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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctatttggatctgtttgtatggcaaagtcacagccaatatcccttttgaaatcctattgatatttttaatatgttaatttgtgttttcttttattgcagTTTACAACTGAAGCAATGCTAGAACATATGAATAAGTTGCTTCAGATACCAGGATCAGAGCTACTATTTGGTGGCAAGGCTTTAGAAAATCATTCGATCC

Basic information

species Vitis vinifera
transcript Vv17s0000g05800.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA05G01290.1 (Glycine max), 3'ss of exon 11
tctatttggatctgtttgtatggcaaagtcacagccaatatcccttttgaaatccta-ttgatatttttaatatgt-taatttgtgttttcttttattgcagTTTACAACTGAAGCAATGCTAGAACATATGAATAAGTTGCTTCAGATACCAGGATCAGAGCTACTATTTGGTGGCAAGGCTTTAGAAAATCATTCGATCC
  |  | |    | ||||  ||| | | |||    |  ||| |  |   |   |    ||  | | ||| | ||   | |||| |  | |  | | |||||| |||| |||||  ||||||| ||||| || |||||||||||| |||||||||||||| || | |||||||| ||  |  |||||||  ||||||| || |
-ttgctggtgcatctttgc-tggaataatcatttgctttattctatgcaatgccaagcttagtttatttgaaattcatgatttttcatcttatatgttgcagGTTACGACTGATTCAATGCTTGAACACATCAATAAGTTGCTTGAGATACCAGGATCAAAGTTGCTATTTGGGGGTCAACCTTTAGAGGATCATTCAATTC

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA17G10610.1 (Glycine max), 3'ss of exon 12
tctatttggatctgtttgtatggcaaagtcacagccaatatcccttttga-aatcctattgatatttttaatatg-ttaatttgtgttttcttttattgcagTTTACAACTGAAGCAATGCTAGAACATATGAATAAGTTGCTTCAGATACCAGGATCAGAGCTACTATTTGGTGGCAAGGCTTTAGAAAATCATTCGATCC
  ||  |||  |   ||  | || | | |      |  ||| |      |  |     ||  | | |||   ||  || |||| |  | || | | |||||| |||| |||||  ||||||| || ||| |||||||||||||| |||||||||||||| || | ||||| || || |   || |||| || ||||| || |
--tagctggtgcatctttgacggaataattgtttgctttattctaagcaatgacaagcttagtttatttggaattcttgatttttcatctcatatgttgcagGTTACGACTGATTCAATGCTTGAGCATGTGAATAAGTTGCTTGAGATACCAGGATCAAAGTTGCTATTCGGGGGTAGTCCTCTAGAGAACCATTCAATTC

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA05G01300.1 (Glycine max), 3'ss of exon 12
tctatttggatctgtttgtatggcaaagtcacagccaatatcccttt-tgaaatcctattgatatttttaatatgttaatttgtgttttcttttattgcagTTTACAACTGAAGCAATGCTAGAACATATGAATAAGTTGCTTCAGATACCAGGATCAGAGCTACTATTTGGTGGCAAGGCTTTAGAAAATCATTCGATCC
   |||||    | |   | ||||| | | |  | |    | | ||  || |||   |    |  ||| ||  | ||||||| | || || | | ||||||| ||| ||||     ||||||||||| | |||||| |||||| |||||||||||||| |||| || ||||| || |   || |||| || ||||| || |
-tcatttgctgatatgcatttggcagaataattgtcttctttctttcatgcaatgacaagtttcatttgaaattcttaatttttcttctcatatgttgcagTGTACGACTGGTATGATGCTAGAACACAAGAATAAATTGCTTGAGATACCAGGATCAAAGCTGCTCTTTGGGGGTAGTCCTCTAGAGAACCATTCAATTC

upper sequence: Vv17s0000g05800.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT5G62530.1 (Arabidopsis thaliana), 3'ss of exon 12
tctatttggatctgtttgtatggcaaagtcacagccaatatcccttttgaaatcctattgatatttttaatatgttaatttgtgttttcttttattgcagTTTACAACTGAAGCAATGCTAGAACATATGAATAAGTTGCTTCAGATACCAGGATCAGAGCTACTATTTGGTGGCAAGGCTTTAGAAAATCATTCGATCC
      ||  | |  |||| |  | |  |    |  |||    ||  ||| ||  |||   ||    | || | || |||  |||||           ||||||||||||| |||||| | || || ||| | ||  |||||||||| || || ||| ||||||| |||||||||||||  ||  | ||||||||||| |
-----gtgagtttcattgtttctccatct-gttgttaat-catctgatgagattgtatcattaaaacttattttttcattattgtttca---------agTTTACAACTGAGGCAATGTTGGAGCACATGGAGAATCTGCTTCAGATTCCTGGCTCAAAGCTACTCTTTGGTGGCAAGGAATTGAAGAATCATTCGATTC

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|33402546|gb|CF208173.1|CF208173
EST:     TTGCTGCAAGAAGGAAGTTAGAAGATCTAACTATTGGACCTGTTCTGAGT                         TTTACAACTGAAGCAATGCTAGAACATATGAATAAGTTGCTTCAGATACCA
genomic: TTGCTGCAAGAAGGAAGTTAGAAGATCTAACTATTGGACCTGTTCTGAGTgtaagcatgg ... tttattgcagTTTACAACTGAAGCAATGCTAGAACATATGAATAAGTTGCTTCAGATACCA
EST: gi|110380514|gb|EC945785.1|EC945785
EST:     TTGCTGCAAGAAGGAAGTTAGAAGATCTAACTATTGGACCTGTTCTGAGT                         TTTACAACTGAAGCAATGCTAGAACATATGAATAAGTTGCTTCAGATACCA
genomic: TTGCTGCAAGAAGGAAGTTAGAAGATCTAACTATTGGACCTGTTCTGAGTgtaagcatgg ... tttattgcagTTTACAACTGAAGCAATGCTAGAACATATGAATAAGTTGCTTCAGATACCA
EST: gi|110731235|gb|EE109223.1|EE109223
EST:     TTGCTGCAAGAAGGAAGTTAGAAGATCTAACTATTGGACCTGTTCTGAGT                         TTTACAACTGAAGCAATGCTAGAACATATGAATAAGTTGCTTCAGATACCA
genomic: TTGCTGCAAGAAGGAAGTTAGAAGATCTAACTATTGGACCTGTTCTGAGTgtaagcatgg ... tttattgcagTTTACAACTGAAGCAATGCTAGAACATATGAATAAGTTGCTTCAGATACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaaatcctattgatatttttaatatgttaatttgtgttttcttttattgcagTTTACAACTGAAGCAATGCTAGAACATATGAATAAGTTGCTTCAGATACCAGGATCAGAGCTACTATTTGGTGGCAAGGCTTTAGAAAATCATTCGATCC
                           tgttaat  putative branch site (score: 3)
                                 tttgtgttttctttt  CT-rich tract
          tattgatatttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctatttggatctgtttgtatggcaaagtcacagccaatatcccttttgaaatcctattgatatttttaatatgttaatttgtgttttcttttattgcagTTTACAACTGAAGCAATGCTAGAACATATGAATAAGTTGCTTCAGATACCAGGATCAGAGCTACTATTTGGTGGCAAGGCTTTAGAAAATCATTCGATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - tgtatgg
- - - - - - - - - - - - - - -cacagcc
- - - - - - - - - - - - - - - - - - - - - - - - - - -cctattg