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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaatttggcagtgccgcacagaacctatttgtttgcttttttagatggcatgaattattttctgcttatattgattatgttatcttttttccaagttagATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGATGGAATACTTGGTTTTGGACAAGCAAATTCGTCTATGCTTTCACAGCTA

Basic information

species Vitis vinifera
transcript Vv04s0023g00730.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AC155377.1_FGT002 (Zea mays), 3'ss of exon 3
-----tcaatttggcagtgccgcacagaacctatttgtttgcttttttagatggc--atgaattattttctgcttatattgattatgttatcttttttccaagttagATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGATGGAATACTTGGTTTTGGACAAGCAAATTCGTCTATGCTTTCACAGCTA
        |  ||     |   || || | | |   ||| || ||| |  || |    |||| | |    ||   |||   || ||    |||| |||||    ||| |||||   | | |||  ||||||  | |||   ||     |||| ||||||||||| ||||||||||| || |||||| |||| ||| | |||||||||
agtagaagagctgattaggaaaca-agcatcaaccggttagcatttgttaataggtgctgaagtgtcaaatggagatac--atgat----tcttctttcctttgtagGTGTGGTGCTCAGCAAGGTGGGGATTTGGGCAACTCAAACCAAGCTCTTGATGGAATTCTTGGTTTTGGTCAGGCAAATACGTCAATGTTATCACAGCTA

upper sequence: Vv04s0023g00730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G36120.1 (Glycine max), 3'ss of exon 1
tcaatttggcagtgccgcacagaacct-atttgtttgcttttttagatggcat----gaattattttctgcttatattgattatgttatcttttttccaagttagATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCA---CTTGATGGAATACTTGGTTTTGGACAAGCAAATTCGTCTATGCTTTCACAGCTA
    || || |     |   | |   | ||    || |      |  |  |||     | || || || | ||||||   ||  | ||   | || |  |   || |||||   |  ||||||||||    | || ||||||||||||| |   |||||||||||| |||||||||||||||||||||| ||| |||||||||||   
---tttaggtaaattggtttataggttgatagagttacagaaaaatgttacattttcaactttttctcggtttatatgtctttggataatctcttgctga--cagGTGTGGTGCTGTACAATCTGGGACATTGGGTTCATCTTCTGAAGAAGCCCTTGATGGAATAATTGGTTTTGGACAAGCAAATTCTTCTGTGCTTTCACAG---

upper sequence: Vv04s0023g00730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G47840.1 (Glycine max), 3'ss of exon 4
tcaatttggcagtgc-cgcacagaacctatttgtttgcttttttagatggcatgaattattttctgcttatattgattatgttatcttttttccaagttagATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCA---CTTGATGGAATACTTGGTTTTGGACAAGCAAATTCGTCTATGCTTTCACAGCTA
|  || |     |      | | | | |  | | ||| |     | ||| ||  | || | ||  | || |||   ||      | || | |    | ||| |||||   |||||||||||||    |  | ||| || ||||  ||   |||||||||||| |||||||||||||||||||||| ||| ||||||||||||  
tatatatatatatatatatatatagctttctaggttgataaag-acatgccacca-ttgtatttggtttttatgacttcctgagtattctcttgctgataggTGTGGTTCTAAACAATCTGGGACATTGAGTTCAACTACTGATACATCCCTTGATGGAATAATTGGTTTTGGACAAGCAAATTCTTCTGTGCTTTCACAGC--

upper sequence: Vv04s0023g00730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G31430.1 (Glycine max), 3'ss of exon 3
--tcaatttggcagtgccgcaca--gaacctatttgtttgcttttttagatggcatgaattattttctgcttatattgattatgttatcttttttccaagttagATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCA---CTTGATGGAATACTTGGTTTTGGACAAGCAAATTCGTCTATGCTTTCACAGCTA
  | |  ||   ||   || |    ||     ||  |      | ||| ||    | || |     | | ||||||   ||  | ||   | || |  |   || |||||   |  ||||||||||    |  | ||||||||||||| |   |||||||||||| |||||||||||||| ||||||| ||| |||||||||||   
atttaggttaataggttcgtaggttgatagagttaatgaaaaatcttacat--tttcaacttccccccgtttatatctctttggataatctcttgctga--cagGTGTGGTGCTGTACAATCTGGGACATTGAGTTCATCTTCTGAAGAAGCCCTTGATGGAATAATTGGTTTTGGACAATCAAATTCTTCTGTGCTTTCACAG---

upper sequence: Vv04s0023g00730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G38480.1 (Glycine max), 3'ss of exon 3
----tcaatt-tggcagtgccgcacagaacctatttgtttgcttttttagatggcatgaattattttctgcttatattgattatgttatcttttttccaagttagATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCA---CTTGATGGAATACTTGGTTTTGGACAAGCAAATTCGTCTATGCTTTCACAGCTA
    ||| || | ||  ||     || |    ||   |   |||   |||||    ||   |||||     |||| ||        |||  | || |  |  ||| |||||   |||||||||||||    |  | ||| |  ||||  ||   |||||||||||| |||||||||||||||||||||| ||| ||||||| |||   
gttttcacttgtcgccatgtgagccaaaggtcatggttacccttccctagatccattg---tatttggcttttatgttttcctgagtattctcttgctga--tagGTGTGGTTCTAAACAATCTGGGACATTGAGTTCAACCACTGATACATCCCTTGATGGAATAATTGGTTTTGGACAAGCAAATTCTTCTGTGCTTTCCCAG---

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|351027232|gb|FQ444481.1|FQ444481
EST:     ATTTCAGGAAACTTTCAAACCACACCAACTAATGGGACTGTAGTATTTGG                         ATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGA
genomic: ATTTCAGGAAACTTTCAAACCACACCAACTAATGGGACTGTAGTATTCGGgtgagtcata ... tccaagttagATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGA
EST: gi|349820946|gb|FQ408654.1|FQ408654
EST:     ATTTCAGGAAACTTTCAAACCACACCAACTAATGGGACTGTAGTATTTGG                         ATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGA
genomic: ATTTCAGGAAACTTTCAAACCACACCAACTAATGGGACTGTAGTATTCGGgtgagtcata ... tccaagttagATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGA
EST: gi|351042013|gb|FQ456223.1|FQ456223
EST:     ATTTCAGGAAACTTTCAAACCACACCAACTAATGGGACTGTAGTATTTGG                         ATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGA
genomic: ATTTCAGGAAACTTTCAAACCACACCAACTAATGGGACTGTAGTATTCGGgtgagtcata ... tccaagttagATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGA
EST: gi|351025817|gb|FQ427829.1|FQ427829
EST:     ATTTCAGGAAACTTTCAAACCACACCAACTAATGGGACTGTAGTATTTGG                         ATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGA
genomic: ATTTCAGGAAACTTTCAAACCACACCAACTAATGGGACTGTAGTATTCGGgtgagtcata ... tccaagttagATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGA
EST: gi|110393757|gb|EC959222.1|EC959222
EST:     ATTTCAGGAAACTTTCAAACCACACCAACTAATGGGACTGTAGTATTTGG                         ATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGA
genomic: ATTTCAGGAAACTTTCAAACCACACCAACTAATGGGACTGTAGTATTCGGgtgagtcata ... tccaagttagATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGA
EST: gi|349819195|gb|FQ412089.1|FQ412089
EST:     ATTTCAGGAAACTTTCAAACCACACCAACTAATGGGACTGTAGTATTTGG                         ATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGA
genomic: ATTTCAGGAAACTTTCAAACCACACCAACTAATGGGACTGTAGTATTCGGgtgagtcata ... tccaagttagATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggcatgaattattttctgcttatattgattatgttatcttttttccaagttagATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGATGGAATACTTGGTTTTGGACAAGCAAATTCGTCTATGCTTTCACAGCTA
                        tattgat  putative branch site (score: 3)
                                 tgttatcttttttcc  putative PPT
                     ttatattgattatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaatttggcagtgccgcacagaacctatttgtttgcttttttagatggcatgaattattttctgcttatattgattatgttatcttttttccaagttagATGTGGAAATAAACAATCTGGGGAGCTAGGCTCATCTTCTGAAGCACTTGATGGAATACTTGGTTTTGGACAAGCAAATTCGTCTATGCTTTCACAGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - ccgcaca
- - - - - - - - - - - - - - - tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - gcatgaa