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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatagttgcaaacatgagaggcgtgcgtttatgacgtgattttcctataatttccattttgtcgtttctgattagggaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA

Basic information

species Vitis vinifera
transcript Vv18s0001g03910.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
tcatagttgcaaacatgagaggcgtgcgtttatgacgtgattttcctataatttccattttgtcgtttctgattagggaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA
        | || ||  |    |  ||       |||  ||     |  ||   | |   ||| | ||  | || ||    |     ||    | ||||||| ||||||||||||||||||||||| || || || ||   ||||| ||  |||| ||| ||||| ||  | || |||||||| || || |  || || |
--------gtaagcactaagcaccagcaacggcaacgccatccgttt-caacgacgacgatgt-gcttacgttttggttcgtgtgcgtg----tgtgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA

upper sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os08g36480.1 (Oryza sativa), 3'ss of exon 3
tcatagttgcaaacatgagaggcgtgcgtttatgacgtgattttccta--taatttccattttgtcgtttctgattagggaaat-aataa--tggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA
                       |||| || ||  |||      || |    |   | || | | ||    ||   |    | |  ||    |||  || ||||||| ||||||||||||||||||||||  || ||    || ||||||  ||  |||| ||| ||||| ||  | || |||||||| || || |  || || |
-------------------gtaggtgc-ttcattccgtctccggccaaggcgacggcgatgtagacgacgatggcaaattcattcgatcggttgggtttttgcagGGGATGATGAACAACTGCTGGTTCAAGGTGAAGGTGAACGTGTGCCGGCCGCACAAGGGTGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCCGGGA

upper sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G02510.1 (Glycine max), 3'ss of exon 3
-------tcatagttgcaaacatgagaggcgtgcgtttatgac-gtg-attttcctataatttccattttgtcgtttctgattagggaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA
          || |||   |  |        |  |||| | |  ||| |   ||  || |   |  || |||  | | |   | || |   |||||||      || |||| |||||||| ||||||||||||||||| |||||||||||||||||||  |||| ||| |||||||| || || || ||||||||||| |  ||||| |
gcatcctctttatttgttgaatttcatttaatatgtttttaatagtgtaaagtctaatgaacccttttgtgttatcttt---ttggaatgcaataatg------tgtagGGCATGATGAATAACTGCTGGTTCAGAGTGAAAACAAATGTGTGCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAGCATCCAACCCAACCAGGCA

upper sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 3
tcatagttg-caaacatgagaggcgtgcgtttatgacgtgat-tttcctataatttccattttgtcgtttctgattagggaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA
|   | |   | |      | | | |    |     |   || ||| ||| | |  ||   ||   |  |||  ||    ||||||   | ||  | | ||||| |||||||||||||||||||||||||| ||||| |||||||||| ||  |||| ||| ||||| || || || || || || || || |  ||||| |
tagcaataaactattgcccgtgacttaaaatctaatcaaaatctttactaaagtgcccgactt--tgagtctattttattaaataagttttgacatgtacagGGCATGATGAACAACTGCTGGTTCAGAGTGAAAACCAATGTGTGCAGGCCCCACAAGGGTGAGATAGGTATAGTGTTTGAACACCCCACCCAACCAGGCA

upper sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
---tcatagttgcaaacatgagaggcgtgcgtttatg---acgtgattttcctataatttccattttgtcgtttctgattagggaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA
   |||  |   |||| |  |    |  || ||| |    | || |      | ||||      |||   |||     || || |   |||||||      || |||| ||||||||||||||||||||||| || |||||||||||   |||||  |||| ||| |||||||| || || || || || || || |  |||| ||
atttcaagggaccaaaaagtattttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttgggaatgcaataatg------tgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA

upper sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G33490.1 (Glycine max), 3'ss of exon 3
--tcatagttgcaaaca-tgagaggcgtgcgtttatgacgtgattt---tcctataatttccattttgtcgtttctgattagggaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA
  |  || ||  || |  |    |   |   | ||  || | |      ||| | ||      || |||    |    || || |   ||| |||      || |||| |||||||||||||||||||  ||||| |||||||||||| |||||| |  || ||| |||||||| ||  | || || |||||| |||  |||||||
ttttttaatttaaagcccttgttgatttttttgtaatacataaaggaagtccaacaaagctttttgtgttacattaatttgggtatgcaatgatg------tgtagGGCATGATGAACAACTGCTGGTATAGAGTGAAAACAAATGTGGGCAAGCCTGCCAAGGGTGAGATTGGCATATTGTTTGAACATCCAGCTCAACCAGGAA

upper sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
tcatagttgcaaacatgagaggcgtg-cgtttatgacgtgattttcc-tataatttccattttgtcgtttctgattagg---gaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA
  | |  |||      | |   | || ||| || || ||  |   |  |  |   |  | ||||     ||   ||  |   |   |     ||| ||  ||||||||||||||||||||||||||||| | || ||        | | ||||    |     | |  ||     | | ||||||||| || ||||  || || |
--agaactgc---tgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA

upper sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S79_76V6.2 (Physcomitrella patens), 3'ss of exon 6
------tcatagttgcaaacatgagaggcgtgcgtttatgacgtgattttcctataatttccattttgtcgtttctgattagggaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA
       |||   | |  |  |||        | |     | | |  ||       ||| | ||  |  |  |||||| |   |   |     |||  |  | ||||||||||||||||||||||||||| | || || |      |   ||||    |       |  |||    |    ||||| || || ||||  ||||| |
tgtttcgcatgcatccccagttgatcattccacatcccccaagcggattcttc---attacaataatcgctgttctgaat---gtcctcgccgtggtgtgctacagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGATCGGCATTACCAAGTCCGAAGACAACGGCATTCATCTGACGTTCGATCACCCGACTCAGCCAGGTA

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|161714940|gb|FC063600.1|FC063600
EST:     GGGATGAGACACTCAACACCCAGCCCGAGAAGCTCATCTGGAACGTCATG                         GGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGT
genomic: GGGATGAGACCCTCAACACCCAGCCCGAGAAGCTCATCTGGAACGTCATGgtatgttcta ... aattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctataatttccattttgtcgtttctgattagggaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA
                     ttctgat  putative branch site (score: 3)
                                 aaataataatggaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatagttgcaaacatgagaggcgtgcgtttatgacgtgattttcctataatttccattttgtcgtttctgattagggaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA

- - - - gcaaaca
- - - - - - - - - - -gcgtgcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaata