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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgataccgtttggttgatttcagtaatttgaatcatgtctatgcattcacttttcttttttttcttttcatgttttcacttttaattcattgtgtggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTGACGCATGTCAACCTTAATGATGGAAGTTGTGCAGGCCTTGCCTATCCTG

Basic information

species Vitis vinifera
transcript Vv04s0044g00550.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g00550.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA04G39390.1 (Glycine max), 3'ss of exon 8
tgataccgtttggttgatttcagtaatttgaatcatgtctatgcattcacttttcttttttttcttttcatgttttcacttt-taattcattgtgtggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTGACGCATGTCAACCTTAATGATGGAAGTTGTGCAGGCCTTGCCTATCCTG
| ||    |||  |         |  |||  ||  ||| |  | |||   || | || ||  |       |||  |||     | ||   |    |||||||| || |||||||| || ||||||||  ||||||| || || ||||| || || ||| |||| || ||||||||||||||||| || ||||| |  || |
ttattttattttatcaggaaacatg-tttccatgttgtattagtattttgttgttttattcatggacctgtgtcatcatgaagtgatatgtaaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTTACTCATATCAATCTAAATGATGGAAGTTGTGCTGGTCTTGCTTTCCCCG

upper sequence: Vv04s0044g00550.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA06G15510.4 (Glycine max), 3'ss of exon 8
tgataccgtttggttgatttcagtaatttgaatcatgtctatgcattcacttttcttttttttcttttcatg-----ttttcacttttaattcat-tgtg---tggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTGACGCATGTCAACCTTAATGATGGAAGTTGTGCAGGCCTTGCCTATCCTG
          | ||   |||   |||   |||  |||| |     ||   || | || || || | |||| |      |  ||   | || | || |||    |||||||| || |||||||| || ||||||||  ||||||| || || ||||| || || ||| |||| || ||||||||||||||||| || ||||| |  ||||
-------aacttgtc--tttttataacaggaaatatgtttccatgttgcattattttgttgttttattcacggacttgtgccatcatgaagtgatatgtaaattggcagAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTTACTCATATCAATCTAAATGATGGAAGTTGTGCTGGTCTTGCTTTCCCTG

upper sequence: Vv04s0044g00550.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA06G15510.3 (Glycine max), 3'ss of exon 8
--------tgataccgtttggttga-tttcagtaatttgaatcatgtctatgcattcacttttcttttttttcttttcatgt-----tttcacttttaattcat-tgtg---tggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTGACGCATGTCAACCTTAATGATGGAAGTTGTGCAGGCCTTGCCTATCCTG
        |  |    |    |||  |||   |||   |||  |||| |     ||   || | || || || | |||| |      |  ||   | || | || |||    |||||||| || |||||||| || ||||||||  ||||||| || || ||||| || || ||| |||| || ||||||||||||||||                  
gttctttttcttgttttaaacttgtctttttataacaggaaatatgtttccatgttgcattattttgttgttttattcacggacttgtgccatcatgaagTGATATGTAAATTGGCAGAACCACAACTATGCTGTTGACCCTGCCACACTGCCGGAAGGAGTGGAGGTTACTCATATCAATCTAAATGATGGAAGTTGTG------------------

upper sequence: Vv04s0044g00550.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA05G32190.1 (Glycine max), 3'ss of exon 8
------tgataccgtttggttgatttcagtaatttgaatcatgtctatgcattcacttttcttttttttcttttcatgttttcacttttaattcattgtgtggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTGACGCATGTCAACCTTAATGATGGAAGTTGTGCAGGCCTTGCCTATCCTG
       |  | | |      ||||  |   || | |||  |   |||  |   |   |   || || |  ||   ||   |  ||||  ||  |||   |||||||| || |||||||| || ||||||||  ||||||| || || ||||| || || |||   || |||||||||||||| ||||| |||||||| |  ||||
agtagaaggcaacataaaaa-gattgtatgcatgtaaatagttattatata---agactgggttgttgttattgtctggcatggctttgtat--attcattggcagAACCACAACTATGCGGTTGACCCTGCCACACTGCCAGAAGGAGTGGAGGTTACTCATAGGAATCTTAATGATGGAAGCTGTGCTGGCCTTGCATTCCCTG

upper sequence: Vv04s0044g00550.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S42_59V6.2 (Physcomitrella patens), 3'ss of exon 9
tgataccgtttggttgatttcagtaatttgaatcatgtctatgcattcacttttcttttttttcttttcatgttttcact-tttaa----ttcattgtgtg-gcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTGACGCATGTCAACCTTAATGATGGAAGTTGTGCAGGCCTTGCCTATCCTG
  ||||  |  |    || |  ||   | || |    || |||| |||  |||  || |||     || |     ||| | |||||    ||| || |||| ||||||||| || ||||| ||||| || |   |||| ||||||||||||||||| || ||| | ||||| |||||||| | |||||| |||||||  |  ||||
--atac-ataagcacaatatttgtctatcga-ttgaatccatgctttcg-tttaattgtttagaagttaactcgatcattatttaacgacttcgtt-tgtgcgcagAATCACAATTATGCTGTAGATCCCGACACACTTCCTGAGGGTGTGGAAGTCACACATATTAACCTGAATGATGGGACTTGTGCTGGCCTTGTATTCCCTG

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|71886013|gb|DT035068.1|DT035068
EST:     ATCATCCAGTTCGTAACCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAG                         AATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTG
genomic: ATCATCCAGTTCGTAACCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAGgtgtgttcac ... tgtgtggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTG
EST: gi|30132674|gb|CB918013.1|CB918013
EST:     ATCATCCAGTTCGTAACCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAG                         AATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTG
genomic: ATCATCCAGTTCGTAACCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAGgtgtgttcac ... tgtgtggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTG
EST: gi|110693364|gb|EE069531.1|EE069531
EST:     ATCATCCAGTTCGTAACCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAG                         AATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTG
genomic: ATCATCCAGTTCGTAACCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAGgtgtgttcac ... tgtgtggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTG
EST: gi|161717391|gb|FC067542.1|FC067542
EST:     ATCATCCAGTTCGTAACCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAG                         AATCATAACTATGCAGTAGCCCCTGCATCACTGCCTGAGGGTGTGGAAGTG
genomic: ATCATCCAGTTCGTAACCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAGgtgtgttcac ... tgtgtggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTG
EST: gi|110402447|gb|EC960203.1|EC960203
EST:     ATCATCCAGTTCGTAACCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAG                         AATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTG
genomic: ATCATCCAGTTCGTAACCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAGgtgtgttcac ... tgtgtggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTG
EST: gi|29783438|gb|CB349597.2|CB349597
EST:     ATCATCCAGTTCGGATCCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAG                         AATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTG
genomic: ATCATCCAGTTCGTAACCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAGgtgtgttcac ... tgtgtggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTG
EST: gi|29783487|gb|CB349677.2|CB349677
EST:     ATCATCCAGTTCGTAACCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAG                         AATCATAACTATGCAGTAGACCCTGCATCCCTGCCTGAGGGTGTGGAAGTG
genomic: ATCATCCAGTTCGTAACCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAGgtgtgttcac ... tgtgtggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacttttcttttttttcttttcatgttttcacttttaattcattgtgtggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTGACGCATGTCAACCTTAATGATGGAAGTTGTGCAGGCCTTGCCTATCCTG
                                  ttttaat  putative branch site (score: 3)
     ttttcttttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgataccgtttggttgatttcagtaatttgaatcatgtctatgcattcacttttcttttttttcttttcatgttttcacttttaattcattgtgtggcagAATCATAACTATGCAGTAGACCCTGCATCACTGCCTGAGGGTGTGGAAGTGACGCATGTCAACCTTAATGATGGAAGTTGTGCAGGCCTTGCCTATCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
tgatacc
- - - - - tggttga
- - - - - - - - - - - - - - - - tcatgtc