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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctcactaatctagtgattttgaaggaaataatatgaatacaagtagagatttttctgtctttcttgaaaattagttttctgaatgatctgtgtcataaatgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAACTGGAAACTGCTGCTTATCCAGC

Basic information

species Vitis vinifera
transcript Vv05s0020g04720.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g53110.1 (Oryza sativa), 3'ss of exon 3
gtatgtctcactaatctagtgattttgaaggaaataatatgaatacaagtagagatttttctgtctttcttgaaaattagttttctgaatgatctgtgtcataaa-tgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAACTGGAAACTGCTGCTTATCCAGC
         |||  | | ||  ||||||  | |||| | |   |     | | ||  |   |   |   |||    ||| | | | | |  | |  | | || || |  ||| ||||||||||||||||| || || |||||  |||||||||||||||| |||||||||| |||||| || || ||  |||| | ||||||||| |||||
------acaactgttgtggttgttttgattgtaatattctatttgttgtttgtgaactccatcaatagtttg----ttaatatcccgcaata-caattttatgaactccagAATCTCCCTTTGAATTCCGCGCACTGGAGGTTACTTTGGAAGCCATTTGCAGTTTTCTTGGTGCACGCACTACTGAGTTGGAGAGTGCTGCTTACCCAGC

upper sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G35260.1 (Glycine max), 3'ss of exon 3
--------------------------gtatgtctcactaatctagtgattttgaaggaaa-taatatgaatacaagtagagatttttctgtctttcttgaaaattagttttctgaatgatctgtgt--cataaatgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAACTGGAAACTGCTGCTTATCCAGC
                             |     || ||  || |||||      |    |  ||| |||  |  |    ||||   | | | |||||     | ||| ||||| ||||||   |  || |||||||||||| ||||||||||||||||| || ||||| ||||| ||||||||||||||||||||||||||||||||||||||| |||| |  ||||||||||| ||
gtacgttacattaaatgatgaaccataagtaatgaacaaacttattgattgcatctgttcctgttataaatctatctttgtatttgcat-tatctcttgct--cttgttatctgagtgatctaaattacacaaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAATTGGAGATGGCTGCTTATCCTGC

upper sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G32350.1 (Glycine max), 3'ss of exon 3
---------------gtatgtctcactaatctagtgattttgaaggaaataatatgaatacaa-----------gtagagatttttctgtcttt-------cttgaaaattagttttctgaatgatctgtgtcata-aatgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAACTGGAAACTGCTGCTTATCCAGC
                 || |     | | | |    |  ||||  || | || ||| | ||             || |  | | | ||| |||       |||      | ||| ||||| ||||||   | ||  ||||||||||| ||||||||||||||||| || ||||| ||||| ||||||||||||||||||||||||||||||||| ||||| |||| |  ||||||||||| ||
gtacgctacatacttacatttaatggtgaaccataagtaatgaacaaactcat-tgattgcatctgttcctcttataaatctatctttgtatttgcattatcttttgctcttgttatctgagtgatctaaattatgcaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACATCAGAATTGGAGATGGCTGCTTATCCTGC

upper sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G09690.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------gtatgtctcactaatctagtgattttgaaggaaataatatgaatacaagtagagatttttctgtctttcttgaaaattagttttctgaatgatctgtgtcataa-atgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAACTGGAAACTGCTGCTTATCCAGC
                               || |  |    | |  |   || ||  |     | ||    | | ||| |   ||    |  ||  ||||   | ||    |  ||||   | ||| |  ||  || |||| || || |||||||||||||| || |||||||| |||||||| |||||||||||||| |||||| | ||||||||||| || |    ||||||||| ||
gtacccctcaaggcctcaacttttgttattttaaggatataaattggaaaaatctttgatcttttgatgcctacataagaactaatgaaccattcactcttttcacttttggtattgaagtgtttgtttgttactatatagAATCCCCGTTTGAATTCCGGGCGCTAGAGGTGGCCTTGGAAGCTATTTGTAGTTTTCTAGCTGCAAGGACAACAGAACTAGAGAAGTTTGCTTATCCTGC

upper sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G09710.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------gtatgtctcactaatctagtgattttgaaggaaata-at------atgaatacaagtagagat--ttttctgtctttcttgaaaattagtt--ttctgaatgatctgtgtcataaatgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAACTGGAAACTGCTGCTTATCCAGC
                  || ||  |  | ||| ||  |||||    | ||| ||      |||  |     || | |   || ||| |    ||||     | ||   |     |||   ||| ||  ||   |||| ||||| |||||||| ||||| || || ||||||||||||||||| ||||||||  | |||||| | ||||||||||| || |   ||| |||||| ||
gtaagtttaaacattacgatctcaaaacattcttgtccttttggcatatatatattttgtaatgcttttccataaaaaccgttctctattcgacttgtcgcgttgtcggtatctgatgtggtgtttc-caatcttagAATCTCCGTTTGAATTTCGGGCACTAGAAGTGGCTTTGGAAGCCATATGTAGTTTCTTAGCTGCAAGAACAACAGAACTAGAGAAGTCTGGTTATCCTGC

upper sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G09720.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------gtatgtctcactaatc--tagtgattttgaagg--aaataatatgaatacaagtagagatttttctgtctttcttgaaaattagttttctgaatgatctgtgtcataa-atgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAACTGGAAACTGCTGCTTATCCAGC
                                 ||   | | | ||   |  |  ||||||     |  |  ||| ||||     ||| |   || |  || | || |   || || ||    ||||| ||  | |||  || |||| ||  | |||||||| ||||| || ||||| ||||||||||| |||||||| || || |||||| | |||| |||| | || |   |||||||||| ||
gtagcccttgaccttagtcatttttagaactcaattcttgatttattcttgatctttttgatacctatgttctataaatatcgtaagaaaaacttgtcactctttttacttttggtatta-atatgat-tgcttgatactatatagAATCCGCGTTTGAATTTCGGGCACTAGAGGTTGCTTTGGAAGCTATTTGTAGCTTCCTAGCTGCAAGGACAATAGAATTAGAGAAGTCTGCTTATCCTGC

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|161719350|gb|FC068970.1|FC068970
EST:     AGATGGGAAAGATTATGGGCACCATGATGTTGAAGCAGGAGAAGAAGATG                         AGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTA
genomic: AGATGGGAAAGATTATGGGCACCATGATGTTGAAGCAGGTGAAGAAGATGgtatgtctca ... ataaatgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTA
EST: gi|161717315|gb|FC065266.1|FC065266
EST:     AGATGGGAAAGATTATGGGCACCATGATGTTGAAGCAGGTGAAGAAGATG                         AGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTA
genomic: AGATGGGAAAGATTATGGGCACCATGATGTTGAAGCAGGTGAAGAAGATGgtatgtctca ... ataaatgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTA
EST: gi|161717936|gb|FC069249.1|FC069249
EST:     AGATGGGAAAGATTATGGGCACCATGATGTTGAAGCAGGTGAAGAAGATG                         AGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTA
genomic: AGATGGGAAAGATTATGGGCACCATGATGTTGAAGCAGGTGAAGAAGATGgtatgtctca ... ataaatgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTA
EST: gi|71857515|gb|DT006570.1|DT006570
EST:     AGATGGGAAAGATTATGGGCACCATGATGTTGAAGCAGGAGAAGAAGATG                         AGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTA
genomic: AGATGGGAAAGATTATGGGCACCATGATGTTGAAGCAGGTGAAGAAGATGgtatgtctca ... ataaatgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctgtctttcttgaaaattagttttctgaatgatctgtgtcataaatgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAACTGGAAACTGCTGCTTATCCAGC
              ttgaaaattagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtctcactaatctagtgattttgaaggaaataatatgaatacaagtagagatttttctgtctttcttgaaaattagttttctgaatgatctgtgtcataaatgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAACTGGAAACTGCTGCTTATCCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT