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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgttaaaatatctacttatacatcttatattcttatgttcctgacataaataatggatagttttgttagaccctgacttgtcataatggtgctttagGTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g00180.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 4
tgctgttaaaatatctacttatacatcttatattcttat----gttcctgacataaataatggatagttttgttagaccctgac-ttgtcataatggtgctttagGTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG
      |  |  ||  || | | ||  ||| | |   ||     |||  ||  || || ||      | ||||  |    | || ||   || |   |    ||||||||||||||||| ||||||||||| ||||| || ||||||||  | |||
----aattgagcatgaacct-tgcaatttacaataccattgcaattcaagaattatattatatgccttcttgtctgtgattcacattaatatgactattgactagGTTTGTACTGGAGCTAAGAGTGAACAACAGTCTAAATTGGCAGCAAGGAAG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G06370.1 (Glycine max), 3'ss of exon 1
tgctgttaaaatatctacttatacatcttatattcttatgttcctgacataaataatggatagttt-tg---ttagaccctgacttgtcataatggtgctttagGTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG
      |||  | |||| ||| | | |  |  |  |   || ||   | |  | | ||  |   || ||   ||  |   | | || | || |   |    ||||||||||||||||| ||||||||||| ||||| || ||||||||  | |||
---ccctaatttttcta-ttacaaaaccaaattaatacggtacccttcttgtaaagtgcttctcttatgaactttaaatttaattttttatgactattgactagGTTTGTACTGGAGCTAAGAGTGAACAACAGTCTAAATTGGCAGCAAGGAAG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 4
--tgctgttaaaatatctacttatacatcttatattcttatgttcctgacataaataatggatagttttgttagaccctgacttgtcataatggtgctttagGTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG
  ||    |      |    | ||   |||||| |  |    ||| ||  ||   |  |   | ||    ||  |   | | || | || |   |    ||||||||||||||||| ||||||||||| || || || ||||||||  | |||
tttgtctcttccgctttctgtaatggctcttatttggtacccttcttgtaatggtttctc--tcgtgaactttaaatttaattttttatgactattgactagGTTTGTACTGGAGCTAAGAGTGAACAACAATCTAAATTGGCAGCAAGGAAG

upper sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 4
tgctgttaaaatatctacttatacatcttatattcttatgttcctgacataaa----taatggata-gttttgttagaccctgacttgtcataatggtgctttagGTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG
   | | |||| |   ||| || || | | |    | |  | | ||  ||       || |   || | | | ||   |||| | ||   ||      |  |||||| |||||||||||||||||||| || ||||| || ||||| ||  | |||
---tttgaaaaaactaactgattcagcatgttgcttcacttgcttgtgatgggcttctatttcttatgctcttttcccccctaaatttaaatctcatgg--ttagGTCTGTACTGGAGCCAAGAGTGAGCAACAGTCTAAATTGGCGGCAAGGAAG

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|161713889|gb|FC062573.1|FC062573
EST:     GGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG                         GTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG
genomic: GGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATGgtaagttatg ... ggtgctttagGTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG
EST: gi|349817400|gb|FQ405404.1|FQ405404
EST:     GGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG                         GTTTGTACTGGAGCCAAGAGTGAACATCACTCCTAGTTGGCAGCTCGAAAG
genomic: GGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATGgtaagttatg ... ggtgctttagGTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG
EST: gi|110721938|gb|EE097741.1|EE097741
EST:     GGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG                         GTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG
genomic: GGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATGgtaagttatg ... ggtgctttagGTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG
EST: gi|71881466|gb|DT030521.1|DT030521
EST:     GGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG                         GTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG
genomic: GGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATGgtaagttatg ... ggtgctttagGTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG
EST: gi|110724394|gb|EE100183.1|EE100183
EST:     GGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG                         GTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG
genomic: GGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATGgtaagttatg ... ggtgctttagGTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG
EST: gi|71881168|gb|DT030223.1|DT030223
EST:     GGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG                         GTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG
genomic: GGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATGgtaagttatg ... ggtgctttagGTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacataaataatggatagttttgttagaccctgacttgtcataatggtgctttagGTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG
     aaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgttaaaatatctacttatacatcttatattcttatgttcctgacataaataatggatagttttgttagaccctgacttgtcataatggtgctttagGTTTGTACTGGAGCCAAGAGTGAACATCAGTCCAAGTTGGCAGCTCGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
tgctgtt
- - - -aaaatat
- - - - - - - - - - - - - - - - - - - - - cctgaca
- - - - - - - - - - - - - - - - - - - - - - - - - aaataat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctgac