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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaacggtgctatcactctgaatcgatgctttttgaatattaatggcctgggtaagaaaactgaatatatataaatttacattttggtatataattgcagGTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTGGTGGGGAAATGGGATGAGGCAATGTATTATGTGTTGGGAGATCCAACAA

Basic information

species Vitis vinifera
transcript Vv01s0137g00290.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os12g18770.1 (Oryza sativa), 3'ss of exon 6
-ca-aacggtg-ctatcactctgaatcgatgctttttgaatattaatggcctgggtaagaaaactgaatatatataaatttacattttggtatataattgcagGTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTGGTGGGGAAATGGGATGAGGCAATGTATTATGTGTTGGGAGATCCAACAA
 || | |  |  |||  | ||||  | |  | ||| | || ||  ||    |||  |      |         | |  |  | | ||||   |     ||||||| ||||||||||||||||||||| |||| ||  |||| || ||||||||  | || ||||||||||| || |||||||||||  | || |||||||   
gcatatcaatatctagtagtctgttttgtggttttataaacat--attaattggacactgttcccagcctcccacat-taaatagtttgaattgctcgtgcagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAGAAAGTTGCTATGTTAATCGGAAAATGGGATGAAGCTATGTATTATGTTCTTGGGGATCCAAGTG

upper sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G156608_T03 (Zea mays), 3'ss of exon 1
-caaacggtgctatcactctgaatcgatgctttttgaata-ttaatggcctgggtaagaaaactgaatatatataaatttacattttggtatataattgcagGTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTGGTGGGGAAATGGGATGAGGCAATGTATTATGTGTTGGGAGATCCAACAA
    | | |   | || ||| | | |   || |   |  | ||||    ||   | |   | |  |   | |   |       || |  |  ||   ||||||| ||||||||||||||||||||| |||| ||  | || |||||||||||  | || ||||||||||| || |||||||||||| | || |||||||   
ggttaagttagcagcagtct-acttgcaactgtacaagcacttaaatatctatttgatcgagcctaggttttgacacaaattgttctaat-catttgtgcagGTGCATGGATTTGTGCAAGATAATAGAACAGGGCAAAAAGTAGCTATGTTAATTGGAAAATGGGATGAAGCTATGTATTATGTGCTTGGGGATCCAAGTG

upper sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 6
---caaacggtgctatcactctgaatcgatgctttttgaatattaatggcctgggtaagaaaactgaatatatataaatttacattttggtatataattgcagGTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTGGTGGGGAAATGGGATGAGGCAATGTATTATGTGTTGGGAGATCCAACAA
    |||     |  ||   | | ||         |     | |         | ||  | |  |  |||    | ||   || |||     |||| |  ||||| ||||| ||||| ||||| ||  ||||||||||||||||||| |||||  | ||||| |||||||| |||||||| |||||  | || |||||||| |
aaataaagaactccgtctagcaggattttcttacctgctgcactttcaattcagttagcacattt--ataagactgaaagaacttttaatcttata-taacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTTGGGGATCCAACCA

upper sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 6
caaacggtgctatcactctgaatcgatgcttt----ttgaatattaatggcctgggtaagaaaactgaatatatataaatttacattttggtatataattgcagGTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTGGTGGGGAAATGGGATGAGGCAATGTATTATGTGTTGGGAGATCCAACAA
  |    |      | ||  |||   |  |||    | |  |||           ||    |   | |  | |  | ||   || |||    ||||| |  ||||| ||||| ||||| ||||| ||  ||||||||||||||||||| |||||  | ||||| |||||||| |||||||| |||||  | || |||||||| |
--agaaatttggcaattccaaatgagtagtttggattcgtctatccgcttttcttgttctgagttttatgagac-tgaaagaacttttaatcatata-taacagGTCCATGGGTTTGTTCAAGACAACAGAACTGGAGAGAAGGTAGCGATGTTAATTGGGAAGTGGGATGAAGCAATGTACTATGTACTCGGGGATCCAACCA

upper sequence: Vv01s0137g00290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 6
caaacggtgctatcactctgaatcgatgctttttgaatattaatggcctgggtaagaaaactgaatatatataaatttacattttggtatataattgcagGTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTGGTGGGGAAATGGGATGAGGCAATGTATTATGTGTTGGGAGATCCAACAA
                  |      ||| |||||  || |   |      | |   |    |||| |    |  |  |  | |||||||      ||||||||||||| ||||||||||| ||  |||| || ||||| ||||||||  || | || ||||||||||| |||||||| ||||| ||||||||||| ||||
-----------------gtagtagaatgattttt--atttctgtctttctgctcgta----tgaacaggcctttaaatggaatttggtaa-----tgcagGTTCATGGGTTTGTGCAAGACAACAGAACCGGGGAGAAAGTAGCTATACTGATAGGCAAATGGGATGAAGCAATGTACTATGTATTGGGAGATCCGACAA

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|110419051|gb|EC985243.1|EC985243
EST:     GTAAGCTGAAGTTCAAGGAGCAGTCTATTATAGACCGAAATCCACATCAG                         GTTCATGGATTTGTG
genomic: GTAAGCTGAAGTTCAAGGAGCAGTCTATTATAGACCGAAATCCACATCAGgtactttgtg ... ataattgcagGTTCATGGATTTGTG
EST: gi|34543569|gb|CF511801.1|CF511801
EST:     GTAAGCTGAAGTTCAAGGAGCAGTCTATTATAGACCGAAATCCACATCAG                         GTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTG
genomic: GTAAGCTGAAGTTCAAGGAGCAGTCTATTATAGACCGAAATCCACATCAGgtactttgtg ... ataattgcagGTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTG
EST: gi|34543484|gb|CF511716.1|CF511716
EST:     GTAAGCTGAAGTTCAAGGAGCAGTCTATTATAGACCGAAATCCACATCAG                         GTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTG
genomic: GTAAGCTGAAGTTCAAGGAGCAGTCTATTATAGACCGAAATCCACATCAGgtactttgtg ... ataattgcagGTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctgggtaagaaaactgaatatatataaatttacattttggtatataattgcagGTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTGGTGGGGAAATGGGATGAGGCAATGTATTATGTGTTGGGAGATCCAACAA
           aaaactgaatatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaacggtgctatcactctgaatcgatgctttttgaatattaatggcctgggtaagaaaactgaatatatataaatttacattttggtatataattgcagGTTCATGGATTTGTGCAAGATAATCGAACTGGAGAGAAGGTAGCTATGTTGGTGGGGAAATGGGATGAGGCAATGTATTATGTGTTGGGAGATCCAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - -tgctatc
- - - - - - - -ctctgaa
- - - - - - - - - - - - - - - - - - - - - - ggcctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa