCAGATTGAAGCTGCAAGGGAGATCTCCCACA

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AC217358.3_FGT005 (Zea mays), 3'ss of exon 4
aatttcaaatactagtttgat--ttggacccctgattgagggtggttcaccttcttttcagtta--cataaattttaaagtaagcaaatctctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA
   |     |  |||||   |  |||      |  |   |  |  ||| |||| |   | | |     | |||       |        ||  |   ||||||||||||||||||||| ||  || |||| || ||||| ||||||||||| || || ||| |  | || ||| | ||||||||| || | || ||  | || |
---tctctgtg-tagttcagtagttgtgtatatactattgcatcattccccttttaccctgatgactctgaatcaccgtctgtctgtgacttgcatttgaacagGGTGAGGCTAAGAGCGCTGAGTTGATTGGCCAAGCCATTGCCAACAACCCCGCCTTCCTGGCTCTGAGACAGATTGAAGCTGCCAGGGAGATCTCCCACA

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G01850.1 (Glycine max), 3'ss of exon 4
aatttcaaatactagtttgatttggacccctgattgagggtggttc--accttcttttcagttacataaatt-ttaaagtaagcaaatctctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA
 ||    | ||||  |||   |   |      |  |||||  |||   ||     | |   |||  || ||     |      |   ||| | |    |||||||||| ||||||||||||||| |||| ||||||||||||||||| ||||| || || |||||  | || |||||||||||| |  | ||||| || || |
-atccatagtact--tttatctacaaaagaatacagagggctgtttttacaactctattgtttatgtatataacctattccttcccttctttttaacaaacagGGTGAAGCTAAGAGTGCCCAGTTGATTGGTCAAGCTATTGCCAATAATCCTGCGTTTATCACCTTAAGGAAAATTGAAGCTGCAAGGGAAATCGCTCAGA

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G11670.2 (Glycine max), 3'ss of exon 5
aatttcaaatactagtttgatttggacccctgattgagggtggttcaccttcttt-tcagttacataaattttaaagtaagcaaatc---------tctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA
         | ||  |||  |    |    | |  |||||   ||   |  || | |   ||| ||| || |  |  ||| |   ||         | | ||   |||||||||| || |||||||||||| |||| ||| ||||||||||||| ||||| || || |||||  | || |||||||||||  |  | ||||| || || |
---------tcctttttttctacaaaagaat-acagagggctatttttcaactctattgtttatatatatatatatataacctgttccttcccttctttttgacaaacagGGTGAAGCCAAGAGTGCCCAGTTGATTGGTGAAGCTATTGCCAATAATCCTGCGTTTATCACCTTAAGGAAAATTGAAGCGGCAAGGGAAATCGCTCACA

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G33520.1 (Glycine max), 3'ss of exon 5
---aatttcaaatactagtttgatttggacccctgattgagggtggttcacct-tcttttcagttacataaattttaaagtaagcaaatctctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA
   | | |    || | | | | |||| |   | |||      ||  || |   | | |||||||          |    ||  | ||||| | |  ||| ||||| || || || |||||||| ||||| || ||||||||||||||||||||||| || ||||| || || || || |||||  |  | || ||||||||||
tagattgtttggtattggct-gttttgcatatcagatcacttttgcatcccaagtgtgttcagttctccctgacctttctta--cgaatcttt-taatgatcagGGAGAAGCAAAAAGTGCCCAACTGATTGGGCAAGCTATTGCCAACAATCCAGCTTTTATCACACTGAGGAAGATAGAAGCCGCAAGGGAGATTGCACATA

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 6
aatttcaaatac-tagtttgatttggacccctgattgagggt-ggttcacctt--cttttcagttacataaattttaaagtaagcaaatctctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA
 ||||   |||  | ||||| | | | |   |  ||||   | ||  ||| ||  | | | |  ||   |  | |    | |      | ||| |  ||||||||| || || || |||||||| || || || || |||||||||||||||||||| || |||||  | || || || |||||| | ||||| ||||||||||
-atttagcatatattgtttgctattggctgtt--ttgattatcggaccacttttgcatcttaagtattcagttctccctg-acctttctttctttaatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCAGCTTTTATCACATTGAGGAAGATAGAAGCTGCACGAGAGATTGCACATA

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G03860.3 (Arabidopsis thaliana), 3'ss of exon 5
aatttcaaatactagtttgatttggacccctgattgagggtggttcacc-ttcttttcagttacataaattttaaagtaagcaaatctctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA
   |   | |  |  | |   ||| |   || ||     | | ||     || |   | |   ||| |  | |          ||||| | ||     ||||| || ||||| ||||| ||||| || || ||||| ||||| |||||||  ||||||||||| || ||||| ||||||||| |  |||| |||||||| |
gtatagcattggtgatcttgattgcaaatctaatgacatgagattagtggttttggcctgaagcattagctctttt-----tgaatctttgtg-----cagGGAGAAGCTAAAAGTGCTCAGCTTATCGGACAAGCAATTGCGAACAATCAGGCATTCATCACTCTGAGAAAGATTGAAGCTGCGAGAGAGATTGCACAGA

upper sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G44140.1 (Arabidopsis thaliana), 3'ss of exon 4
aatttcaaatactagtttgatttggacccctgattgagggtggttcaccttcttttcagttacataaattttaaagtaagcaaatctctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA
            ||| ||   |||      || || ||  |  |    ||    || | |   | || || |   ||||  | |  | | || |  |||||| || ||||||||||| || || ||||| ||||||||||| ||||||  ||| ||||| || || || || ||||||||| |  |||| ||||| || |
-----------gtaggttatcttg--tttttgtttaagcattatgtgtctctggtttatt---agaagttgtgt-gtaatgacaattatgtgattcacagGGAGAAGCTAAGAGTGCTCAACTCATAGGGCAAGCTATTGCGAACAATGAAGCTTTCATTACTCTGAGGAAGATTGAAGCTGCAAGAGAGATTGCTCAGA

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|30320841|gb|CD004103.1|CD004103
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|110400766|gb|EC967344.1|EC967344
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|110414101|gb|EC979926.1|EC979926
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|110708454|gb|EE086015.1|EE086015
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGC
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGC
EST: gi|30297423|gb|CB974217.1|CB974217
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|110421504|gb|EC987802.1|EC987802
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|18459675|gb|BM437953.1|BM437953
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|110699664|gb|EE076859.1|EE076859
EST:     TTGTGGGAAAAGCTGAGCAAGACAAGA-GAGTGCTATTATCAGAGCACAG                         GGTGAAGCTAAAAGTG
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTG
EST: gi|110381432|gb|EC934441.1|EC934441
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|110367206|gb|EC931133.1|EC931133
EST:     TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAG                         GGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
genomic: TTGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACAGgtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCA
EST: gi|110718347|gb|EE095076.1|EE095076
EST:     TGTGGAAAAAGCTGAGCCAGACAAGAAGAGTGCTATTATCAGAGCACAAG                         GGTGAGGCTAAGAGTGCCCAGCTGATA
genomic: TGTGGAAAAAGCTGAGCAAGACAAGAAGAGTGCTATTATCAGAGCACA-Ggtgagaaata ... tggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccttcttttcagttacataaattttaaagtaagcaaatctctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA
                                       tctctct  CT-rich tract
       ttttcagttacataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttcaaatactagtttgatttggacccctgattgagggtggttcaccttcttttcagttacataaattttaaagtaagcaaatctctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - -caaatac
- - - - - - - - - - - - - cccctga
- - - - - - - - - - - - - - - - - -gagggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagcaaa