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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtgccactttttcattttcaattattgctcctctcctatttgctatcacaggcgttgtaatcatgtgctcgatgtggtgctgaatgccttgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTC

Basic information

species Vitis vinifera
transcript Vv03s0038g00460.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g36870.1 (Oryza sativa), 3'ss of exon 4
-------cgtgccactttttcattttcaattattgctcctctcctatttgctatcacaggcgttgtaatcatgtgctcgatgtggtgctgaatgccttgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTC
         |||||   |  | ||   |||| |         | ||| |  ||    |  |    | |   ||| || ||  |   | | |||  | |      ||||| ||||| || || || || ||||| ||||||||||| ||||| |||||||| |||||||| ||| | || || || ||||| || ||||| ||||| |
tgcaatgaatgccataatgcccttgcaaattgtaatcttgtgcatatattttactcaaatctgcatgagactgttct-gacatatggattaatatcat------tagGTGGCAGAACCGTTGAGGGCTATGGTGATGGGAGCTCCTTTGGAAGATGCTCGCCATCTTGCCCAAAGATACGACAGGATGCGTCAGGAAGCCGAAGCAC

upper sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G002859_T03 (Zea mays), 3'ss of exon 3
---------cgtgccactttttcattttcaattattgctcctctcctatttgctatcacaggcgttgtaatcatgtgctcgatgtggtgctgaatgccttgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTC
          ||||||   | || |||   | | | |  | | |  |  |  | |||| |  ||    || | |||  |  | |||  ||  | || | |       |||||||||| ||  | || || ||||| ||||||||||| |||||||||||||| || ||||||||| | || || |||||||| |||||||||||||| |
ttacccgtaagtgccataatatcctttcatact-tcgtacatttttttctaacaatcaaacccggacaaagcttgtttt--aagtgaagcgaactgacat------cagGTTGCAGAACCTCTGAGGGCTATGGTTATGGGAGCTCCTTTGGAGGATGCTCGCCACCTTGCTCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC

upper sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G123624_T01 (Zea mays), 3'ss of exon 4
--cgtgccactttttc---attttcaattattgctcctctcctatttgctatca-caggcgttgtaatcatgtgctcgatgtggtgctgaatgccttgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTC
    | |||  | | |   | | ||  || |  ||     | | |||  ||  | ||  | | |  |     || |  | ||  | |  | || | |       |||||||||| ||| | ||||| ||||| ||||||||||| ||||||||||| || || || || ||| | || || |||||||| |||||||||||||| |
atttttccatgtgtgccataatatcctttgtcactttgtacatttttcttaaaatcaaacctggacaaagcttgttttaagtaatacaaactgtcat------cagGTTGCAGAACCACTGAGAGCTATGGTTATGGGAGCTCCTTTGGAGGATGCCCGCCACCTCGCCCAAAGGTACGACAGAATGCGTCAAGAAGCTGAAGCGC

upper sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AC216073.3_FGT001 (Zea mays), 3'ss of exon 1
-----cgtgccactttttcattttcaattattgctcctctcctatttgctatcacaggcgttgtaatcatgt-gctcgatgtggtgctgaatgccttgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTC
     |  |  | |     | | |   ||  | || |   | | |||   |  |      | |||   || | | |  | |||  ||  | || | |       |||||||||| ||  | || || ||||| |||||||||||  ||||||||||||  || || || ||| | || || |||||||| |||||||||||||| |
ttttacccgtaagtgccataatattctttcatacttcgtacatttttctaacaatcaaactcgtacaaatattgttttaagtgaagcaaactgacat------cagGTTGCAGAACCCCTGAGGGCTATGGTTATGGGAGCTCCTATGGAGGATGCTCACCACCTCGCCCAAAGGTACGATAGAATGCGTCAAGAAGCTGAAGCGC

upper sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G04210.1 (Glycine max), 3'ss of exon 4
-------cgtgccactttttcattttcaattattgctcctctcctat-ttgctatcacaggcgttgtaatcatgtgctcgatgtggtgctgaatgccttgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTC
         | |   |   |||| ||   ||  |   |||    | | |||| |||  || | |  |||| ||||| | || ||  || | |||||  |||||   ||||||||||||||||||| || |||||  ||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||| ||||||||||| |
ctctatctatactggtggctcatatt--gttgatttacctagtgtgtgttgccatcttagcc-taataattatgtgattgaagtcatggtcaatgc--tgatt---agGTTGCAGAGCCATTAAGGGCAATGGTGGTGGGAGCTCCATTGGAGGATGCTCGGCATCTTGCTCAACGTTATGACAGAATGCGACAGGAAGCTGAAGCCC

upper sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G01120.2 (Glycine max), 3'ss of exon 4
cgtgccactttttcattttcaattattgc--tcctctcctatttgctatcacaggcgttgtaatcatgtgctcgatgtggtgctgaatgccttgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTC
  |    ||   ||||| ||||||  | |  |     | |  ||  | |  | | | |  |  |  || |   ||     |   ||||  ||||||   |||||||||||||| |||||||| ||||| ||||||||||||||||||||||| || |||||||||||||| ||||| |||||||| || ||||| ||||| |
-atat-gctggctcattgtcaatttatccagtttgtgcttgatttttttatctgacataatgtttctgcgagtgaacattttaagaattgcttgatgcttagGTTGCAGAGCCCTTAAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCCC

upper sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G11950.3 (Glycine max), 3'ss of exon 4
-------cgtgccactttttcattttcaattattgctcctctcctat-ttgctatcacaggcgttgtaatcatgtgctcgatgtggtgctgaatgccttgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTC
         | |   |   |||| ||  |||  |   |||    | | |||| |||  || | |  |||  ||||| | || ||  || | ||||||  ||||   ||||||||||||||||||| || |||||  ||||||||||||||||||||||| | |||||||||||||| ||||| ||||||||||| ||||| ||||| |
cgctatctatactggtggctcatatt--attgatttacctagtgtgtgttgccatcttagcc-taataactatgtgattgaagtcatggtcaatgcc--gatt---agGTTGCAGAGCCATTAAGGGCAATGGTGGTGGGAGCTCCATTGGAGGATGCTAGGCATCTTGCTCAACGTTATGACAGAATGCGACAGGAAGCGGAAGCCC

upper sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G01100.2 (Glycine max), 3'ss of exon 4
cgtgccactttttcattttcaattattgc---tcctctcctatttgctatcacaggcgttgtaatcatgtgctcgatgtggtgctgaatgccttgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTC
       ||   ||||| ||||||  | |   |  |     ||||  | |  | ||| |  |  |  || |   ||     |   | ||  ||||||   |||||||||||||| || ||||| ||||| ||||||||||||||||||||||| || |||||||||||||| ||||| |||||||| || ||||| ||||| |
---tatgctggctcattgtcaatttatccaatttgtgcttgattttttttatctggcataatgtttctgcgagtgaacattttaagtattgcttgatgcttagGTTGCAGAGCCCTTGAGAGCAATGGTGATGGGAGCTCCATTGGAGGATGCCCGGCATCTTGCTCAACGTTATGACAGAATGCGGCAGGAAGCCGAAGCAC

upper sequence: Vv03s0038g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G34660.2 (Arabidopsis thaliana), 3'ss of exon 4
cgtgccactttttcattttcaattattgctcctct-cctatttgctatcacaggcgttgtaatcatgtgctcgatgtggtgctgaatgccttgattt-ctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTC
      ||| ||| |   ||||||| ||      |    | ||| |          |||   |   |         |  |     |  |||  ||||  |||||||| ||||||||| | || |||||  ||||||||||||||||||||||| |||||||||||||||||||||| |||||||| ||||||||||||||||
--acatactctttaaaagtcaattaatgtcatggtgttcacttggttctttctttattgcggtttggctactacaatcatatgtcaatcctgaatttgttagGTTGCTGAGCCATTACGGGCAATGGTTTTGGGAGCTCCATTGGAGGATGCTAGACATCTTGCTCAACGCTATGACAGAATGCGCCAAGAAGCTGAAGCTC

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|351024745|gb|FQ430570.1|FQ430570
EST:     CCCAAATTGAGAAAGAACGTGGAAATCTATTGAAAGCTCTTGGTACACAG                         GTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCT
genomic: CCCAAATTGAGAAAGAACGTGGAAATCTATTGAAAGCTCTTGGTACACAGgtttggccaa ... tgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCT
EST: gi|351035615|gb|FQ463460.1|FQ463460
EST:     CCCAAATTGAGAAAGAACGTGGAAATCTATTGAAAGCTCTTGGTACACAG                         GTTGCAGAGCCATTAAGAGCGTTGGTAATGGGAGCTCCATTGGAGGATGCT
genomic: CCCAAATTGAGAAAGAACGTGGAAATCTATTGAAAGCTCTTGGTACACAGgtttggccaa ... tgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCT
EST: gi|349826387|gb|FQ417884.1|FQ417884
EST:     CCCAAATTGAGAAAGAACGTGGAAATCTATTGAAAGCTCTTGGTACACAG                         GTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCT
genomic: CCCAAATTGAGAAAGAACGTGGAAATCTATTGAAAGCTCTTGGTACACAGgtttggccaa ... tgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCT
EST: gi|351023475|gb|FQ432858.1|FQ432858
EST:     CCCAAATTGAGAAAGAACGTGGAAATCTATTGAAAGCTCTTGGTACACAG                         GTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCT
genomic: CCCAAATTGAGAAAGAACGTGGAAATCTATTGAAAGCTCTTGGTACACAGgtttggccaa ... tgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCT
EST: gi|351040290|gb|FQ425376.1|FQ425376
EST:     CCCAAATTGAGAAAGAACGTGGAAATCTATTGAAAGCTCTTGGTACACAG                         GTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCT
genomic: CCCAAATTGAGAAAGAACGTGGAAATCTATTGAAAGCTCTTGGTACACAGgtttggccaa ... tgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcacaggcgttgtaatcatgtgctcgatgtggtgctgaatgccttgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTC
                                          ccttgat  putative branch site (score: 5)
                                                tttct  CT-rich tract
          ttgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtgccactttttcattttcaattattgctcctctcctatttgctatcacaggcgttgtaatcatgtgctcgatgtggtgctgaatgccttgatttctagGTTGCAGAGCCATTAAGAGCGATGGTAATGGGAGCTCCATTGGAGGATGCTCGACATCTTGCTCAACGCTATGAAAGAATGCGACAAGAAGCTGAAGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- -gccactt
- - - - - - - - - - - - - - - -ctctcct
- - - - - - - - - - - - - - - - - - - - - - - -cacaggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgcc