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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCAGATTCAAAGGCCTCAACAGAGAGTGTTTACAATGCTGCATTAGCCCTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGAgtaagtttcttatgatgcagaaatctccactgaactaggaagaaaaattcaattctttgtcatgttttctttgctccaagataatcattcgtaattgggg...

Basic information

species Vitis vinifera
transcript Vv12s0028g00960.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os12g43130.1 (Oryza sativa), 5'ss of exon 4
CACCAGATTCAAAGGCCTCAACAGAGAGTGTTTACAATGCTGCATTAGCCCTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGAgtaagtttct-tatgatg--cagaaatctccactgaactaggaagaaaaattcaattctttgtcatgttttctttgctccaagataatcattcgtaattgggg
| || || || ||||||||||| ||||| || ||||| |||||  |||| |||||||| ||||| ||||| || || || |||||||| || || || ||||||||  |  | || |    |  |   |   ||      |    || ||||  |  ||||  |||| |   | ||      || |  || |    ||||   
CCCCCGACTCGAAGGCCTCAACCGAGAGCGTGTACAACGCTGCGCTAGCTCTTGGGATCGCCAACCAGCTGACGAATATTCTCAGAGACGTAGGCGAAGAgtaagtaccaatgtgctcactaccagcatgttctttttctgagttaataattgcagactttcacatgataaatatgtagtttgacacccaatatgtattg---

upper sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA02G45270.1 (Glycine max), 5'ss of exon 4
CACCAGATTCAAAGGCCTCAACAGAGAGTGTTTACAATGCTGCATTAGCCCTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGAgtaagtttcttatgatgcagaaatctc----cactgaactaggaagaaaaattcaattctttgtcatgttttctttgctccaagataa-tcattc-gtaattgggg
|||||||  |||| || |||||||||||  |||| ||||||||||| || || || || || ||||| || |||||||||||||||||||| || ||||||||||||||||   |  |   ||| ||     | | ||| |  || |  ||   |||    | | |  |  |     ||| | | ||  |||  |  |||      
CACCAGAAGCAAATGCTTCAACAGAGAGCATTTATAATGCTGCATTGGCTCTAGGCATTGCAAATCAACTTACTAACATACTCAGAGATGTTGGAGAGGAgtaagtttctttgaacacttcaatgtcatgcaattaaaccaaaaaaagtaaagaaatgacatttgaaatcatgcc-actcaagggtatctcaccccataac-----

upper sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA08G41890.1 (Glycine max), 5'ss of exon 5
CACCAGATTCAAAGGCCTCAACAGAGAGTGTTTACAATGCTGCATTAGCCCTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGAgtaagtttcttatgatgcagaaatctccactgaactaggaagaaaaattcaattctttgtcatg-ttttctttgctccaagataatcattcgtaattgggg
||||||| ||||||||  |||||||||| ||||| ||||||||||| || ||||| ||||| ||||| || || ||||| |||||||| || || || |||||||  ||||   |||||  ||| ||   | |  |      ||| ||  || |     | |    |  | |||       |  |||| |   | | |   
CACCAGAATCAAAGGCTACAACAGAGAGCGTTTATAATGCTGCATTGGCACTTGGCATAGCTAATCAACTTACCAACATTCTCAGAGACGTTGGAGAAGAgtaaggatctttaaatgcaataatatcttgt-atttgaacctaaatatagaagttagaattacaactcaccttgtagtttaagtatcagtgacattcgttc

upper sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA18G13700.1 (Glycine max), 5'ss of exon 4
-CACCAGATTCAAAGGCCTCAACAGAGAGTGTTTACAATGCTGCATTAGCCCTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGAgtaagtttcttatgatgcagaaatctccactgaactaggaagaaaaattcaattctttgtcatgttttctttgctccaagataatcattcgtaattgggg--
 ||||||| |||||||| || ||||||||||| || ||||||||||| || ||||| || || ||||| || || ||||| |||||||| || || || |||||||  ||||   || ||  ||| ||   |    |    || |  | | |  |   |          ||    ||||||| | |   ||  ||        
GCACCAGAATCAAAGGCTTCGACAGAGAGTGTCTATAATGCTGCATTGGCACTTGGCATTGCTAATCAACTTACCAACATTCTCAGAGACGTTGGAGAAGagtaaggatctttaaatacaacaatatcttgtagtttt---agtatgactgacattcatacataaaaacctcaattccaagaaagtatatctcaacaataaag

upper sequence: Vv12s0028g00960.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA14G03500.1 (Glycine max), 5'ss of exon 4
CACCAGATTCAAAGGCCTCAACAGAGAGTGTTTACAATGCTGCATTAGCCCTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGAgtaagtttcttatgatgc----agaaatctccactgaactaggaagaaaaattcaattctttgtcatgttttctttgctccaagataatcattcgtaattgggg
||||||| ||||| || ||| |||||||  |||| ||||||||||| || || || || || ||||| || || |||||||| |||||||| || || ||||||| |||||   |  |    |   ||  | | | ||| |  || || ||   |||    | | |  | || |   ||| | | || ||   | | |      
CACCAGAATCAAATGCTTCATCAGAGAGCATTTATAATGCTGCATTGGCTCTAGGCATTGCAAATCAACTTACCAACATACTTAGAGATGTTGGAGAAGAgtaaggttctttgaacacttcaatgcattgcaattaaaccaaaaacaataaacaaatggcatttaacatcttgtc-actcaagggta-tctcacatcacacc--

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|29785566|gb|CB342702.2|CB342702
EST:     CTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGA                         TGCTAGGAGGGGAAGAATATATCTCCCACAGGATGAGCTTGAACGAGCAGG
genomic: CTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGAgtaagtttct ... attatatcagTGCTAGGAGGGGAAGAATATATCTCCCACAGGATGAGCTTGAACGAGCAGG
EST: gi|110716794|gb|EE092085.1|EE092085
EST:     CTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGA                         TGCTAGGAGGGGAAGAATATATCTCCCACAGGATGAGCTTGAACGAGCAGG
genomic: CTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGAgtaagtttct ... attatatcagTGCTAGGAGGGGAAGAATATATCTCCCACAGGATGAGCTTGAACGAGCAGG
EST: gi|110382672|gb|EC946989.1|EC946989
EST:     CTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGA                         TGCTAGGAGGGGAAGAATATATCTCCCACAGGATGAGCTTGAACGAGCAGG
genomic: CTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGAgtaagtttct ... attatatcagTGCTAGGAGGGGAAGAATATATCTCCCACAGGATGAGCTTGAACGAGCAGG
EST: gi|28963735|gb|CB342768.1|CB342768
EST:     CTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGA                         TGCTAGGAGGGGAAGAATATATCTCCCACAGGATGAGCTTGAACGAGCAGG
genomic: CTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGAgtaagtttct ... attatatcagTGCTAGGAGGGGAAGAATATATCTCCCACAGGATGAGCTTGAACGAGCAGG
EST: gi|26262970|gb|CA814033.1|CA814033
EST:     CTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGA                         TGCTAGGAGGGGAAGAATATATCTCCCACAGGATGAGCTTGAACGAGCAGG
genomic: CTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGAgtaagtttct ... attatatcagTGCTAGGAGGGGAAGAATATATCTCCCACAGGATGAGCTTGAACGAGCAGG
EST: gi|30126994|gb|CB912333.1|CB912333
EST:     CTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGA                         TGCTAGGAGGGGAAGAATATATCTCCCACAGGATGAGCTTGAACGAGCAGG
genomic: CTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGAgtaagtttct ... attatatcagTGCTAGGAGGGGAAGAATATATCTCCCACAGGATGAGCTTGAACGAGCAGG
EST: gi|28958977|gb|CB339489.1|CB339489
EST:     CTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGA                         TGCTAGGAGGGGAAGAATATATTTCCCACAGGATGAGCTTGAACGAGCAGG
genomic: CTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGAgtaagtttct ... attatatcagTGCTAGGAGGGGAAGAATATATCTCCCACAGGATGAGCTTGAACGAGCAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCAGATTCAAAGGCCTCAACAGAGAGTGTTTACAATGCTGCATTAGCCCTTGGGATAGCCAATCAGCTCACTAACATACTCAGAGATGTCGGGGAGGAgtaagtttcttatgatgcagaaatctccactgaactaggaagaaaaattcaattctttgtcatgttttctttgctccaagataatcattcgtaattgggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagataa