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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cataagatttgactgtaatggatgtgaggagcttattacttattactcattaggacttcaattttcatagaggtttttctaagataaaattaatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATATTTTCGGCGCCTAATTATTGTGGGGAGTTTGATAATGCTGGTGCCATGA

Basic information

species Vitis vinifera
transcript Vv14s0036g00370.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g57450.2 (Oryza sativa), 3'ss of exon 2
cataagatttgactgtaatggatgtgaggagcttattacttattactcattaggacttcaattttcatagaggtttttctaagataaaattaatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATATTTTCGGCGCCTAATTATTGTGGGGAGTTTGATAATGCTGGTGCCATGA
          |      |||      |  | || |    ||  |  |  |||  |  | ||||    ||   ||| ||||    |      ||||  |||||||| || ||||| || || |||||||| ||||| ||||||||||| ||||| ||||| |||||||| ||||| || ||||||||||||||||||||||
----------gtgccccatgctcacaattacctgacctttttatttttcttaccaagtgaattgatttatcagttattcttgccttgttggaatt--cagGTTGTCGAAGATGGGTACGAGTTCTTTGCTAACCGCCAACTTGTAACAATATTCTCGGCCCCTAATTACTGTGGAGAATTTGATAATGCTGGTGCCATGA

upper sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G390076_T03 (Zea mays), 3'ss of exon 2
cataagatttgactgtaatggatgtgaggagcttattacttattactcattaggacttcaatt-ttcatagaggtttttctaagataaaattaatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATATTTTCGGCGCCTAATTATTGTGGGGAGTTTGATAATGCTGGTGCCATGA
     | | ||     || |  |||||    |||||| | |  ||      ||    ||||   || |   | ||||||      | |||||      |||||||| || ||||| ||||| || || || | ||| ||||| ||||| || ||||| || ||||| || ||||| || |||||||| |||||||||||||
--gttgctgtgctctgaaagagtgtgacctacttattcccttataa-----agtgtatcaaccgtttactcatgtttttgccctgttaaatt------cagGTTGTCGAAGATGGATATGAGTTTTTCGCTAGCCGCCAACTCGTAACAATGTTTTCAGCCCCTAACTACTGTGGAGAATTTGATAACGCTGGTGCCATGA

upper sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G41200.1 (Glycine max), 3'ss of exon 2
cataagatttgactgta-atggatgtgaggagcttattacttattactcattaggacttcaattttcatagaggtttttctaagataaaattaatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATATTTTCGGCGCCTAATTATTGTGGGGAGTTTGATAATGCTGGTGCCATGA
 |    |  || || ||  |  |  |  || | |  |        |   | || |   |  |   | | |  | ||||| |         ||  ||  |||||||| || ||||| || || |||||||| || || ||||||||||| |||||||| || ||||||||||||||||||||||| ||||||||||| ||||
tactgtacatgcctttatgtttagatcgggggatagtaggcctcgatcaactatgctattgaaagtaa-attgttttttgttttcggcctttttttaccagGTTGTGGAAGATGGATACGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAGTTTGACAATGCTGGTGCTATGA

upper sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G43800.1 (Glycine max), 3'ss of exon 2
----cataagatttgactgtaatggatgtgaggagcttattacttattactcattaggacttcaattttcatagaggtttttctaagataaaattaatttgc-agGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATATTTTCGGCGCCTAATTATTGTGGGGAGTTTGATAATGCTGGTGCCATGA
     |    |  || || ||      |   || |  || ||  | | | |||     |||    | || | |    ||| | |    |    ||  ||| | ||||||| || ||||| ||||| |||||||| || || ||||||||||| |||||||| || ||||||||||||||||| ||||| ||||||||||| ||||
tttgtaccgtacatgcctttatgtttagatcgggggatagtaggtgtcaatca-----actatgctattgaaaataatttattttttttggccttcttttaccagGTTGTGGAAGATGGATATGAGTTCTTTGCTAATCGACAACTTGTAACAATATTTTCAGCACCTAATTATTGTGGGGAATTTGACAATGCTGGTGCTATGA

upper sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G30970.1 (Glycine max), 3'ss of exon 2
--cataagatttgactgtaatggatgtgaggagcttatta-cttattactcattaggacttcaatt--ttcatagaggtttttctaagataaaattaatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATATTTTCGGCGCCTAATTATTGTGGGGAGTTTGATAATGCTGGTGCCATGA
      | | ||  |  |     |||  |    ||||||| ||||| |  | | |    ||   ||  | |||  |  ||    |||  |  | ||  |   ||||| || |||||||| || || |||||||| |||||||| |||||||| |||||||| || |||||||||||||| |||||||| |||||||| || ||||
gaggctaaacttctccctttcaaatgcca----cttattagcttatgatgcttcattctttacgttcctgcatttaaattggattaatgttgagttt-tgaccagGTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATATTTTCAGCACCTAATTATTGTGGAGAGTTTGACAATGCTGGCGCTATGA

upper sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G36510.1 (Glycine max), 3'ss of exon 2
----cataagatttgactgtaatggatgtgaggagcttattacttattactcattaggacttcaattttcatagaggtttttctaagataaaattaatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATATTTTCGGCGCCTAATTATTGTGGGGAGTTTGATAATGCTGGTGCCATGA
      ||   |    |  | ||  |  |  | ||  || ||  ||| | ||       ||   |  || | |  || ||    | | |   | |  |   ||||| || || ||||| ||||| |||||||| |||||||| |||||||| |||||||| || |||||||||||||| |||||||| |||||||| || ||||
attctttacattcctgcatttatttacatt-gaaggatagtatctatcaatccgctctgctattaaatttaaattggatta---atgttttgacttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATATTTTCAGCACCTAATTATTGTGGAGAGTTTGACAATGCTGGCGCTATGA

upper sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
-cataagatttgactgtaatggatgtgaggagcttattacttattactcattaggacttcaattttcatagaggtttttctaagataaaattaatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATATTTTCGGCGCCTAATTATTGTGGGGAGTTTGATAATGCTGGTGCCATGA
    |  | || ||| |  | | || |  | | |  |   |  |||  |  ||    |  |  | | |||     |    |  |    | |     ||||||| || |||||||||||||||||||| || || || || || || || || || || || || ||||| ||||| || ||||||||||| ||||||||||
attgattaatttacttttttcgttgggtagggatcgtagatggttaaaccgtaat-ttagagatctgataattaatgacttgcgtgggattccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA

upper sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S97_286V6.1 (Physcomitrella patens), 3'ss of exon 3
cataagatttgactgtaatggatgtgaggagcttattacttattactcattaggacttcaattttcatagag---gtttttctaagataaaattaatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATATTTTCGGCGCCTAATTATTGTGGGGAGTTTGATAATGCTGGTGCCATGA
      ||||||   |    |||| ||    | | |  |||    | |  ||    |  | | ||  || |    | |  |||  |    |  | |  | ||||| |||||||||||||||||||| || || || || ||||| || ||||| ||||| || || ||||||||||| || ||||||||||| ||||| ||||
-gacgaatttgaacct--ccgatgcgattgacatgtctcttccaccaccatacttttatattctttgtatactatgctgatctgtgtgggatgttacatacagGTAGTAGAGGATGGTTATGAATTTTTCGCTAAGCGCCAACTGGTTACCATTTTTTCTGCTCCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA

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|351051974|gb|FQ450665.1|FQ450665
EST:     CAGAGTTTCTTGAGAAGCATGATCTGGACCTTGTTTGTCGTGCTCATCAG                         GTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATA
genomic: CAGAGTTTCTTGAGAAGCATGATCTGGACCTTGTTTGTCGTGCTCATCAGgtatcaaact ... taatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATA
EST: gi|352798401|gb|FQ480426.1|FQ480426
EST:     CAGAGTTTCTTGAGAAGCATGATCTGGACCTTGTTTGTCGTGCTCATCAG                         GTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATA
genomic: CAGAGTTTCTTGAGAAGCATGATCTGGACCTTGTTTGTCGTGCTCATCAGgtatcaaact ... taatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATA
EST: gi|71880840|gb|DT029895.1|DT029895
EST:     CAGAGTTTCTTGAGAAGCATGATCTGGACCTTGTTTGTCGTGCTCATCAG                         GTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATA
genomic: CAGAGTTTCTTGAGAAGCATGATCTGGACCTTGTTTGTCGTGCTCATCAGgtatcaaact ... taatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATA
EST: gi|110426835|gb|EC993260.1|EC993260
EST:     CAGAGTTTCTTGAGAAGCATGATCTGGACCTTGTTTGTCGTGCTCATCAG                         GTTGTAGAGGATGGTTATGAATTCTTTGCAA
genomic: CAGAGTTTCTTGAGAAGCATGATCTGGACCTTGTTTGTCGTGCTCATCAGgtatcaaact ... taatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAA
EST: gi|351053762|gb|FQ441528.1|FQ441528
EST:     CAGAGTTTCTTGAGAAGCATGATCTGGACCTTGTTTGTCGTGCTCATCAG                         GTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATA
genomic: CAGAGTTTCTTGAGAAGCATGATCTGGACCTTGTTTGTCGTGCTCATCAGgtatcaaact ... taatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATA
EST: gi|71880054|gb|DT029109.1|DT029109
EST:     CAGAGTTTCTTGAGAAGCATGATCTGGACCTTGTTTGTCGTGCTCATCAG                         GTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAAC
genomic: CAGAGTTTCTTGAGAAGCATGATCTGGACCTTGTTTGTCGTGCTCATCAGgtatcaaact ... taatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcattaggacttcaattttcatagaggtttttctaagataaaattaatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATATTTTCGGCGCCTAATTATTGTGGGGAGTTTGATAATGCTGGTGCCATGA
                                          aattaat  putative branch site (score: 3)
                            tttttctaagataaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cataagatttgactgtaatggatgtgaggagcttattacttattactcattaggacttcaattttcatagaggtttttctaagataaaattaatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATATTTTCGGCGCCTAATTATTGTGGGGAGTTTGATAATGCTGGTGCCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - -tgactgt
- - - - - - - - - -ggatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gataaaa