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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTCGTTGCATTGGTGGTGGAGGTGCAACTGATAATGCTGATAGTGACAGTGACCTGGAAGTGGTTGCAGATTTCTTTACTGTCAATCTACGATGTCCTgtaagtaatgctgtgtgtgtgaaaaacaaccatgcatcatctttatatattcaaatatgttgagcaatcaagctatgcactgtcccaaaggaaatatcac...

Basic information

species Vitis vinifera
transcript Vv06s0004g03180.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g03180.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os05g03430.3 (Oryza sativa), 5'ss of exon 8
TCGTCGTTGCATTGGTGGTGGAGGTGCAACTGATAATGCTGATAGTGACAGTGACCTGGAAGTGGTTGCAGATTTCTTTACTGTCAATCTACGATGTCCTgtaagtaatgctgtgtgtgtgaaaaacaaccatgcatcatctttatatattcaa-atatgttgagcaatcaagctatgcactgtcccaaaggaaatatcac-
||| || ||  | || |||||||   |  | || ||||||||||||||||||||  ||||||||||||| || |   |||| ||||| || || || ||||| |||  |  | |  || | |      |    || | |  | | | | || |   ||   |     ||  || |||   |  ||    |||  || | |  
TCGGCGCTGTCTCGGAGGTGGAGACACTGCAGAGAATGCTGATAGTGACAGTGATTTGGAAGTGGTTGCGGAGTCTGTTACAGTCAACCTTCGTTGCCCTgtgagtttttgt-tacgtataactgtttagttagcttaacatatgtttgttaagtgtacactacagtatgcagatatagtcattctatcaggttat-tgatg

upper sequence: Vv06s0004g03180.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G155123_T02 (Zea mays), 5'ss of exon 12
TCGTCGTTGCATTGGTGGTGGAGGTGCAACTGATAATGCTGATAGTGACAGTGACCTGGAAGTGGTTGCAGATTTCTTTACTGTCAATCTACGATGTCCTgtaagtaatgctgtgtgtgtgaaaaacaaccatgcatcatctttatatattcaaatatgttg-agca-atcaa-gctatgcactgtcccaaaggaaatatcac----
|||||| ||  |||| ||||||||||| || || |||||||||||||| || ||||||||||||||| | || |   |||| ||||| || || || |||||  ||  || | ||  | |    | |     |    ||| |||   | ||    | ||||  |  |  |||   | ||  ||  |    ||     | ||      
TCGTCGCTGTCTTGGAGGTGGAGGTGCTACGGACAATGCTGATAGTGATAGCGACCTGGAAGTGGTTACTGAATCTGTTACAGTCAACCTTCGTTGCCCTgtgcgtcttgttctgcatat----atcttttttatgacattttt---tgtttggctttgttacaatatgtcactaccatttacctttttcaattttttttcttcata

upper sequence: Vv06s0004g03180.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA11G15880.1 (Glycine max), 5'ss of exon 13
TCGTCGTTGCATTGGTGGTGGAGGTGCAACTGATAATGCTGATAGTGACAGTGACCTGGAAGTGGTTGCAGATTTCTTTACTGTCAATCTACGATGTCCTgtaagtaatgctgtgtgtgtgaaaaacaaccatgcatcatctttatatattcaaatatgttgagcaatcaagctatgcactgtcccaaaggaaatatcac
  | |||||  |||| || |||  |||| ||||| |||||||||||||||||||  ||||||||||| |||||   || ||| |||| || |||||||||||| |       |  |   | || |      ||| || || ||   | |||||   |        |||||   | |    | |      | |||| | | 
CTGCCGTTGTGTTGGGGGAGGAAATGCAGCTGATGATGCTGATAGTGACAGTGATTTGGAAGTGGTTTCAGATACTTTCACTATCAACCTTCGATGTCCTgtatg-------gctttcatcaatag-----atgaattattttagca-attcatgaagtcctcctaatcagttttttt--ttttttggtgaaaattttag

upper sequence: Vv06s0004g03180.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA12G07590.1 (Glycine max), 5'ss of exon 13
TCGTCGTTGCATTGGTGGTGGAGGTGCAACTGATAATGCTGATAGTGACAGTGACCTGGAAGTGGTTGCAGATTTCTTTACTGTCAATCTACGATGTCCTgtaagtaatgctgtgtgtgtgaaaaacaaccatgcatcatctttatatattcaaatatgttgagcaatcaagctatgcactgtcccaaaggaaatatcac
  | |||||  |||| ||||||  ||||  |||| |||||||||||||||||||  ||||||||||| |||||   || |||||||| || || ||||||||| |       |  |   | || |      ||| || || ||   | |||||   |     |  ||||| | | |  | | |      | |||| | | 
CTGCCGTTGTGTTGGGGGTGGAAATGCAGTTGATGATGCTGATAGTGACAGTGATTTGGAAGTGGTTTCAGATACTTTCACTGTCAACCTTCGTTGTCCTgtatg-------gctttcatcaatag-----atgaattattttagca-attcatgaagtcctactaatca-gttttttattttt--ggtgaaaattttag

upper sequence: Vv06s0004g03180.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA12G29270.1 (Glycine max), 5'ss of exon 9
TCGTCGTTGCATTGGTGGTGGAGGTGCAACTGATAATGCTGATAGTGACAGTGACCTGGAAGTGGTTGCAGATTTCTTTACTGTCAATCTACGATGTCCTgtaagtaatgctgtgtgtgtgaaaaaca-accatgcatcatctttatatattcaaatatgttgagcaatcaagctatgcactgtcccaaaggaaatatcac
  || ||||  |||| ||||||  ||||| |||||||||||||||||| |||||  ||||||| ||| |||||   ||||   ||||||| || || || |||||   |    ||| |  ||  |    |  |  |||    ||| ||||    | |   |   |  || ||  | |  ||  |    ||    |||    
CTGTTGTTGTGTTGGGGGTGGAAATGCAAATGATAATGCTGATAGTGATAGTGATTTGGAAGTTGTTTCAGATACTTTTAGCATCAATCTCCGTTGCCCAgtaag-gctttcatgtattggattattttagtactcatggagttt-tataaatcagttcctgaggtcat-aaattttatacgcttgtgaaatttatag---

upper sequence: Vv06s0004g03180.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA13G40320.1 (Glycine max), 5'ss of exon 9
TCGTCGTTGCATTGGTGGTGGAGGTGCAACTGATAATGCTGATAGTGACAGTGACCTGGAAGTGGTTGCAGATTTCTTTACTGTCAATCTACGATGTCCTgtaagtaatgctgtgtgtgtgaaaaacaaccatgcatcatctttatatattcaaatatgttgagcaatcaagctatgcactgtcccaaaggaaatatcac
  || ||||  |||| ||||||  ||||| |||||||||||||||||| |||||  ||||||| ||| ||||    ||||   ||||||| || || || |||||   | | |    | | |     |  |||| |     |||||| ||   | |   |  ||  || ||  | |  ||  |    ||    |||    
CTGTTGTTGTGTTGGGGGTGGAAATGCAAATGATAATGCTGATAGTGATAGTGATTTGGAAGTCGTTTCAGACACGTTTAGCATCAATCTCCGTTGCCCAgtaaggctttcagacacttttag---tactcatggagt---tttataaatc--agttcctgaagtcataaaattttatacacttgtgaaatttatag---

upper sequence: Vv06s0004g03180.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT5G60410.4 (Arabidopsis thaliana), 5'ss of exon 13
TCGTCGTTGCATTGGTGGTGGAGGTGCAACTGATAATGCTGATAGTGACAGTGACCTGGAAGTGGTTGCAGATTTCTTTACTGTCAATCTACGATGTCCTgtaagtaatgctgtgtgtgtgaaa-aacaaccatgc--atcatctttatatattcaaatatgttga--gcaatcaagctatgcactgtcccaaaggaaatatcac
 || || |||||||| |||||||||| |  ||||||||| || ||||| |||||| | ||||| ||||| ||||||||   ||||||||| || |||||||||||| |      |   ||     |      || |  ||| ||||  ||     |  | ||  ||  | | |     |||   || | |     |    || | 
CCGCCGATGCATTGGAGGTGGAGGTGGAGATGATAATGCCGACAGTGATAGTGACATTGAAGTTGTTGCTGATTTCTTCGGTGTCAATCTTCGGTGTCCTgtaagttactaatagctcgtagcccagtttttatacttatcctcttcctagggctatct-tgcagactgaattttttttattgtcttttctgtttgcgtcattag

upper sequence: Vv06s0004g03180.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: PP1S10_326V6.1 (Physcomitrella patens), 5'ss of exon 10
TCGTCGTTGCATTGG-TGGTGGAGGTGCAACTGATAATGCTGATAGTGACAGTGACCTGGAAGTGGTTGCAGATTTCTTTACTGTCAATCTACGATGTCCTgtaagtaatgctgtgtgtgtgaaaaacaaccatg-catcatctttatatattcaaatatgttgagcaatcaagctatgcact-gtcccaaagg--aaatatcac
 | ||  || |  || | ||  |||       |   ||| ||| |||||||||||  ||||||| || ||||||||  |||||||||| |||||||| || || ||    | | | | | ||  |  || |  |  |   |   |  | |  |  | |||  |   | || |   | | | || || |||   |   | | | | 
-CATCAATGGAGGGGGTAGTCAAGGGTTGGGGGCCGATGATGACAGTGACAGTGATTTGGAAGTTGTGGCAGATTTTATTACTGTCAACCTACGATGCCCGgtgagaggcgttttat-tatgtgatccatctctaacgctactctcgtttgctacattattctc--ccatgatagtgttctcttgttccatctgttgactttga-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGTCGTTGCATTGGTGGTGGAGGTGCAACTGATAATGCTGATAGTGACAGTGACCTGGAAGTGGTTGCAGATTTCTTTACTGTCAATCTACGATGTCCTgtaagtaatgctgtgtgtgtgaaaaacaaccatgcatcatctttatatattcaaatatgttgagcaatcaagctatgcactgtcccaaaggaaatatcac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaat