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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatatcagagaggcaatgagttttcttttttttcttttttctgttttattctttaaatggcaagggattcagcctgatgcattttgaacttgtatgcagCAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGATCCCCCAAGGAGACCAGGTGGTGGTTCCATGACGATAAAGTCTAATTTG

Basic information

species Vitis vinifera
transcript Vv04s0023g02620.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 5
gaatatcagagaggcaatgagttttcttttttttcttttttctgttttattctttaaatggcaagggattcagcctgatgcattttgaacttgtatgcagCAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGATCCCCCAAGGAGACCAGGTGGTGGTTCCATGACGATAAAGTCTAATTTG
             |  ||     |||  | | | || |   |||||| | |    |    |||   ||         |||  | ||  |  |   |||||||||||||||  || ||||| || ||||| ||||||||| | ||||| || || || |||||||||||||||||||| ||||| || ||||| | ||| |
-------------gttatagagcttcactgtgtcctctc--ctgtttaaatggagatcatgcatctgaccatattatatgtttattatatgttggtgcagCAACGTCCTGCCGACAATGATCGCTATGTCAGGAACTGCCGCAATGGGAGGTCGCCGAAGGAGACCAGGTGGTGGTTTCATGATGACAAAGTGTGATTGG

upper sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 5
gaatatcagagaggcaatgagttttcttttttttcttttttctgttttattctttaaatggcaagggattcagcctgatgcattttgaacttgtatgcagCAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGATCCCCCAAGGAGACCAGGTGGTGGTTCCATGACGATAAAGTCTAATTTG
   ||| | | |   | | |      |    |||  |||  |||    |      |||    ||  | |  | | || |  | | ||    ||| |||||||||| ||| |||| |||||||| ||||| ||||| ||| | ||||| || || || ||||||||||| |||||||||||||| || ||||| |||   |
-gttattatatata-actaacacccttcccattttctttcgctgaccaa------aaacattaaaaggt--atcttgctataatgtgg---tgtttgcagCAACGCCCTCAAGACAATGACCGCTATGTTAGGAATTGCCGCAATGGGAGGTCGCCGAAGGAGACCAGATGGTGGTTCCATGATGACAAAGTGTAAGAGG

upper sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G018447_T01 (Zea mays), 3'ss of exon 5
gaatatcagagaggcaatgagttttcttttttttcttttttctgttttattctttaaatggcaagggattcagcctgatgcattttgaacttgtatgcagCAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGATCCCCCAAGGAGACCAGGTGGTGGTTCCATGACGATAAAGTCTAATTTG
| |      ||    | | | |  ||  | | ||      || ||    |   |  |    ||   || ||   ||     |   || | |||| ||||||||||||| |  || |||||||| ||||| ||||||||| | || || || || || ||||||||||| ||||||||||||||||| |  || |||||  
gtagcgtttagtcttactaactactcgatctattaaaacctcagtgccctgactccataatca---gactctaactagctaacaatgcatttgt-tgcagCAACGTCCAGTGGACAATGACCGCTATGTCAGGAACTGCCGCAACGGGAGGTCGCCGAAGGAGACCAGATGGTGGTTCCATGACGACACGGTGTAATTGA

upper sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G018447_T02 (Zea mays), 3'ss of exon 5
gaatatcagagaggcaatgagttttcttttttttcttttttctgttttattctttaaatggcaagggattcagcctgatgcattttgaacttgtatgcagCAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGATCCCCCAAGGAGACCAGGTGGTGGTTCCATGACGATAAAGTCTAATTTG----------
| |      ||    | | | |  ||  | | ||      || ||    |   |  |    ||   || ||   ||     |   || | |||| ||||||||||||| |  || |||||||| ||||| ||||||||| | || || || || || ||||||||||| ||||||||||||||||| |  || |||||            
gtagcgtttagtcttactaactactcgatctattaaaacctcagtgccctgactccataatca---gactctaactagctaacaatgcatttgt-tgcagcaacgtccagTGGACAATGACCGCTATGTCAGGAACTGCCGCAACGGGAGGTCGCCGAAGGAGACCAGATGGTGGTTCCATGACGACACGGTGTAATTGAGCGCCTGTCA

