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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctggcattggcttatgctttgttcttcatgtcattccaaactacttcttacaagcttcagtatggagtttacatgttaatctttaatgatatttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACGAGGCTGCCCAAAGGGGCACATCTGTCTACCTTGTTGAGCGCAGAATTGA

Basic information

species Vitis vinifera
transcript Vv07s0031g02190.t01
intron # 11
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os03g03710.1 (Oryza sativa), 3'ss of exon 11
---ctggcattggcttatgctttgtt--cttca-tgtcattccaaactacttcttacaagcttcagtatggagtttacatgttaatctttaatgatatttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACGAGGCTGCCCAAAGGGGCACATCTGTCTACCTTGTTGAGCGCAGAATTGA
      | |||  |  | |   ||||   |||| | | ||| ||  | || | ||| |   ||   | ||||| || |||     |  || |       | |  ||| |||||||| || || || |||||||| ||||| ||||| |||||||| |||||  | ||||||||||| ||||| || |||||||  |   |||||||
tgatatgaattttcacacgtcatgtttctttcacttttatttcacgc-accttttatactgtttgatttggagattgcat-----ttcttgactcgggatgactagATATTGCTGACGTCACTAACTTTGTTCATCCTGGTACTCCTCTTGATGAGGAGGCCTCACAAAGGGGCACTTCTGTATATCTTGTTGGACAGCGAATTGA

upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G031859_T03 (Zea mays), 3'ss of exon 11
ctggcattggcttatgctttgttct--tcatgtcattccaaactacttcttacaagcttcagtatggagtttacatgttaatctttaatgatatttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACGAGGCTGCCCAAAGGGGCACATCTGTCTACCTTGTTGAGCGCAGAATTGA
||   | |   |||   || ||     |||   | || |   |    || | ||  ||    ||  || |  | |   |    ||   |||  |    | ||| || |||||||| || ||||||||||||||||| || || |||||||| || ||||| ||||||||||| ||||| || ||||||| ||   | |||||
cttcaactaatttacttttggtctcggtcacaacttttctgtcctggtcattcactctgtgctactga-tacatagactg-cattccttgacttgagctgagATATCGCTGATGTCACTAATTTTGTTCACCCTGGTACCCCTCTTGATGAGGAAGCTGCGCAAAGGGGCACTTCTGTTTATCTTGTTGGGCAGCGGATTGA

upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA06G14870.2 (Glycine max), 3'ss of exon 11
ctggcattggcttatgctttgttcttcatgtcattccaaactacttcttacaagcttcagtatggagt----ttacatgttaatctttaatgatatttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACGAGGCTGCCCAAAGGGGCACATCTGTCTACCTTGTTGAGCGCAGAATTGA
    | |   |    ||   | |     |||  ||| |  || ||||    |   |    |||  | |     || | ||| |||||||||||  ||   ||||| ||||||||||| |||||||||||||| |||||||||||||||||||| |||||||| |||||||| |||||||||||||||||||||||  | || ||
---tcctcttcaacagccaagcttcatttgtttttctaccct-cttcccctagcttatgctatctaatccctctataggttcatctttaatgaatttctgtcagATATTGCTGATGTGACAAATTTTGTTCATCCTGGCACTCCCCTTGATGATGAGGCTGCACAAAGGGGTACATCTGTCTACCTTGTTGAGCGGCGGATAGA

upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA04G39980.1 (Glycine max), 3'ss of exon 11
ctggcattggcttatgctttgttcttcatgtcattccaaactacttcttacaagcttcagtatggagtt----tacatg-ttaatctttaatgatatttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACGAGGCTGCCCAAAGGGGCACATCTGTCTACCTTGTTGAGCGCAGAATTGA
  || | ||  || |  | |  | | ||||  |||  | ||||     |  |   |    |||| | |     || ||| || ||||||||||   ||   ||||| ||||||||||| || ||||||||| | |||||||||||||||||||| |||||||| |||||||| || ||||||||||||||||||||  | || ||
--ggtagtgctttct--tctagtgtgcatga-attgtatactaacgtatgaagcttatgctatgtaatccctctatatggttcatctttaatggatttctgtcagATATTGCTGATGTGACTAATTTTGTTTATCCTGGCACTCCCCTTGATGATGAGGCTGCACAAAGGGGTACGTCTGTCTACCTTGTTGAGCGGCGGATAGA

upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT2G17510.1 (Arabidopsis thaliana), 3'ss of exon 11
ctggcattggcttatgctttgttcttcatgtcattccaaactacttcttacaagcttcagtatggagtttacatgtta---atctttaatgatatttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACGAGGCTGCCCAAAGGGGCACATCTGTCTACCTTGTTGAGCGCAGAATTGA
   | || ||  | | |     | |  |  |  ||||    || |   | |  |  |  | |  || | || ||| |    ||| || |  || ||| || |||||||||||||||||| ||||||||||||||||| |||||  | ||||| |||||  |  |||| ||||||||||||||||||||||||||| | |||||
---gaatcggtatcttccagaatttgtagctagttccgttgtattctcttcttgtcttgggagtgaatatatatgatgcttatccttgaccatgtttgattagACATTGCTGATGTAACGAATTTTGTTCACCCTGGTACTCCTTTGGATGATGAGGCATCAAAAAGAGGCACATCTGTCTACCTTGTTGAGCGCCGTATTGA

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|32268690|gb|CD717849.1|CD717849
EST:     TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTC                         ACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGATG
genomic: TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTCgtatcctcca ... atttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACG
EST: gi|32249460|gb|CD715279.1|CD715279
EST:     TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTC                         ACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGATG
genomic: TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTCgtatcctcca ... atttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACG
EST: gi|32247182|gb|CD713001.1|CD713001
EST:     TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTC                         ACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGATG
genomic: TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTCgtatcctcca ... atttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACG
EST: gi|110357405|gb|EC920922.1|EC920922
EST:     TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTC                         ACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGATG
genomic: TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTCgtatcctcca ... atttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACG
EST: gi|32248522|gb|CD714341.1|CD714341
EST:     TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTC                         ACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGATG
genomic: TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTCgtatcctcca ... atttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACG
EST: gi|32267807|gb|CD716966.1|CD716966
EST:     TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTC                         ACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGATG
genomic: TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTCgtatcctcca ... atttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACG
EST: gi|32267641|gb|CD716604.1|CD716604
EST:     TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTC                         ACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGATG
genomic: TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTCgtatcctcca ... atttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACG
EST: gi|32248261|gb|CD714080.1|CD714080
EST:     TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTC                         ACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGATG
genomic: TGCACTGCATTGTACAACTCTTCCGAATGGAAATTTTGAAGTGGGAGTTCgtatcctcca ... atttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttacaagcttcagtatggagtttacatgttaatctttaatgatatttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACGAGGCTGCCCAAAGGGGCACATCTGTCTACCTTGTTGAGCGCAGAATTGA
                                 atctttaat  putative branch site 
                      tttacatgttaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctggcattggcttatgctttgttcttcatgtcattccaaactacttcttacaagcttcagtatggagtttacatgttaatctttaatgatatttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACGAGGCTGCCCAAAGGGGCACATCTGTCTACCTTGTTGAGCGCAGAATTGA

- - - - - cttatgc
- - - - - - - - - - - - -tcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - -acaagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgtt