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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcaatcttcatacaatgcagttaaccttcctcctcctcctctctctctctctcccaaaaagaagaaaaactaatctggatccatttatttattttcagTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTAATGCTTT

Basic information

species Vitis vinifera
transcript Vv14s0068g01000.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os11g32490.1 (Oryza sativa), 3'ss of exon 5
---atgcaatcttcatacaatgcagttaaccttcctcctcctcctctctctctctctcccaaaaagaagaaaaactaatctggatccatttatt-tattttcagTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTAATGCTTT
   |    ||  | ||   || || || |   |     | |   | | ||  |    |  || |    | | |||||||    |  |||  |   |  || |||||  | || ||  | || ||||||||||| || || ||| |||||||||| |||||||||||||||||  | || || |||||  | |||  |    |  
gatacctcatgatgatggcatacatttgatgataaa--tgcatttttttcagttctacataatatattgcataactaattatca--catcaaccatgcttgcagTACATTATATTTCGGCGGGGCATTGGAATCGACCGGACAACTGATTACTTCTTCATGGAGAAAGTGGATGTAATAATATCACGGGTGTGGAGATCATTGC

upper sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G011136_T03 (Zea mays), 3'ss of exon 5
----------------------------------------------------------atg-caatcttcatacaatgcagttaaccttcctcctcctcctctctctctctctcccaaaaagaagaaaaactaatctggatccatttatttattttcagTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTAATGCTTT
                                                          |||   |      ||||||    ||     |  || || |||||| | | |   || ||         || ||  ||         |  |  | || | ||||| | |||||  | || ||||||||||| ||||||||| |||| ||||||||||| |||||||| ||  | || || || ||    |||       |  
gtattattcgttcatgcaacttttcttttcatcctgatgatacttatgtttatgagggatgattagaaatctacaatagcattggatgttttcatcatcctctgttttt---tctcatggtttcctaagacacattcttcattgtccacatcttgt-agTATATCATCTTTCGTCGGGGCATTGGAATTGATCGAACAACTGACTACTTTTTCATTGAGAAAGTAGATGTAATGATATCCCGAGCTTGGAGGTCATTGC

upper sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G527387_T01 (Zea mays), 3'ss of exon 5
atgcaatcttcatacaatgcagttaaccttcctcctcctcctctctctctctctcccaaaaagaagaaaaactaatctggatccatttatttattttcagTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTAATGCTTT
|     | | | |    |    ||  | |  |   |  |  |  |||  | | |    | |      |  | | || |     ||   |  | ||| |||||| | |||||| | || |||||||| || ||||| ||| |||| ||||| |||||||||||||||||  | ||||| || ||   ||||       |  
aatttgtttgcttgttctaattttgtcttcacaagtattatttcctcggtattttattatagttttcagcagttatttcacgtcaccaacatctttacagTATATTATCTTCCGTCGGGGCATTGGGATTGATCGGACAACTGACTACTTCTTCATGGAGAAAGTGGATGTCATCATATCCCGAGCATGGAGGTCATTGC

upper sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G052279_T01 (Zea mays), 3'ss of exon 2
atgcaatcttcatacaatgcagttaaccttcctcctcctcctctctctctctctcccaaaaagaagaaaaactaatctggatccatttatttattttcagTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTAATGCTTT-------------
                 |   |  |     ||    | |  |  | |||          |   |  |   | | | |||    ||| | ||  ||  || ||||| || ||  |  | ||||||||| | || || ||     | |  || ||||||||||||||||||||||||||  | |||  ||||  || | |               
-----------------tagtggcattgcgccgttacttagtacccctcagatgttttgattaactacttatttagctgacatcatcttttatttgccaatatgttatatttcgtagGGGCATTGGATTGGACCGCACTAGCAACTTTTTCTTCATGGAGAAAGTGGACATGATCATAGCTCGTGCATGGCGAAGGTTCCTTGAGAAGACAAG

upper sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G161168_T02 (Zea mays), 3'ss of exon 5
-atgcaatcttcata-caatgcagttaaccttcctcctcctcctctctctctctctcccaaaaaga-agaaaaactaatctggatccatttatttattttcagTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTAATGCTTT
  | |  |  |  |  || ||||      |||  | | ||||   | | |   |   | |   |   ||   |  |||||    |  ||||    ||| ||||||||| || ||  |  | ||||||||| | || || ||     | |  || ||||||||||||||||||||||||||  | |||  ||||  || | |  
tcttctcttctggtggcattgcaccgttacttagtacccctcagatgttttgattaactacttatttagctgacataatcc---tttatttgccaattgtcagTATGTTATATTTCGTAGGGGCATTGGATTGGACCGCACTAGCAACTTTTTCTTCATGGAGAAAGTGGACATGATCATAGCTCGTGCATGGCGAAGGTTCC

upper sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G26360.1 (Glycine max), 3'ss of exon 5
atgcaatcttcatacaatgcagttaaccttcctcctcctcctctctctctctc--tcccaaaaag---aagaaaaactaatctggatccatttatttattttcagTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTA-ATGCTTT
 ||  | || |||| | || ||  |||  ||    |  |  | | |    |||  |   |    |     |||     || ||  |  |||    ||||||| ||||| | || ||  | || ||||||||||| ||||||||| ||||||||||| |||||||||||||||||||| ||||  ||||| | |||| | ||   | 
-tg-gacctgcatagattg-agacaacaatcagaattatttttttttaaactcgattttagtctgttcgtgaagtggcaagcta-acacatcctgttatttt-agTATATTATTTTTCGGCGTGGCATTGGAATTGATCGAACAACTGATTACTTTGTCATGGAGAAAGTGGACATGCTCATAGCACGTTTTTGGTCATATATAT-

upper sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 5
-----atgcaatcttcatacaatgcagttaaccttcctcctcctcctc--tctctctctctcccaaaaagaagaaaaactaatctggatccatttatttattttcagTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTAATGCTTT
      ||   | ||| |  |    | |   | |   |  |  |  ||     ||   |||       | | | |||||||||        | | || |  ||| ||||||| |||||  |||| ||||||||||| ||||||||| |||| |||||| | |||||||||||||||||| | |||  |||  | |||  |   || |
gattgttgttttgttccttgagcttattctgcttgtttttttttaatcagcagcttattctgtttgtgaaatggaaaactaata-------aatcatattattttagTATGTTATCTTTCGACGTGGCATTGGAATTGATCGAACAACTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT

upper sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G07370.1 (Glycine max), 3'ss of exon 5
atgcaatcttcatacaatgcagt--taaccttcctcctcctcctctctctctctctcccaaaaag---aagaaaaactaatctggatccatttatttattttcagTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTA-ATGCTTT
     | || |||| | ||       || |    |  |  |  | |    |||  |   ||   |     |||     |||||  |  |||    ||||||| ||||| | || ||  | || ||||||||||| ||||||||  | ||||||||| |||||||||||||||||||| ||||  ||||| | |||| | ||   | 
---ggacctgcatagattgggacaacaatcacaatgttttttttttaaaactcgattttaatctgtttgtgaagtggcaatcta-acacatcctgttatttt-agTATATTATTTTTCGGCGTGGCATTGGAATTGATCGAACGACCGATTACTTTGTCATGGAGAAAGTGGACATGCTCATAGCACGTTTTTGGTCATATATGT-

upper sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G05180.1 (Glycine max), 3'ss of exon 5
------atgcaa-tcttcatacaatgcagttaaccttcctcctcctcctctctctctctctcccaaaaagaagaaaaactaatctggatccatttatttattttcagTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTAATGCTTT
       ||||| |    |  |   ||     |   |  |  |  ||||    ||   | |       | | | ||| |||||        | | || |  ||| ||||||| |||||  | || ||||||||||| ||||||||| |||| |||||| | |||||||||||||||||| | |||  |||  | |||  |   || |
ctgaacctgcaaatacaaacgccgagctaaagattgtagttttgttccttgagcttattatgtttgtgaaatggaaagctaata-------aatcatattattttagTATGTTATCTTTCGGCGTGGCATTGGAATTGATCGAACAGCTGACTACTTTGTGATGGAGAAAGTGGACATGCTTATTGGACGCTTTTGGGCATATCTAT

upper sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G19340.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------atgcaatcttcatacaatgcagttaaccttcctcctcctcctctctctctctctcccaaaaagaagaaaaactaatctggatc-catttatttattttc------agTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTAATGCTTT
           |     |||  | |  | ||| || |   |  |  |   |      || |||        | | ||  | |    |    ||   |||||    |||||      ||||||| ||||||||||| || |||||| | |||  |||  | ||||| ||||||||||||||| ||||  |||||||||||||| | ||||   | ||  
gtacagtttttagtttgtctgtagatga-gcatttcaagattatagtttcctaaagactttcttgatggtcatgtagcgacatgtgttgatatagtatttaccctttttcttatatagTATGTCATCTTCAGACGTGGTATTGGATTGGATAAAACCACAGATTATTTTTTCATGGAGAAATTGGATGTGATCATTTCACGTTTTTGGTCCTTTCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctctctcccaaaaagaagaaaaactaatctggatccatttatttattttcagTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTAATGCTTT
                        aactaat  putative branch site (score: 2)
                                            tttattttc  putative PPT
                                   atccatttatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcaatcttcatacaatgcagttaaccttcctcctcctcctctctctctctctcccaaaaagaagaaaaactaatctggatccatttatttattttcagTATGTAATCTTCAGACGCGGCATTGGAATAGATCGAACATCTGATTACTTTTTCATGGAGAAAGTGGACATGATCATTTCACGTCTATGGTTAATGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
-tgcaatc
- - - - - - - caatgca
- - - - - - - - - - - - - ccttcct
- - - - - - - - - - - - - - - cctcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatcca