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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtggcattctgacaaattatgcaaagatagccgtctcattgctcctcagtcccattctatgaatgattggacttacatcttcttgccttttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAACAGATCATAGAACACATAGACCTGTGGCTGTCCCAGTGCCAGGCCACAGG

Basic information

species Vitis vinifera
transcript Vv04s0023g03020.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA16G24270.1 (Glycine max), 3'ss of exon 12
tgtggcattctgacaaattatgcaaagatagccgtctcat-tgctcctcagtcccattctatgaatgattggactta-catcttcttgccttttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAACAGATCATAGAACACATAGACCTGTGGCTGTCCCAGTGCCAGGCCACAGG
  |   ||  | | |   ||   |     |  |   | || || ||     |     |   | ||  |     || |   |||  |||    ||   ||||||| |||  ||||||||   ||| |||||||||||||||||||| ||||||||||| | |||||| || ||| ||||||| ||  ||||||| |      |
--taaaataataatattatagcaagcagcaatcaaattatgtgatcaatgattgtgctgagtaaactaacattctgaatttctggttgtgaattttgttcagGTAATGAGAAGAACTGCTCCTCACCTGATGCAGTTCACAAAGTAAGGCAACAGATTACAGAACATATGGACTTGTGGCTATCTGAGTGCCAAGAAGGCAG

upper sequence: Vv04s0023g03020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA16G24290.1 (Glycine max), 3'ss of exon 11
----tgtggcattctgacaaattatgcaaagatagccgtctcattgctcctcagtcccattctatgaatgattggacttacatcttcttgccttttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAACAGATCATAGAACACATAGACCTGTGGCTGTCCCAGTGCCAGGCCACAGG
    |     ||||  | |||| |   |||   |  |    ||   ||    |  |    |  |   || |    || | |   ||  ||  ||||  |||||||| |||  || ||||| | |||||||||||||||||||||||| |||||| ||||   |||||| || ||| ||||| | ||  | |||   | ||||||
tccatacataattc--ataaatgacaaaaaaggaaacaaaaca--acttaaaatactgcctacacatatcaaccaacattctaatttgtggattttcttttcagGTAATGAGAAAAACTGCACCTCTCCTGATGCAGTTCACAAAGTAAGGCAAAAGATTTCAGAACATATGGACTTGTGGTTATCTGAATGCGTCGACACAGG

upper sequence: Vv04s0023g03020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G36190.1 (Arabidopsis thaliana), 3'ss of exon 11
-----------------tgtggcattctgacaaattatg-caaagatagccgtctcattgctcctcagtcccattctatgaatgattggacttacatcttcttgccttttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAACAGATCATAGAACACATAGACCTGTGGCTGTCCCAGTGCCAGGCCACAGG-
                 | |    ||| ||    | | | ||| || |  | ||  |       | |     ||   |||    |||    |    | || || |||     || ||||||||||| |||| || || || || ||||||||  ||||||| |||||||| || ||| ||||||| ||| ||||||| ||  |||| |  |  | ||| 
gtatattaccggcttcttctctgtttccgatgcctgaagtcaatgacaagcatcagaacaactgttaagaaaatatgatgtcccattcttttcctgttttttt-cctcccatttgcagGTGATGCCCAGAATTGCAGTTCACCAGATGCAGTGAACAAAGTGAGGCAACATATGATAAAACACATCGACTTGTGGCTCTCTGAGTGTCGTGG-ATAGGT

upper sequence: Vv04s0023g03020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT2G18080.1 (Arabidopsis thaliana), 3'ss of exon 11
tgtggcattctgacaaattatgcaaagatagccgtctcattgctcctcagtcccattctatgaatgattggacttacatcttcttgccttttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAACAGATCATAGAACACATAGACCTGTGGCTGTCCCAGTG---CCAGGCCACAGG
                           |||  | | |   ||    |    |  |  |||  ||  |   | |||  |    |     |||   |||||||| |  | || || || ||||  || |||   ||  ||||||| |||||||||||  |||||||||| ||| ||||||||||  ||||   |||  | |    
-------------------------gtataagcatttgtgtgtgttttgtccaaaaactaaaaaaaaagagtcttgaaataacaaat-tttcattttcagGTAAATCAAATAATTGCAGCTTACCCGATTATGTAAACAAAGTAAGGCAACAGATGGTAGAACACATTGACTTGTGGCTGTCTGAGTGTCGCCAATCTAT---

upper sequence: Vv04s0023g03020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G36195.2 (Arabidopsis thaliana), 3'ss of exon 11
-----------------tgtggcattctgacaaattatg-caaagatagccgtctcattgctcctcagtcccattctatgaatgattggacttacatcttcttgccttttggt-ttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAACAGATCATAGAACACATAGACCTGTGGCTGTCCCAGTGCC----AGGCCACAGG-----------------------------
                 | |  | ||| ||    | | | |||||| || | |   ||||   |      |  ||  |  |||  |     |  |  ||| || | || |  | |||||||||| ||||||| || || || |||||||||||  ||||||| |||||||| ||  |||| || || ||| ||||||| ||  |||| |    |||    |||                             
gtatattactggcctcttctctctttccgatccctgaagtcaaagacagac-tagtattggaacaa----ctgttaaaaaaatattatttttccctgcttttttcattctcatattcaggtgattccaagaattgcagttcacctgatgcagTGAACAAAGTGAGGCAACATATAGTAGATCATATGGACTTGTGGCTCTCTGAGTGTCGTGGAGGGATTAGGAGTTCCATGTAAAGAGTCACACGAAGTCA

upper sequence: Vv04s0023g03020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G36195.1 (Arabidopsis thaliana), 3'ss of exon 11
-----------------tgtggcattctgacaaattatg-caaagatagccgtctcattgctcctcagtcccattctatgaatgattggacttacatcttcttgccttttggt-ttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAACAGATCATAGAACACATAGACCTGTGGCTGTCCCAGTGCCAGGCCACAGG
                 | |  | ||| ||    | | | |||||| || | |   ||||   |      |  ||  |  |||  |     |  |  ||| || | || |  | |||||||||| ||||||| || || || |||||||||||  ||||||| |||||||| ||  |||| || || ||| ||||||| ||  |||| |  |       
gtatattactggcctcttctctctttccgatccctgaagtcaaagacagac-tagtattggaacaa----ctgttaaaaaaatattatttttccctgcttttttcattctcatattcagGTGATTCCAAGAATTGCAGTTCACCTGATGCAGTGAACAAAGTGAGGCAACATATAGTAGATCATATGGACTTGTGGCTCTCTGAGTGTCGTGGAGGGAT

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|45770356|gb|CN006208.1|CN006208
EST:     CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAG                         GTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
genomic: CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAGgtatgttaac ... ttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
EST: gi|22010957|gb|BQ795991.1|BQ795991
EST:     CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAG                         GTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
genomic: CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAGgtatgttaac ... ttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
EST: gi|22011128|gb|BQ796162.1|BQ796162
EST:     CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAG                         GTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
genomic: CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAGgtatgttaac ... ttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
EST: gi|30126977|gb|CB912316.1|CB912316
EST:     CCATGGAACTGACCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAG                         GTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
genomic: CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAGgtatgttaac ... ttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
EST: gi|33403028|gb|CF208655.1|CF208655
EST:     CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAG                         GTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
genomic: CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAGgtatgttaac ... ttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
EST: gi|46918655|gb|CN547984.1|CN547984
EST:     CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAG                         GTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
genomic: CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAGgtatgttaac ... ttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
EST: gi|110705809|gb|EE083079.1|EE083079
EST:     CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAG                         GTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
genomic: CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAGgtatgttaac ... ttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
EST: gi|110375447|gb|EC940435.1|EC940435
EST:     CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAG                         GTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
genomic: CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAGgtatgttaac ... ttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
EST: gi|71872346|gb|DT021401.1|DT021401
EST:     CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAG                         GTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
genomic: CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAGgtatgttaac ... ttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
EST: gi|22012959|gb|BQ797993.1|BQ797993
EST:     CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAG                         GTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC
genomic: CCATGGAACTGATCTGCGAGGATGTCCCCAATCTCCTTTAAGCCCTGAAGgtatgttaac ... ttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcagtcccattctatgaatgattggacttacatcttcttgccttttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAACAGATCATAGAACACATAGACCTGTGGCTGTCCCAGTGCCAGGCCACAGG
                         gacttac  putative branch site (score: 2)
                               catcttcttgcctttt  CT-rich tract
         attctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtggcattctgacaaattatgcaaagatagccgtctcattgctcctcagtcccattctatgaatgattggacttacatcttcttgccttttggtttcagGTGATGCCAAGAACTGTAGCTCTCCTGATGCAGTTCACAAAGTTAGGCAACAGATCATAGAACACATAGACCTGTGGCTGTCCCAGTGCCAGGCCACAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - gcattct
- - - - - - acaaatt
- - - - - - - - - - - -aaagata
- - - - - - - - - - - - - - - - - - - - - ctcctca
- - - - - - - - - - - - - - - - - - - - - - - - - -cccattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattgg