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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggctagatgatctgtatgcagcactatgttattcattctggcttggattatttttttgattgttgacatattagggttttttttttttttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAGTAATGGAGTTTCTGCTGATGAATCATCCTTTGGATTGTCCAATTTGTGA

Basic information

species Vitis vinifera
transcript Vv14s0006g02020.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g50540.1 (Oryza sativa), 3'ss of exon 1
-------ttggctagatgatctgtatgcagcactatgttattcat-tctggcttggattatttttttgattgttgacatattagggttttttttttttttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAGTAATGGAGTTTCTGCTGATGAATCATCCTTTGGATTGTCCAATTTGTGA
        | | | ||  |  || ||| |  | ||   | |     | |  || | |  ||||    || |  | | |  || | |    || || |  |      |||||||||||||||||| |  || ||||| ||||| || ||||| || || || |||||||| ||| |||||||||||||  |||| || ||||| |||||
gctagtgatagttggactaattgaatg-attagtagagtgtgtgcgtttatctagtaggatttgcaggagttctta-acgttggagcgccttgttgtaat------agGGATGAAGATTAAGACAAACACGCCAGTAGCAAAGAAAGCCAGGGAGGGTGTCATGGAGTTCCTGTTGATGAATCATCCGCTGGACTGCCCAATCTGTGA

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G126038_T01 (Zea mays), 3'ss of exon 1
ttggctagatgatctgtatgcagca-ctatgttattcattctggcttggattat-ttttttgattgttgacatattagggttttttttttttttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAGTAATGGAGTTTCTGCTGATGAATCATCCTTTGGATTGTCCAATTTGTGA
    | |   ||  ||| || || | |||  |   |||   ||   |   |||  | | | |||| |||    | |  |  || |   | ||  |   |||||||||||||||||||| |  || ||||| ||||| ||||| || || || || ||||||||  |||||||||| |||||  | || || ||||| |||||
cataccatcagaaatgtttggagaaactagatacctcaaattgatgtaccttaggtctgtggatttttggagcactgag--ttatcactgttgctggattagGGATGAAGATTAAGACAAACACCCCAGTGGCAAAGAAGGCAAGGGAGGGTGTCATGGAGTTCTTGCTGATGAACCATCCACTCGACTGCCCAATCTGTGA

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA11G33480.1 (Glycine max), 3'ss of exon 1
ttggctagatgatctgtatgcagcactatgttattca--ttctggcttggattatttttttgattgttg--acatattagggttttttttttttttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAGTAATGGAGTTTCTGCTGATGAATCATCCTTTGGATTGTCCAATTTGTGA
      |||| | |    |       | | ||| | |  || |      | || ||  | ||||| |||  | | ||      |  |    |  |  | |||||||||||| ||||||||    ||||| |||||||| |||||  |||||||||| ||||||||| |  ||||||||||||| || ||||| |||||||||||
---aacagataagcatccttggattttgttttaatgaggtttttaaccag-ttgttgctatgattcttgttaaagatgtaatctaatgagatgctcatctttagGGATGAAAATTAAGACTGACACACCTGTTGCAAAGAAGGCTCGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGA

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 1
ttggctagatgatctgtatgcagcactatgttattcattctggcttggattatttttttgattgttg--acatattagggttttttttttttttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAGTAATGGAGTTTCTGCTGATGAATCATCCTTTGGATTGTCCAATTTGTGA-
   | ||    |||  |         | |  |     || |  |  |  |||||  | ||||| |||  | | ||      |  |    |  |  | |||||||||||| ||||||||    ||||| || ||||| ||||| ||||||||||| ||||||||| |  ||||||||||||| || ||||| ||||||||||| 
acagataagc-atccttggattttgttctaatgaggtttttaaccag--ttattgctatgattcttgttaaagatgtaatctaatgagatgctcatctttaggGATGAAAATTAAGACTGACACACCTGTGGCAAAGAAGGCTAGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGAT

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 1
ttggctagatgatctgtatgcagcactatgttattcattctggcttggattatttttttgattgttg--acatattagggtttttttttttt--------ttttttt--tagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAGTAATGGAGTTTCTGCTGATGAATCATCCTTTGGATTGTCCAATTTGTGA
       | |  |  |  | ||| |  || |   |  |  ||| |||  ||   |  ||||||| ||  | ||||| || |||  |  | ||        ||||| |   ||||||||||||||||||   ||||||  | || || ||||| || || ||||| ||||||||| || |||||||||| |||||||||||||| ||||||||
-------gttagttcgattccaggaaaatttctatgctgatggattgattttgatcgttgattggtggaatatatttggatttggtgctattgctaagagtttttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAGTGATGGAGTTTTTGTTGATGAATCACCCTTTGGATTGTCCTATTTGTGA

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|37187544|gb|CF606897.1|CF606897
EST:     AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTG                         GGATGAAGATTAAGACCAGTAC
genomic: AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTGgttagggttt ... ttttttttagGGATGAAGATTAAGACCAGTAC
EST: gi|110731198|gb|EE109146.1|EE109146
EST:     AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTG                         GGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
genomic: AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTGgttagggttt ... ttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
EST: gi|352781338|gb|FQ467784.1|FQ467784
EST:     AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTG                         GGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
genomic: AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTGgttagggttt ... ttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
EST: gi|110732595|gb|EE108017.1|EE108017
EST:     AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTG                         GGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
genomic: AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTGgttagggttt ... ttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
EST: gi|161712112|gb|FC061484.1|FC061484
EST:     AGATAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTG                         GGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
genomic: AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTGgttagggttt ... ttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
EST: gi|71855139|gb|DT004194.1|DT004194
EST:     AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTG                         GGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
genomic: AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTGgttagggttt ... ttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
EST: gi|352769322|gb|FQ471471.1|FQ471471
EST:     AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTG                         GGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
genomic: AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTGgttagggttt ... ttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
EST: gi|110723230|gb|EE100308.1|EE100308
EST:     AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTG                         GGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
genomic: AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTGgttagggttt ... ttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
EST: gi|352765257|gb|FQ465954.1|FQ465954
EST:     AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCACGCCCGCTCTTCCTG                         GGATGAAGAATTAAGACCAGGACACC
genomic: AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTGgttagggttt ... ttttttttagGGATGAAGA-TTAAGACCAGTACACC
EST: gi|110688867|gb|EE067907.1|EE067907
EST:     AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTG                         GGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
genomic: AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTGgttagggttt ... ttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
EST: gi|352772818|gb|FQ473856.1|FQ473856
EST:     AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTG                         GGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
genomic: AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTGgttagggttt ... ttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
EST: gi|110699724|gb|EE076975.1|EE076975
EST:     AGAGAAGTCGCCTAAGCCCGTTTTTTCCCGCGCCATGCCCGCTCTTCCTG                         GGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG
genomic: AGAGAAGTCGCCTAAGCCCGTCGCTTCCTGCGCCATGCCCGCTCTTCCTGgttagggttt ... ttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggattatttttttgattgttgacatattagggttttttttttttttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAGTAATGGAGTTTCTGCTGATGAATCATCCTTTGGATTGTCCAATTTGTGA
                 tgttgac  putative branch site (score: 3)
                                 tttttttttttttttt  putative PPT
                   ttgacatattagggtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggctagatgatctgtatgcagcactatgttattcattctggcttggattatttttttgattgttgacatattagggttttttttttttttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAGTAATGGAGTTTCTGCTGATGAATCATCCTTTGGATTGTCCAATTTGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
-tggctag
- - - - - - - -gtatgca
- - - - - - - - - - - -cactatg
- - - - - - - - - - - - - - - - - - - - tggcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgac