Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatgctttatactattctactagttgaatatatatggaagtcatgtgtaaattttaacagaattctaataagcattcttgtgattttgctgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTTGGGTTCCCAAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g06920.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 17
---------------------------------------taatgctttatactattctactagttgaatatatatggaagtcatgtgtaaattttaacagaattctaataagcattcttgtgattttgctgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTTGGGTTCCCAAAG
                                        ||    ||||   | | ||  | ||| | ||  | |   || | |   |     ||| ||| |   | |      | || | ||| | |||  |||||||||||||| ||||| || ||||| |||||||| || ||||||||||| ||||| |||||||||
gtacgtaatctcttgattgaattgcattgtttctagaggcaacttcttatgtcagtatagcatttggagatgaa-gactgtaaaggagatgagctaatagagtgagagtctctcatttt-taattattctgatgtttagATATGGACCAGCACGCTTCAGAGGACAATTTTGACAGCAAGTCCAATAGTTGGATTCCCAAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 17
taatgctttatactattctactagttgaatatatatggaagtcatgtgtaaattttaacagaattctaataagcattcttgtgattttgctgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTTGGGTTCCCAAAG-------------------------------------
      |   || | | | | |  || |||    |||||  | |   | |     |||||       || |       |||  ||| |    | |||||||||||||| || || || |||||||||||||| || ||||||||||||||||| ||||| |||                                     
-----gtaagtattttccca-tgatttaatg---atggatctgaccagca-----taacatgggctgaaaa------tttgcaattatcgaattgtttagATATGGACCAGTACCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAGGTATTTGGTTACACGATTTAGGAGTCTTCTTAAAGAA

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G021846_T01 (Zea mays), 3'ss of exon 17
taatgctttatactattctactagttgaatatatatggaagtcatgtgtaaattttaacagaattctaataagcattcttgtgattttgctgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTTGGGTTCCCAAAG
      |   || | | | | |  || |||    |||||  | |   | |     |||||       || |       |||  ||| |    | |||||||||||||| || || || |||||||||||||| || ||||||||||||||||| ||||| |||
-----gtaagtattttccca-tgatttaatg---atggatctgaccagca-----taacatgggctgaaaa------tttgcaattatcgaattgtttagATATGGACCAGTACCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 15
taatgctttatactattctactagttgaatatatatggaagtcatgtgtaaattttaacagaattctaataagcattcttgtgattttgctgtggttt-agATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTTGGGTTCCCAAAG
                         | | |||         |  | | |  | |  |   ||| | | || |  |||  ||||      |  || ||| ||||||||||||||||||| ||||||||||| ||||| |||  ||| ||  |||| || ||||||
------------------------gtaagtatgccatttgcttctctattcagtgaaggggaaatatcattaa-atttatgtg---caacgatgatttcagATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 17
taatgctttatactattctactagttgaatatatatggaagtcatgtgtaaattttaacagaattctaataagcattcttgtgatt-ttgctgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTTGGGTTCCCAAAG
                          | |    |||   |   ||||| ||| | |     |||  | |   |  || |  || || |   ||  || |||||||||||||| ||||||||| |||||||||| || ||| |||||||||||||||| ||||||
--------------------------gtaagcttataataaatatgtgcaaaatat--tgaaatgatgaatggt-ttgtgatgtttgtaaatggtgtctagATATGGACTAGTACACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 28
taatgctttatactattctactagttgaatatatatggaagtcatgtgtaaattttaacagaattctaataagcattcttgtgattttg-ctgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTTGGGTTCCCAAAG
                         | |   |||    ||   ||||| ||| | |     |||  | |  ||  || |  || || |  |||  || |||||||||||||| ||||||||| |||||||||| || ||| |||||||||||||||| ||||||
------------------------gtaagcttatcataaatatatgtgcaaaatat--tgaaatgatgaatagt-ttgtgatgtttgtaactggtgtctagATATGGACTAGTACACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAG

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|30322291|gb|CD005553.1|CD005553
EST:     AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGANAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|352764397|gb|FQ472754.1|FQ472754
EST:     AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|71882349|gb|DT031404.1|DT031404
EST:     AAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: AAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|352769630|gb|FQ468558.1|FQ468558
EST:     CCTGAAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: CCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|71888454|gb|DT037509.1|DT037509
EST:     AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|352768928|gb|FQ468119.1|FQ468119
EST:     AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGTTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|71889378|gb|DT038433.1|DT038433
EST:     AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|71890359|gb|DT039414.1|DT039414
EST:     AACTTTCTACCTTCGTGGAAAAGAGACTGAAACTTGAAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|30321972|gb|CD005234.1|CD005234
EST:     AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|27580319|gb|CB003014.1|CB003014
EST:     AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|27581545|gb|CB004240.1|CB004240
EST:     AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|32250239|gb|CD716058.1|CD716058
EST:     AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|110360631|gb|EC923892.1|EC923892
EST:     AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|30321898|gb|CD005160.1|CD005160
EST:     AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTG
genomic: AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTG
EST: gi|352781433|gb|FQ468277.1|FQ468277
EST:     AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|71888451|gb|DT037506.1|DT037506
EST:     CGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: CGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|27582400|gb|CB005095.1|CB005095
EST:     GACTGAAACCTGAAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: GACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
EST: gi|30321402|gb|CD004664.1|CD004664
EST:     AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCT                         ATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT
genomic: AACTTTCTACCTTCGTGGAAAAGAGACTGAAACCTGAAAGGGCTGCTTCTgtaagtttca ... tgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtaaattttaacagaattctaataagcattcttgtgattttgctgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTTGGGTTCCCAAAG
                  ttctaat  putative branch site (score: 2)
                                       ttttgct  putative PPT
     aattttaacagaattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatgctttatactattctactagttgaatatatatggaagtcatgtgtaaattttaacagaattctaataagcattcttgtgattttgctgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTTGGGTTCCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - catgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aacagaa