upper sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 5
gaatatcagagaggcaatgagttttcttttttttcttttttctgttttattctttaaatggcaagggattcagcctgatgcattttgaacttgtatgcagCAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGATCCCCCAAGGAGACCAGGTGGTGGTTCCATGACGATAAAGTCTAATTTG
   |  ||   || ||      |   |  | | |         | |    ||  |  || || ||   |  | |  | |  | | |    |||| |||||||||| || |  || |||||||| ||||| ||||||||| | || || || || || |||||||| || ||||||||||||||||| |  || ||||   
--gtgacacttagtcatcatactacttgatctattcaaacctcggtgctctcactccatagccagac-tctaactagctagaatgta---ttgtttgcagCAACGCCCGGCGGACAATGACCGCTATGTTAGGAACTGCCGCAACGGGAGGTCGCCAAAGGAGACTAGATGGTGGTTCCATGACGACACGGTGTAATGAT

upper sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 5
gaatatcagagaggcaatgagttttcttttttttcttttttctgttttattctttaaatggcaagggattcagcctga-tgcattttgaacttgta-----tgcagCAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGATCCCCCAAGGAGACCAGGTGGTGGTTCCATGACGATAAAGTCTAATTTG
                          ||   | | |  | |   | |  || || ||  ||   |   | |   |||| |||| |    || ||||     |||||||||| || |  ||||| || || ||||| ||||||||  | ||||| || || || |||||||||| |||||||||||||||||| |  || | ||  |
-------------------------gttacatatttcctctacatatccttgttcaatcggtgggtcttgctttctgactgcaatacatacatgtaccgattgcagCAACGCCCAGCCGATAACGATCGCTATGTCAGGAACTGTCGCAATGGGAGGTCACCAAAGGAGACCACGTGGTGGTTCCATGACGACACTGTGTGATGGG

upper sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 5
gaatatcagagaggcaatgagttttcttttttttcttttttctgttttattctttaaatggcaagg----gattcagc--ctgatgcattttgaacttgtatgcagCAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGATCCCCCAAGGAGACCAGGTGGTGGTTCCATGACGATAAAGTCTAATTTG
  || | | |   ||    | |    ||  ||    |  || || ||||   | |  |    |||     ||||   |  ||||| |   |||  |||| |     ||  | ||    ||| | || |||||||||||||| ||| | ||||||||||| |||||||| ||  |||||||||| |||||||||||||| | | || 
--attttacattcgcgtcaaatgaatttccttcaagtaattttgatttaccatgtgcaatttaagtattcgattggactactgatactcgttg--cttgaacagGCCA--GACCACCTGATGACGATCGTTATGTGAGGAAATGCCGAAATGGCAGATCTCCCAAGGAAACACGGTGGTGGTTTCATGACGATAAAGTATGAGTTA

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|71861276|gb|DT010331.1|DT010331
EST:     GTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAG                         CAACGTCCTGAAGATAATGACCGTTATGTGGGGAACTGCAGGAATGGCAGA
genomic: GTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAGgttcttgtcc ... ttgtatgcagCAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGA
EST: gi|30297123|gb|CB973917.1|CB973917
EST:     GTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAG                         CAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGA
genomic: GTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAGgttcttgtcc ... ttgtatgcagCAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGA
EST: gi|37183496|gb|CF602850.1|CF602850
EST:     GTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAG                         CAACGTCCTGA
genomic: GTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAGgttcttgtcc ... ttgtatgcagCAACGTCCTGA
EST: gi|26262225|gb|CA813288.1|CA813288
EST:     GTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAG                         CAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGA
genomic: GTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAGgttcttgtcc ... ttgtatgcagCAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGA
EST: gi|30305051|gb|CB981845.1|CB981845
EST:     GTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAG                         CAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGA
genomic: GTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAGgttcttgtcc ... ttgtatgcagCAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattctttaaatggcaagggattcagcctgatgcattttgaacttgtatgcagCAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGATCCCCCAAGGAGACCAGGTGGTGGTTCCATGACGATAAAGTCTAATTTG
                           gcctgat  putative branch site (score: 4)
     tctttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatatcagagaggcaatgagttttcttttttttcttttttctgttttattctttaaatggcaagggattcagcctgatgcattttgaacttgtatgcagCAACGTCCTGAAGATAATGACCGTTATGTGAGGAACTGCAGGAATGGCAGATCCCCCAAGGAGACCAGGTGGTGGTTCCATGACGATAAAGTCTAATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - caatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aatggca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agcctga