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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaaatagcaacctttttttattttttatttctttttcttgatttattattagtatcatttattcatttcatttcacttaatgtttctttcaacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG

Basic information

species Vitis vinifera
transcript Vv11s0052g01840.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G073380_T01 (Zea mays), 3'ss of exon 3
caaaatagcaacctttttttatttttt--atttctttttcttgatttattatt---agtatcatttattcatttcatttcacttaatgtttctttcaacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG
 ||  |  |||  | | | | ||||||  ||  | |      |  | ||  ||     |||      |  | || ||||||  | |   |   |    |    |||||||||||||| ||||| || |||||||| |  |||| |||||||||| | || ||||| ||| ||||||| || |||||||| || 
-aagctcacaatttctctgttttttttggatagcgtacgtagggatcatccttccgcatatagagcgtgaaattaatttcatctgacactctatgatgc----agTGTGAGGGCAATCGTTGCATTAAATCTTCACAATTATGCAAGTGGAAGAAACCCTTGGGGAAATTTGAAGCCTGAATATTTGGAGAAA

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G01360.2 (Glycine max), 3'ss of exon 9
caaaatagcaacctttttttattttttatttctttttcttgatttattattagtatcattta-ttcatttcatttcacttaatgtttctttcaacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG
|    |||  |  ||        |   |   ||   |||   ||| | |    | |  |||  | |||||    | |  |  |  | || |   |||  ||||| ||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||| |  || ||||| ||||||||||||
ctgcctagagaatttagcaagagtcacacaactcaatctct-tttgtgaagtttttggtttggtccattttgcatgatatggttatgctatttcctttcagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAATCCATGGGGTAAACCAAAACCAGAATATTTGGAAAAG

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA17G07480.1 (Glycine max), 3'ss of exon 9
--caaaatagcaacctttttttattttttatttc--tttttcttgatttattattagtatcatttattcatttcatttcacttaatgtttctttcaacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG
  |    |||  |   |  |     |   |  ||  | | | | |     || || ||    ||  | |||||    | |  |  |  |  | |   |||  ||||| |||||||||||||||||||| |||||||||||||||||||||||| ||||||||||||| |  || ||||| ||||||||||||
tactgcctagtgaatgtagtaagagtcacaactcagtctctttcgtgaagtttttggt----ttggtccattttgcatgatatggttatgttatttcctttcagTGTAAGGGCAATAGTTGCTTTGAACCTTCATAGCTATGGAAGTGGAAGAAATCCATGGGGTAAACCAAAACCAGATTATTTGGAAAAG

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA06G30040.1 (Glycine max), 3'ss of exon 2
caaaatagcaacctttttttattttttatttctttttcttgatttattatta--gtatcatt---tattcatttcatttcacttaatgtttctt--tcaacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG
        |||  || || ||  ||  |||  | |      |||| || |||  || |||||     ||  | |||||| |  ||| |||   |  |    ||  ||||| || |||||||||||| | ||||||||||| ||||||||||||||| |||||||||||||| |||  || || ||||| || |||
-------tcaaagttcttatagcttacattagtgtgataaaatttgttcttatggtctcattagaggtttgtctcattttaaataaggttatgtcatttgttttcagTGTAAGAGCAATAGTTGCTCTAAATCTTCATAGTTATGGAAGTGGAAGAAATCCATGGGGTAATTTGACACCTGAGTATTTAGAGAAG

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA18G22370.1 (Glycine max), 3'ss of exon 2
caaaatagcaacctttttttattttttatttctttttcttgatttattatta--gtatcattt---attcatttcatttcacttaa--tgtttctttcaacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG
          |   | || || | |  |||  | |      | || || |||  || || |||    ||  | || ||| | | |   | | || ||    |||| |||| || |||||||||||| | || |||||||| ||||||||||||||| |||||||||||||| | |  || || ||||| || |||
------tttgaagctcttatagtatacattagtgtgataacaattgttcttatggtttcgttttgggtttctctcttttaaataaggttatgtcctttgctttca-gTGTAAGAGCAATAGTTGCTCTAAACCTTCATAGTTATGGAAGTGGAAGAAATCCATGGGGTAATTTAACACCTGAGTATTTAGAGAAG

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT4G30340.1 (Arabidopsis thaliana), 3'ss of exon 6
caaaatagcaacctttttttattttttatttctttttcttgatttattattagtatcatttattcatttcatttcacttaatgtttctttcaacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG
               ||  |||        |||| |  |||||| |  | ||  |  ||   |||| ||    || ||     ||| |||     |  || || ||  | || || |  ||||||||| ||| ||||||||||||||||||||||||||||||||| |  ||| | ||||| || |||
--------------gttcatataaaactaatcttatctttgattaaa-actaaaaaaatggcttcacttataatctctctggttttgttttggtgt--agCGTAAGATCTATTGTGGTGTTGAATCTTTATAACTATGGAAGTGGAAGACATCCATGGGGTAATCTCAGACCAAAATATTTAGAGAAG

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G18730.1 (Arabidopsis thaliana), 3'ss of exon 9
caaaatagcaacctttttttattttttatttctttttcttgatttattattagtatcatttattcatttcatttcacttaatgtttctttcaacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG
      |  |||  ||||  || | | |||| | | |    || |    ||  ||||| |  || |    |  | |    |||  | | ||   ||  ||||||||  |||| || || ||||||||||| ||||||||||||||||| ||||| ||||| ||||| || || |||||| | || |||
---gtaaaaaacagttttcgatatatgatttatgtattacaatct----ttgatatcaatgcttaaa---acctgatgctatggatttctc---ttgtagTGTGAGATCAATTGTCGCATTGAATCTTCACAGCTATGGAAGTGGAAGCCATCCTTGGGGCAATCTAAAACCGGACTATCTAGAGAAG

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G57690.1 (Arabidopsis thaliana), 3'ss of exon 7
-------caaaatagcaacctttttttattttttatttctttttcttga-tttattattagtatcatttattcatttcatttcacttaatgtttctttcaacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG
       || ||||| |||        |  |   |        | || | | |  || | |  |   | ||  |     | |   ||  |  || ||   ||    ||||| || ||| | ||||| |||||||| ||||||||||||||||||||| | || ||||| ||||| || | ||| ||| | ||||| 
gtatctacagaatagaaacaagaacacaaatgagacagaacacttttaaatctcataattgggtttctaatgaaagatgtgt-gtttgcttgtttttgggac----agTGTAAGAGCAGTTGTTGCATTGAATCTACATAGCTATGGAAGTGGAAGAAACCCTTGGGGAAATCTCAAACAAGATTATCTTGAAAAA

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|110400722|gb|EC967297.1|EC967297
EST:     ATTAAAAAGGTCAATTGTTCAGAATGGGAGCAGATTCGAGTTCCTTCAAG                         TGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACA
genomic: ATTAAAAAGGTCAATTGTTCAGAATGGGAGCAGATTCGAGTTCCTTCAAGgtatagttct ... caacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACA
EST: gi|30303616|gb|CB980410.1|CB980410
EST:     ATTAAAAAGGTCAATTGTTCAGAATGGGAGCAGATTCGAGTTCCTTCAAG                         TGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACA
genomic: ATTAAAAAGGTCAATTGTTCAGAATGGGAGCAGATTCGAGTTCCTTCAAGgtatagttct ... caacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACA
EST: gi|30304336|gb|CB981130.1|CB981130
EST:     ATTAAAAAGGTCAATTGTTCAGAATGGGAGCAGATTCGAGTTCCTTCAAG                         TGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACA
genomic: ATTAAAAAGGTCAATTGTTCAGAATGGGAGCAGATTCGAGTTCCTTCAAGgtatagttct ... caacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACA
EST: gi|83276057|gb|DV940065.1|DV940065
EST:     AAAAAGGTCAA-TGTTCAGAATGGGAGCAGATTCGAGTTCCTTCAAG                         TGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACA
genomic: AAAAAGGTCAATTGTTCAGAATGGGAGCAGATTCGAGTTCCTTCAAGgtatagttct ... caacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attattagtatcatttattcatttcatttcacttaatgtttctttcaacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG
                              acttaat  putative branch site (score: 4)
                                      tttctttcaacttc  CT-rich tract
        tatcatttattcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaaatagcaacctttttttattttttatttctttttcttgatttattattagtatcatttattcatttcatttcacttaatgtttctttcaacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
caaaata
- - - - caacctt