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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttgaggaataatttcttcttcctttttttttttttgataaaagcttgtcttcagtatctgatgtgctagcttttcatcattcttttaacattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCATACAGATTGGATGAAAAAACTGGATATATTGACTATGACCAG

Basic information

species Vitis vinifera
transcript Vv18s0001g07960.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
atttgaggaataatttcttct-tcctttttttttttttgata-aaagct-----tgtcttcagtatctgatgtgctagcttttcatcattcttttaacattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCATACAGATTGGATGAAAAAACTGGATATATTGACTATGACCAG
   ||||         | ||  | |||  || | ||  |||| || |||     |    |||   ||  |||   ||| | |||| | |  |  |      |||||||| || || |||||||| || || || || ||||| |||||||||||||| ||||||||||||||||  ||||| |  ||||| ||||| |||
---tgagtttcttccccctcaattcttagttatgttcagatataatgctcttggtactctcatcctcccatggcttagttgttcaacttcttgatgg----ttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
atttgaggaataatttcttcttcctttttttttttttgataaaagcttgtcttcagtatct-gatg-tgctagcttttcatcattcttttaacattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCATACAGATTGGATGAAAAAACTGGATATATTGACTATGACCAG
|| ||   |  |||  | | ||||  |   || ||    ||| |    |   | |   ||| |||  | |||    |  |   ||||    ||  ||||||||| ||||| ||||||||||||||    || |||||||||||||||||||| ||||||||||||||||  |||||||  ||||| || || |||
atctgcaaatgaatgacattttcccataaattctt--agtaacattcagatatgatgctctagatactcctatagctcaaaggttctacctactgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G135283_T01 (Zea mays), 3'ss of exon 6
atttgaggaataatttcttcttcctttttttttttttgataaaagcttgtcttcagtatct-gatg-tgctagcttttcatcattcttttaacattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCATACAGATTGGATGAAAAAACTGGATATATTGACTATGACCAG-------
|| ||   |  |||  | | ||||  |   || ||    ||| |    |   | |   ||| |||  | |||    |  |   ||||    ||  ||||||||| ||||| ||||||||||||||    || |||||||||||||||||||| ||||||||||||||||  |||||||  ||||| || || |||       
atctgcaaatgaatgacattttcccataaattctt--agtaacattcagatatgatgctctagatactcctatagctcaaaggttctacctactgtttgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGGTCATTT

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 6
---atttgaggaataatttcttcttcctttttttttttttgataaaagcttgtcttcagtatctgatgtg-ctagcttttcatcattcttttaacattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCATACAGATTGGATGAAAAAACTGGATATATTGACTATGACCAG
     || |  |  |||| |   | |  | ||||||   ||    ||   ||| | |  |||    |||  | || |||| || |||  |||    |  ||||||| ||||||||||||||||| ||||| |||||||||||||| |||||||||||||||||| |||| |  ||||| ||||| || |||||||||
aaccattcattagcaattccccttgcactcttttttaactgtagcaa---tgtgtgccatattctttgtaacaagtttttgattatttgtttg-tgtcatgcagACTGACACCAAGAAGATATCAGCTGTATCTATATTTTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 6
---atttgaggaataatttcttcttcctttttttttttttgataaaagcttgtcttcagtatctgatgtg-ctagcttttcatcattcttttaacattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCATACAGATTGGATGAAAAAACTGGATATATTGACTATGACCAG
    ||| |  |  || | |   | |   | ||||   |||    ||   ||| | |  |||    |||  | || |||| || |||  |||   ||  ||||||| ||||||||||||||||| ||||| |||||||| ||||| |||||||||||||||||| |||| |  ||||| ||||| || |||||||||
agcctttcattagcaactccccttgcacctcttttaaattgtagcaa---tgtgtgccatattctttgtaacaagattttgattatttgtttg-tatcatgcagACTGACACCAAGAAGATATCGGCTGTATCTATATTCTTTGAAACAATGCCATACAGATTGAATGAGAGCACTGGTTATATCGATTATGACCAG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 6
--atttgaggaataatttctt---cttcctttttttttttttgataaaagcttgtcttc------agtatctgatgtgctagcttttcatcattcttttaacat-----tttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCATACAGATTGGATGAAAAAACTGGATATATTGACTATGACCAG
  | ||| |   || | |||    |||  |   |   | |||||       || || ||       | |  |||| |  || |||||| |||||  ||| |  |     | ||||||| ||||| ||||| ||||| ||||| || || |||||||||||||||||||||||||||||||| || ||||| || ||||| |||||||||
gtacttgggttctagtctctctagcttggtcagtcagtatttgactttcttttctcatctctttgtggaattgatattgtatcttttcctcatttcttttatttgctcttgtgcagACTGACACGAAGAAAATATCGGCTGTATCCATCTTTTTTGAGACAATGCCATACAGATTGGATGAGAACACTGGTTACATTGATTATGACCAG

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|352776821|gb|FQ472708.1|FQ472708
EST:     TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAG                         ACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAGgtgcttatga ... cattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCA
EST: gi|71862434|gb|DT011489.1|DT011489
EST:     TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAG                         ACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAGgtgcttatga ... cattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCA
EST: gi|161708846|gb|FC059632.1|FC059632
EST:     TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAG                         ACCGACACCAAGAAGATATCTGCTGTGTCT
genomic: TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAGgtgcttatga ... cattttgcagACCGACACCAAGAAGATATCTGCTGTGTCT
EST: gi|352781776|gb|FQ469074.1|FQ469074
EST:     TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAG                         ACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAGgtgcttatga ... cattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCA
EST: gi|110359383|gb|EC920779.1|EC920779
EST:     TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAG                         ACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAGgtgcttatga ... cattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCA
EST: gi|294966030|gb|GW837397.1|GW837397
EST:     CATGGCACTTGATCTTCCTCATGGTGGGGCATCTTTCACATGGTTATCAG                         ACCGACACCAAGAAGATATCTGCTGTGTCTATANNNNNNNGAGACAATGCC
genomic: CATGGCACTTGATCTTCCTCATGGTGGG-CATCTTTCACATGGTTATCAGgtgcttatga ... cattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTT-GAGACAATGCC
EST: gi|352768688|gb|FQ467900.1|FQ467900
EST:     TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAG                         ACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAGgtgcttatga ... cattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCA
EST: gi|71859287|gb|DT008342.1|DT008342
EST:     TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAG                         ACCGACACCAAGAAGATATCTGCTGTGTCTATA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAGgtgcttatga ... cattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATA
EST: gi|161713667|gb|FC062807.1|FC062807
EST:     TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAG                         ACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGGCATCTTTCACATGGTTATCAGgtgcttatga ... cattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtcttcagtatctgatgtgctagcttttcatcattcttttaacattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCATACAGATTGGATGAAAAAACTGGATATATTGACTATGACCAG
                                       ttttaac  putative branch site (score: 2)
                                   attcttttaacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttgaggaataatttcttcttcctttttttttttttgataaaagcttgtcttcagtatctgatgtgctagcttttcatcattcttttaacattttgcagACCGACACCAAGAAGATATCTGCTGTGTCTATATTTTTTGAGACAATGCCATACAGATTGGATGAAAAAACTGGATATATTGACTATGACCAG

- - - ggaataa
- - - - - - - - -ttcttcc
- - - - - - - - - - - - - - - - - - -gataaaa
- - - - - - - - - - - - - - - - - - - - - - gcttgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatgt