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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgattggtgtttgagagtatcgatgttgaataacatacaaactttcattaaaaaaatatgaattacacgtaaccttctgaaatttgtcttctgtttcagTGGCATACAAATTGTCGAAAAGGAAGAGCGATGACACTTTTAAATTGCTTCATACCATTCTCTTTGGAAGGAGAGGAAAG

Basic information

species Vitis vinifera
transcript Vv19s0015g00430.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g00430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G44130.1 (Glycine max), 3'ss of exon 3
---ttgattggtgtttgaga-gtatcgatgttgaataacatacaaact-ttcattaaaaaaatatgaattacacgtaaccttctgaaatttgtcttctgtttcagTGGCATACAAATTGTCGAAAAGGAAGAGCGATGACACTTTTAAATTGCTTCATACCATTCTCTTTGGAAGGAGAGGAAAG
    | ||     ||    | ||   || ||       |||      | ||| ||| || |     || |  | |   | |  || |     | ||||| || ||||||||  || || || | ||||||||  || || || || |||||||| ||||| ||||||||||||||||||||||||
gttcttatatacattcattatgttgtgaagtgtggatgcatgtttcttcttctttagaacagctaaaactttatgactcttgttgca-----ttttctgctttagTGGCATTTAAGTTATCTAGAAGGAAGACTGAAGATACGTTCAAATTGCTCCATACAATTCTCTTTGGAAGGAGAGGAAAG

upper sequence: Vv19s0015g00430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G08640.1 (Glycine max), 3'ss of exon 3
ttgattggtgtttgagagtatcgatgttgaataacatacaaactttcattaaaaaaatatgaattacacgtaaccttctgaaatttg--tcttctgtttcagTGGCATACAAATTGTCGAAAAGGAAGAGCGATGACACTTTTAAATTGCTTCATACCATTCTCTTTGGAAGGAGAGGAAAG-
 | ||     ||    |   ||  | |   || |  |   ||      ||       |    |  |     ||| |  |||  ||||  | ||||| || ||||||||  ||||| || | ||||||||  ||||| || || |||||||| ||||| |||||||||||||||||||| ||| 
-ttatatacattgattacattcattatgttatgaagtgtgaatgcatgtttcttc--ttcagaacagctaaaacttaatgacttttgcattttctgctttagtGGCATTTAAATTATCTAGAAGGAAGACTGATGATACCTTCAAATTGCTCCATACAATTCTCTTTGGAAGGAGAGGGAAGG

upper sequence: Vv19s0015g00430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G44120.2 (Glycine max), 3'ss of exon 3
ttgattggtgtttgagagtatcgatgttgaataacatacaaactttcattaaaaaaatatgaattacacgtaaccttctgaaatttg--tcttctgtttcagTGGCATACAAATTGTCGAAAAGGAAGAGCGATGACACTTTTAAATTGCTTCATACCATTCTCTTTGGAAGGAGAGGAAAG
 | ||     ||    |   ||| | |   || | | |||||   || ||        | |||  ||    ||| |  |||   |||  | ||||| || ||||||||  || || || | ||||||||  ||||| || || |||||||| ||||| |||||||||||||||||||| |||
cttatatacattgattacattcgttatgctatgaaacacaaatgctcgtttgttcttca-gaacaac-taaaacttaatgactcttgcattttctgctttagTGGCATTTAAGTTATCTAGAAGGAAGACTGATGATACCTTCAAATTGCTCCATACAATTCTCTTTGGAAGGAGAGGGAAG

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|26261738|gb|CA812801.1|CA812801
EST:     GGGACTGCACTGAAAGATATACTTAATG                         TGGCATACAAATTGTCGAAAAGGAAGAGTGATGACACTTTTAAATTGCTTC
genomic: GGGACTGCACTGAAAGATATACCTAATGgtatggttct ... tctgtttcagTGGCATACAAATTGTCGAAAAGGAAGAGCGATGACACTTTTAAATTGCTTC
EST: gi|351031373|gb|FQ445398.1|FQ445398
EST:     GGTCGTGGGACTGCACTGAAAGATATACCTAATG                         TGGCATACAAATTGTCGAAAAGGAAGAGCGATGACACTTTTAAATTGCTTC
genomic: GGTCGTGGGACTGCACTGAAAGATATACCTAATGgtatggttct ... tctgtttcagTGGCATACAAATTGTCGAAAAGGAAGAGCGATGACACTTTTAAATTGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattaaaaaaatatgaattacacgtaaccttctgaaatttgtcttctgtttcagTGGCATACAAATTGTCGAAAAGGAAGAGCGATGACACTTTTAAATTGCTTCATACCATTCTCTTTGGAAGGAGAGGAAAG
                      acgtaac  putative branch site (score: 3)
                                      tttgtcttctgtttc  putative PPT
     aaaaaaatatgaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgattggtgtttgagagtatcgatgttgaataacatacaaactttcattaaaaaaatatgaattacacgtaaccttctgaaatttgtcttctgtttcagTGGCATACAAATTGTCGAAAAGGAAGAGCGATGACACTTTTAAATTGCTTCATACCATTCTCTTTGGAAGGAGAGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
-tgattgg
- - - - - - - - - - - - - - gaataac
- - - - - - - - - - - - - - - - - -atacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctga