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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatattttgtagccatggaatcagttttatttataaaaacaatcttatgcttaagctttgatctttagtaaaatattaaatgctcccatgacttttccagGCTGAAAACATGATTGCCCATAAGGATGATATCTACTCACGCCCTAAAAGAACCTGGTTTGCAACAGAAAAGGAGAAGAAGTCTGTGGCAAAGGCAGCAA

Basic information

species Vitis vinifera
transcript Vv18s0001g14540.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g14540.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os12g29660.1 (Oryza sativa), 3'ss of exon 14
----------------------tatattttgtagccatggaatca-gttttatttataaaaacaatc----ttatgc-ttaagctttgatctttagtaaaatattaaatgctcccatgacttttc------cagGCTGAAAACATGATTGCCCATAAGGATGATATCTACTCACGCCCTAAAAGAACCTGGTTTGCAACAGAAAAGGAGAAGAAGTCTGTGGCAAAGGCAGCAA
                       | ||||  | |  |   ||||| |||||  ||  || |   ||     ||| |  |||     || | | |||   || |     | || |||   |||| |      ||||| ||||| ||||| || ||||||||||| || |||||| | || || |||||||||||||| || || ||||| |||||   | |||||||||| || |
gtagtatttctttacaagtttcgaaatttccttgataacaaatcatgttttgcttgcaatagttattactattaagtgttatttaatgctatatagattaacacctttttctgccaaatctttacaactatcagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCAAGACCAAAGAGAACCTGGTTTGCTACTGAGAAGGAAAAGAAACTTTTGGCAAAGGCTGCTA

upper sequence: Vv18s0001g14540.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G420865_T01 (Zea mays), 3'ss of exon 14
-----------------------------tatattttgtagccatggaatcagttttatttataaaaacaatcttatgctt--aagctttgat--ctttagtaaaatattaaatgctcccatgacttttccagGCTGAAAACATGATTGCCCATAAGGATGATATCTACTCACGCCCTAAAAGAACCTGGTTTGCAACAGAAAAGGAGAAGAAGTCTGTGGCAAAGGCAGCAA
                              |||  ||  | |    |  | | ||| | |||    ||||      |||||   || | |||   | || |||   |    | ||| |   ||| | | | |||| ||||| ||||| || ||||||||||| || |||||||| || || |||||||||||||| || |||| |||||||||   | |||||   || || |
gttataatttttttacgttattttaccaaaataaatta-atctcccgtgtgaatttcagttacttgaacagagccgtgcttcagagttctgaatacatttgtacctttgccattgcacatttgaatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAGAAGAAACTTTTGGCAGCAGCGGCTA

upper sequence: Vv18s0001g14540.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM5G804064_T01 (Zea mays), 3'ss of exon 14
------------------------------tatattttgtagccatggaatcagttttatttataaaaacaatcttatgctt---aagctttgat-ctttagtaaaatattaaatgctcccatgacttttccagGCTGAAAACATGATTGCCCATAAGGATGATATCTACTCACGCCCTAAAAGAACCTGGTTTGCAACAGAAAAGGAGAAGAAGTCTGTGGCAAAGGCAGCAA
                               |||  |||      |    | | ||| | |||    |||         |||   ||   |  || | || |||   |    | | |     ||| | | | |||| ||||| ||||| || ||||||||||| || |||||||| || || |||||||||||||| || |||| ||| ||||||  | ||| |   || || |
gttatatattttaaagttcagttttacgtaaataaattgatttttttttgtgaatttcaattactttaactgatccgcacttcagaattctcaatacatttgtacctttgccattacatatttgaatatacaagGCAGAAAATATGATAGCTCATAAGGATGAGATATACTCACGGCCAAAGAGAACCTGGTTTGCTACTGAAAGGGAAAAGAAGCTTTTGGTAGCAGCTGCTA

upper sequence: Vv18s0001g14540.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA18G11950.1 (Glycine max), 3'ss of exon 14
---tatattttgtagcca-----tggaatca-gttttatttataaaaacaatcttatgcttaagctttgatctttagtaaaatattaaatgctcccatgacttttccagGCTGAAAACATGATTGCCCATAAGGATGATATCTACTCACGCCCTAAAAGAACCTGGTTTGCAACAGAAAAGGAGAAGAAGTCTGTGGCAAAGGCAGCAA
   | |||| | |  |||     ||||| |   | ||  || |    |   ||| || |||||  |||   ||| | | ||||     |||| |  ||     |  |||||||||||||||||||| |||| ||| || ||||  || ||||| ||||||||||||||||  ||||| |||||||| |||  ||   |||| ||| | |
aattttattgtatgaccaggctttggaaccccatattgattgttttcattttctaatccttaacattttcccttcaatgaaatc----atgcacttat-----tggcagGCTGAAAACATGATTGCACATAGGGAAGAGATCTTTTCCCGCCCCAAAAGAACCTGGTTTGTCACAGAGAAGGAGAAAAAGCTTGCTTCAAAAGCATCCA

upper sequence: Vv18s0001g14540.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA02G25240.1 (Glycine max), 3'ss of exon 14
tatattttgtagccatggaatcagttttatt-tataaaaacaatcttatgcttaagctttgatctttagtaaaatat-taaatgctcccatg-acttttc--cagGCTGAAAACATGATTGCCCATAAGGATGATATCTACTCACGCCCTAAAAGAACCTGGTTTGCAACAGAAAAGGAGAAGAAGTCTGTGGCAAAGGCAGCAA
   |   |     ||   |   | ||||||| |||   |   ||  | |  | |   | | ||| |||  |   |   | |||      ||| |||| |   ||||| |||||||||||||| |||| ||| || ||||  || ||||| ||||||||||||||||  ||||| |||||||| |||  ||  ||||| ||| | |
---aaagtagcatcacttagaaaattttattgtatggtattgat--tgttttcattttctaatccttaacattttccctcaataaaattatgcacttattggcagGCCGAAAACATGATTGCACATAGGGAAGAGATCTTTTCCCGCCCCAAAAGAACCTGGTTTGTCACAGAGAAGGAGAAAAAGCTTGCTGCAAAAGCATCCA

upper sequence: Vv18s0001g14540.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA09G15220.1 (Glycine max), 3'ss of exon 14
tatattttgtagccatggaatcagttttatt-tataaaaacaatcttatgcttaagctttgatctttagtaaaatat-taaatgctcccatg-acttttc--cagGCTGAAAACATGATTGCCCATAAGGATGATATCTACTCACGCCCTAAAAGAACCTGGTTTGCAACAGAAAAGGAGAAGAAGTCTGTGGCAAAGGCAGCAA
   |   |     ||   |   | ||||||| |||   |   ||  |    | |   | | ||| |||  |   |   | ||| |    ||| |||| |   ||||| |||||||||||||| |||| ||| || ||||  || ||||| ||||||||||||||||  ||||| |||||||| |||  ||  ||||| ||| | |
---aaagtagcatcacttagaaaattttattgtatggtattgat--tgctttcattttctaatccttaacattttccctcaatacaattatgcacttattggcagGCCGAAAACATGATTGCACATAGGGAAGAGATCTTTTCCCGCCCCAAAAGAACCTGGTTTGTCACAGAGAAGGAGAAAAAGCTTGCTGCAAAAGCATCCA

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|349812869|gb|FQ410511.1|FQ410511
EST:     GGAAGAGAGAATCCTCAGAAAAGCTGAAATGGAAGCAACAAAG                         GCTGAAAACATGATTGCCCATAAGGATGATATCTACTCACGCCCTAAAAGA
genomic: GGAAGAGAGAATCCTCAGAAAAGCTGAAATGGAAGCAACAAAGgtttgacact ... acttttccagGCTGAAAACATGATTGCCCATAAGGATGATATCTACTCACGCCCTAAAAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgcttaagctttgatctttagtaaaatattaaatgctcccatgacttttccagGCTGAAAACATGATTGCCCATAAGGATGATATCTACTCACGCCCTAAAAGAACCTGGTTTGCAACAGAAAAGGAGAAGAAGTCTGTGGCAAAGGCAGCAA
          ctttgat  putative branch site (score: 5)
                                              cttttcc  putative PPT
           tttgatctttagtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatattttgtagccatggaatcagttttatttataaaaacaatcttatgcttaagctttgatctttagtaaaatattaaatgctcccatgacttttccagGCTGAAAACATGATTGCCCATAAGGATGATATCTACTCACGCCCTAAAAGAACCTGGTTTGCAACAGAAAAGGAGAAGAAGTCTGTGGCAAAGGCAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - ccatgga
- - - - - - - - - - - - - - - - ataaaaa
- - - - - - - - - - - - - - - - - - - - - -cttatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatat