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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttgatcttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC

Basic information

species Vitis vinifera
transcript Vv06s0004g06860.t01
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
---aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttgatcttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
    ||  |       |  |  ||| |||   |  || || |  ||     ||  ||  || | | |  ||  | | | |       | |||| |     ||||| ||||||||||| ||||| ||||| || ||||||||||| ||||| || ||||| || || || |||||||| |||||  | ||| |||| ||||| |
gtatatatacaggagcaacctgttagaactaaaacatatttcagtac----aagtcttttcttatctagattttttctaacaccc--ttttttgta----tagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 24
---aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttgatcttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
    ||  |     | |  |  ||| |||   |  || || |  ||     ||  ||  || | | |  ||  | | | |       | |||| |     ||||| ||||||||||| ||||| ||||| || ||||||||||| ||||| || ||||| || || || |||||||| |||||  | ||| |||| ||||| |
gtatatatacaggaccaacctgttagaactaaaacatatttcagtac----aagtcttttcttatctagattttttctaacacccttttttttgta----tagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 1
-------------aatgca-gctagctattcatttataacctcagtatgttactctatttagaatcctagt--cctgtttgaatcctctttgatcttggatattttatgat--tctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
             |   ||  || | || |  ||| ||   || |  |  ||    |  |   |||   ||   || |||   |  | | | || |  | | || |||  |  | ||||| ||||| ||||||||||||||||| || ||||| || || |||||||| ||||| |||||  ||||||||||||||||  | ||| | ||||||||||
gtatacaagtaggagcacatacttgataattttttgtagtatctgctttatagcagagcttctatcactgtgatctattt---ttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
lower sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
-aatgcagctagctattca---tttataacctcagtatgttactctatttagaa------tcctagtcctgt--ttgaatcctctttgatcttggatattttatgatt--ctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
  || ||  |||     ||   || ||||  |   | |  ||     |||| |       | |||   || |  |  | |  | | | || |  | | || |||  ||   ||||| ||||| ||||||||||||||||| || ||||| || || |||||||| ||||| |||||  ||||||||||||||||  | ||| | ||||||||||
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
-aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgt--ttgaatcctctttga--tcttggatattttatgatt--ctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
  || ||  |||     |||   | |      | | |       |||| ||      | || |  |  | | || | |||  | |  ||| || |||  ||   ||||| ||||| ||||||||||||||||| || |||||||| || |||||||| | ||| || ||  ||||||||||||||||  | ||| | ||||||||||
gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
-aatgcagctagctattca---tttataacctcagtatgttactctatttagaatcctagtcctgt--ttgaatcctctttg--atcttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
  || ||  |||     ||   || || |  |     |  |  |   ||||         | || |  |  | | || | ||  ||    | | |||| |   | ||||| || ||  |||||||||||||||| || ||||||||||| |||||||| | ||| || ||  ||||||||||||||||  | ||| | ||||||||||
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 9
-------------------------------------------------------------------------aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgt--ttgaatcctctttgatcttg--gatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
                                                                          || ||  |||     |||   | |  |     | ||  |   ||||         | || |  |  | | || | |||  | |  | | |||| |  || ||||| |||||  | |||||||||||||| || ||||||||||| |||||||| | ||| || ||  ||||||||||||||||  | ||| | ||||||||||
gtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtt-tagGTTGATGACCTCGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 22
aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttgatcttggatatt--ttatgattct--agGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
| ||      |     ||||   |||    |   | ||  || || |  |   |  |  | | ||     | |||||      ||  |  |||| ||| |  ||||||||||||||||||| || ||||| | ||| |||||||| |||||||||||||| ||||||||||| |||||||||||| | ||| |||| ||||| |
attgggaaatgtagaacattggcaacaagtgccagatagactgttgattagtttgttattttctg----ttgtttgactgctaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttgatcttggatatt--ttatgattct--agGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
| ||      |     ||||   |||    |   | ||  |  || |  |   |  |  | | ||     | ||||||     ||  |  |||| ||| |  ||||||||||||||||||| || ||||| | |||||||||||| |||||||||||||| || |||||||| |||||||||||| | ||| |||| ||||| |
attgggaaatgtagaacattggcaacaagtggcagatagacagttgattagtttgttattttctg----ttgtttgattactaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 24
----------aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttgatcttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
          ||| |    | | | | |   | || ||   |   || || ||| ||   |  | |   ||| ||||| |    | ||||   ||||      |||  |||||||||||||||| || || || || ||||| || ||||| |||||||| ||||| ||||||||||| ||||||||||| || |||||||| |||||||
ctagtagcaaaatactaa-aacaagtgacagaaaaactt--ttgattgctttatctaaccttttggcgttgtctgaataccaact-atctgttatat------attgaagGTGGATGATTTGGAGGAGGTTAGCGAGTATTATCAAAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 24
---------aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttgatcttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
         ||| |    | | | | |   | || ||   |   || || | | ||   |  |   | ||| ||||| ||   | ||||      |||||| |||  |||||||||||||||| || || || || || || |||||||| |||||||| ||||| ||||||||||| ||||||||||| || |||||||| |||||||
tagtagcaaaatactaaaaacaagtgacagaaaaactt--ttgattgctttgtctaaccttttgaccttgtctgaatacttact-atct-----gttttat-attgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 12
aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttg-atcttggatattttatgattct--agGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
   | |  | | |  ||   |  ||    ||||||    |  |||| |  | || |     |   || |   | |  | | ||   ||  |    || |  ||||||| ||||||||||| |||||||| ||||||||||| || ||  ||||| |||||||||| || || ||||| |||||  | || ||||| || || |
ggagta-ttggattctctggtccaagtagagtatgca--ttgattttgttttctggaaggctagaaaacaattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 24
aatgcagctagctattcatttataacctcagtat--gttactctatttagaatccta----gtcctgtttgaatcctctttgat------cttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
            | ||  || ||| | ||| ||   |||   ||  |   | || ||    || |||  |||   | |||| ||      ||| |  ||    |  | | ||||||| || ||||||||||||||| | || || ||||||||||| || |||   ||||| || ||||| |||||||||||  | ||  |||| |||||||
-----------ttgttt-ttgatatcatcattactagtttggctggtggcattcttatgcagtgctggatgagatcactttaataaaccgctttgtaatggggttttaccagGTGGACGACTTGGAAGAAGTCAGTCAGTACTATCAGAACAGGGGTTGTTTTGTGGAGCTTATCTCTCTTATGGAGAGTGGGCTTGGGCTGGAGCGTGCAC

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 3'ss of exon 12
-----aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctct-ttgatcttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
       || |   ||        |  || |||      |||    | | | |||| ||   |  ||   |  ||  | |||||  ||   | | | ||     |||| |||||| ||||||| ||||| || |||||||||||||||||  ||||| | |||||||| || || ||||| |||||  | || ||||| ||||| |
atccttgtggaaaaagagcagagatattatcctgcaacggttgtgttgtatggaatactg--caagtaaaataccggtattgattgtgcgaaatctgtg----cagGTTGATGATCTGGAAGAGGTCAGCGAATATTACCAGAACAGGGGTCGCTTTGACGAGCTCATTTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGTGCCC

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttgatcttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
                                  || |  ||||      | || ||  |  |  |    |  ||| |||    | || | | | || |||||||||||||||| ||||| |||||||| |||||||| |||||| | ||  |||| || || ||||| ||||| |||||  | ||| | || || ||||
----------------------------------gtaaggctat---agtttctggttatactctatctttggttggtctaatctgttat-taaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC

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|161712003|gb|FC060856.1|FC060856
EST:     CTGAGGAATTTCGCTTGGCTCAGATATGTGGGCTCAACATCATCATACAG                         GTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTT
genomic: CTGAGGAATTTCGCTTGGCTCAGATATGTGGGCTCAACATCATCATACAGgtggaggttc ... atgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaatcctagtcctgtttgaatcctctttgatcttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC
                          ctttgat  putative branch site (score: 5)
                                      atattttatgattcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttgatcttggatattttatgattctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
aatgcag
- - - - - -ctattca
- - - - - - - - - - - -aacctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgttt