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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attggtatccatatagataagtttattatcttcttccttttggtctcaaataagattttattccttttttgcttacaatggtgcataacactgcttgcagGTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGATGAGAAGTGCATGTGGAAAAATCTCTCTGTGGAGGAAAGCCAAAGACTT

Basic information

species Vitis vinifera
transcript Vv12s0028g03370.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G002687_T01 (Zea mays), 3'ss of exon 2
--attggtatccatatagataagtttattatcttcttccttttggtctcaaataagattttattccttttttgcttacaatggtgcataacactgcttgcagGTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGATGAGAAGTGCATGTGGAAAAATCTCTCTGTGGAGGAAAGCCAAAGACTT
   |    | |  |  || |  ||||  || |||   | |     ||| |  |  | | || |   |  | |      ||   | || ||   | ||| ||| |||||||| || || |||||||| || || ||||||||||| ||||| |||||||||| | ||||||||||  |  || |  |||||||  |||| |||
atctacacaacactcaagttttgtttgataacttgcacgtcgctttcttagttctggtcttgtaagtgatgtttcattaactat-cagaatctttctt-cagATACTTGCAGGAGGCTTTTAAGGTGCCCCTAGTTATACAACTGACTGACGATGAGAAGTACTTGTGGAAAAACTTGACTATTCAGGAAAGTAAAAGGCTT

upper sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G11390.1 (Glycine max), 3'ss of exon 2
attggtatccatatagataagtttattatcttcttccttttggtctcaaataagattttattccttttt-tgcttacaatggtgcataacactgcttgcagGTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGATGAGAAGTGCATGTGGAAAAATCTCTCTGTGGAGGAAAGCCAAAGACTT
 || |   |  ||    |   |      |     |     ||   || ||     | | ||| ||     || ||      |||    | |  |  || ||||| ||||||||||  |||||||||||||| |||||||| || |||||||||||||||| | | |||||||||||  || | || ||  ||  |||||||
-ttagatgctttagttttggatcaggcttgaaaatgaaggtgagttctaaatcattgtgattgctgggaatgtttgttgatgtggtggaaatggtgtgtagGTATTTGCAAGATGTGTTTAAGGTTCCTCTGGTTATACAGCTCACTGATGATGAGAAGTTCTTCTGGAAAAATCTTACTATAGAAGAGTGCAGAAGACTT

upper sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 2
---attggtatccatatagat-aagtttattatcttcttccttttggtctcaaataagattttattccttttt-tgcttacaatggtgcataacactgcttgcagGTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGATGAGAAGTGCATGTGGAAAAATCTCTCTGTGGAGGAAAGCCAAAGACTT
     || | |   | | ||| ||| ||   |     |     |  ||   ||||  | | | ||| ||     || ||      |||    | |  |  || ||||| ||||||||||  |||||||||||| | |||||||| || |||||||||||||||| | | ||||||||||| ||| | || ||  ||| |||||||
ttagatgcttttgttttggatcaagcttgaaaa----tgaaggtgagttctaaatt-gttgtgattgctggggatgtttgttgatgtggtggaaatggtgtgtagGTATTTGCAAGATGTGTTTAAGGTTCCTTTGGTTATACAGCTCACTGATGATGAGAAGTTCTTCTGGAAAAATCTTTCTATAGACGAGTGCCGAAGACTT

upper sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 3
attggtatccatatagataagtttatt-atcttcttccttttggtctcaaataagattttattccttttttgcttacaatggtgcataacactgcttgcagGTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGATGAGAAGTGCATGTGGAAAAATCTCTCTGTGGAGGAAAGCCAAAGACTT
             ||  | || |  |  | ||  |    | |   |     || |  |||  |   || |   |     |  | | | | |  | |||||| ||||||||||| || || |||||||| ||||||||||| || || |||||||| ||  | || ||||| ||  | || ||||||||||| |||||||||
------------gtaagtgagatcctggagctagtattgtcttaccatgtttacggatttggtagattgtgcttgctctttatacttgaaatggtttgcagATACTTGCAAGAAGCTTTCAAGGTTCCCCTTGTTATACAGCTCACGGATGATGAAAAAAGTATATGGAAGAACTTATCGGTGGAGGAAAGTCAAAGACTT

upper sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ23832 (Selaginella moellendorffii), 3'ss of exon 2
attggtatccatatagataagtttattatcttcttccttttggtctcaaataagattttattccttttttgcttacaatggtgcataacactgcttgcagGTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGATGAGAAGTGCATGTGGAAAAATCTCTCTGTGGAGGAAAGCCAAAGACTT
                                                 |   |     |||  ||||||  || ||  | |        || || | || || ||||| ||||| || |||||||| ||||| ||||| || || || ||||||||||| |||||||| |||||    |||||||| | | | ||||||
-----------------------------------------------gtaggtgtcggcattttttttttttttccatcgct------tgcttct-gtagATATTTGCAGGATGCTTTCAAGGTTCCGCTTGTCATACAGCTCACAGACGATGAGAAGTGTATGTGGAAGAATCTGAGCGTGGAGGAGACCAAGAGACTT

upper sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ24416 (Selaginella moellendorffii), 3'ss of exon 2
attggtatccatatagataagtttattatcttcttccttttggtctcaaataagattttattccttttttgcttacaatggtgcataacactgct-tgcagGTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGATGAGAAGTGCATGTGGAAAAATCTCTCTGTGGAGGAAAGCCAAAGACTT
                                                  || |  |       |||| |  ||    |  | |||  |  |  | || || || ||||| ||||| || |||||||| ||||| ||||| || || || ||||||||||| |||||||| |||||    |||||||| | | | ||||||
-------------------------------------------------gtaggtgtcggcattttttattttt----ttttccatcgctttcttctgtagATATTTGCAGGATGCTTTCAAGGTTCCGCTTGTCATACAGCTCACAGACGATGAGAAGTGTATGTGGAAGAATCTGAGCGTGGAGGAGACCAAGAGACTT

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|161717337|gb|FC065270.1|FC065270
EST:     TCTTCTGAGGCTTTGCATTTGGGGCATTTGGTTCCTTTCATGTTCACCAA                         GTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGA
genomic: TCTTCTGAGGCTTTGCATTTGGGGCATTTGGTTCCTTTCATGTTCACCAAgtatgtgttt ... ctgcttgcagGTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGA
EST: gi|110709548|gb|EE085106.1|EE085106
EST:     TCTTCTGAGGCTTTGCATTTGGGGCATTTGGTTCCTTTCATGTTCACCAA                         GTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGA
genomic: TCTTCTGAGGCTTTGCATTTGGGGCATTTGGTTCCTTTCATGTTCACCAAgtatgtgttt ... ctgcttgcagGTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGA
EST: gi|71855398|gb|DT004453.1|DT004453
EST:     TCTTCTGAGGCTTTGCATTTGGGGCATTTGGTTCCTTTCATGTTCACCAA                         GTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGA
genomic: TCTTCTGAGGCTTTGCATTTGGGGCATTTGGTTCCTTTCATGTTCACCAAgtatgtgttt ... ctgcttgcagGTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGA
EST: gi|294967200|gb|GW840075.1|GW840075
EST:     TCTTCTGAGGCTTTGCGTTTGGGGCATTTGGTTCCTTTCATGTTCACCAA                         GTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTCATACAACTTACTGATGA
genomic: TCTTCTGAGGCTTTGCATTTGGGGCATTTGGTTCCTTTCATGTTCACCAAgtatgtgttt ... ctgcttgcagGTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGA
EST: gi|110710091|gb|EE086125.1|EE086125
EST:     TCTTCTGAGGCTTTGCATTTGGGGCATTTGGTTCCTTTCATGTTCACCAA                         GTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGA
genomic: TCTTCTGAGGCTTTGCATTTGGGGCATTTGGTTCCTTTCATGTTCACCAAgtatgtgttt ... ctgcttgcagGTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGA
EST: gi|71860975|gb|DT010030.1|DT010030
EST:     TCTTCTGAGGCTTTGCATTTGGGGCATTTGGTTCCTTTCATGTTCACCAA                         GTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGA
genomic: TCTTCTGAGGCTTTGCATTTGGGGCATTTGGTTCCTTTCATGTTCACCAAgtatgtgttt ... ctgcttgcagGTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaataagattttattccttttttgcttacaatggtgcataacactgcttgcagGTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGATGAGAAGTGCATGTGGAAAAATCTCTCTGTGGAGGAAAGCCAAAGACTT
         attttattcctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attggtatccatatagataagtttattatcttcttccttttggtctcaaataagattttattccttttttgcttacaatggtgcataacactgcttgcagGTACTTGCAAGATGCCTTTAAGGTTCCTCTTGTTATACAACTTACTGATGATGAGAAGTGCATGTGGAAAAATCTCTCTGTGGAGGAAAGCCAAAGACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - gtatcca
- - - - - - - - - - - - - - - ttcttcc
- - - - - - - - - - - - - - - - - - - - - - - caaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcata