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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtagtactacattataattatttttttttgatagggtagtaatacgttataattaccttcaccagactaatcttttctcgtactggattaaatttctagAATCCAGTTGAGTTGGATGGATTAAGAAAGGCACACATTCGGGATGGTGCAGCTGTTGTGCAATATCTTGTTTGGCTGGATAAGCAG

Basic information

species Vitis vinifera
transcript Vv04s0023g01300.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g01300.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G169095_T01 (Zea mays), 3'ss of exon 6
-----agtagtactacattataattatttttttttgatagggtagtaatacgttataattaccttcaccagactaatcttttctcgtactggattaaatttctagAATCCAGTTGAGTTGGATGGATTAAGAAAGGCACACATTCGGGATGGTGCAGCTGTTGTGCAATATCTTGTTTGGCTGGATAAGCAG
        | |  |     | |  || ||   | ||| |  |||    |  |   | | || ||    |     |||  |||||  |  || |  ||   | ||||| ||    ||  |||||||||| || ||||| || ||||| |||||||| |||||||| || || |||| |||||||||||| |||
cctttttcatttgtgatccacagataattagctatgaaactgtaactcttggaatttagtatctgtttcc--tcaat--tttcttat-ttgcaacaatggtgtagAACCCCACAGAACTGGATGGATTGAGGAAGGCGCATATTCGAGATGGTGCCGCTGTTGTACAGTACCTTGCTTGGCTGGATAATCAG

upper sequence: Vv04s0023g01300.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G38410.4 (Glycine max), 3'ss of exon 6
agtagtactacatta---taattatttttttttgatagggtagtaatacgttataattacctt-caccagactaatcttttctcgtactggattaaat--ttctagAATCCAGTTGAGTTGGATGGATTAAGAAAGGCACACATTCGGGATGGTGCAGCTGTTGTGCAATATCTTGTTTGGCTGGATAAGCAG
 || |||     |||   |||| |    || |  |||   | | | |       | || | |  ||  | ||| | ||| | |  |  |   |  |||  || |||||  | || ||||||||||| |||| ||||||||| ||||||||||||||||| ||||||||||||||||| |||||||||||| ||
-gttgtatgcagttaatttaataaaaaattatatatatctttggatttttccccattttcatcacatgaaacttagcttatttttttataactccaataattttagAACTCGGTGGAGTTGGATGGGTTAAAAAAGGCACATATTCGGGATGGTGCAGCAGTTGTGCAATATCTTGTCTGGCTGGATAAGAAG

upper sequence: Vv04s0023g01300.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G06900.1 (Glycine max), 3'ss of exon 6
------------------agtagtac-tacat-tataattatttttttttgatagggtagtaatacgttataatt-------accttcacc-----agactaatctt-ttctcgtactggattaa-atttctagAATCCAGTTGAGTTGGATGGATTAAGAAAGGCACACATTCGGGATGGTGCAGCTGTTGTGCAATATCTTGTTTGGCTGGATAAGCAG
                  | || ||  || || ||||  ||| | | | |       ||   |||  ||  ||||       |  |||| |     | ||| | ||| || |  || |     || | || |||||  | || || ||||| || ||||  |||||||| ||||||||||||||||| || ||||| |||||||| |||||||||||| ||
gttgtatgcagttaatttaataatatatatatatatatatatatatatatatatatatatatatatctttgaattttttcccattttcatctcttgaaacttagcttatttttttattactccaatacttttagAACTCGGTGGAATTGGACGGGTTAAAGAAGGCACATATTCGGGATGGTGCAGCGGTCGTGCAGTATCTTGTCTGGCTGGATAAGAAG

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|110726497|gb|EE102329.1|EE102329
EST:     ATAAGGTTGTTTTGCAGCAATCACCTTTGGCCATTGCAAAAGCTATCAAG                         AATCCAGTTGAGTTGGATGGATTAAGAAAGGCACACATTCGGGATGGTGCA
genomic: ATAAGGTTGTTTTGCAGCAATCACCTTTGGCCATTGCAAAAGCTATCAAGgtagcatatc ... aaatttctagAATCCAGTTGAGTTGGATGGATTAAGAAAGGCACACATTCGGGATGGTGCA
EST: gi|110694334|gb|EE071348.1|EE071348
EST:     CAAAAGCTATCAAG                         AATCCAGTTGAGTTGGATGGATTAAGAAAGGCACACA-TCAGGGATGGTGC
genomic: CAAAAGCTATCAAGgtagcatatc ... aaatttctagAATCCAGTTGAGTTGGATGGATTAAGAAAGGCACACATTC-GGGATGGTGC
EST: gi|161706319|gb|FC055464.1|FC055464
EST:     ATAAGGTTGTTTTGCAGCAATCACCTTTGGCCATTGCAAAAGCTATCAAG                         AATCCAGTTGAGTTGGATGGATTAAGAAAGGCACACAT-CAGGGATGGTGC
genomic: ATAAGGTTGTTTTGCAGCAATCACCTTTGGCCATTGCAAAAGCTATCAAGgtagcatatc ... aaatttctagAATCCAGTTGAGTTGGATGGATTAAGAAAGGCACACATTC-GGGATGGTGC
EST: gi|110712732|gb|EE088034.1|EE088034
EST:     ATAAGGTTGTTTTGCAGCAATCACCTTTGGCCATTGCAAAAGCTATCAAG                         AATCCAGTTGAGTTGGATGGATTAAGAAAGGCACACATTCGGGATGGTGCA
genomic: ATAAGGTTGTTTTGCAGCAATCACCTTTGGCCATTGCAAAAGCTATCAAGgtagcatatc ... aaatttctagAATCCAGTTGAGTTGGATGGATTAAGAAAGGCACACATTCGGGATGGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttataattaccttcaccagactaatcttttctcgtactggattaaatttctagAATCCAGTTGAGTTGGATGGATTAAGAAAGGCACACATTCGGGATGGTGCAGCTGTTGTGCAATATCTTGTTTGGCTGGATAAGCAG
                    gactaat  putative branch site (score: 2)
                                                tttct  putative PPT
                                          attaaatttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtagtactacattataattatttttttttgatagggtagtaatacgttataattaccttcaccagactaatcttttctcgtactggattaaatttctagAATCCAGTTGAGTTGGATGGATTAAGAAAGGCACACATTCGGGATGGTGCAGCTGTTGTGCAATATCTTGTTTGGCTGGATAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttcac