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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccctaccacaggctttttctcttacacttgcacacacatagcttctgctcctctttcttttgaaaattcaggaatgacattgtctttttttatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACATAGAGCTGCAGTTTGCAACCAACCATTTAG

Basic information

species Vitis vinifera
transcript Vv02s0025g03380.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g03380.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G01870.1 (Glycine max), 3'ss of exon 1
ccctaccacaggctttttctctt-acacttgcacacacatagcttctgctcctctttcttttgaaaattcaggaatgacattgtctttttttatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACATAGAGCTGCAGTTTGCAACCAACCATTTAG
  ||      ||| | ||   |  | |    | |     |    | || |  |    | ||||||  |  | |||  | ||  ||||| |||  || ||||||||||||||||||| ||||| |||||||||  ||||||||| ||||| || ||  ||||||| |||||||| |||||||
aactcttgttggcatattgcatggaaagaaactcctctgtttaatgtgttgattgcacatttgaagttgaaagaaata-atattctttctttcctttgaagTAACAATGCAGGGGTGATGGCAACTCCATTCACGCTTTCCCAAGACAATATTGAATTGCAGTTCGCAACCAATCATTTAG

upper sequence: Vv02s0025g03380.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G37720.1 (Glycine max), 3'ss of exon 2
----ccctaccacaggctttttctcttacacttgcacacacatagcttctgctcctctttcttttgaaaattcaggaatgacattgtctttttttatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACATAGAGCTGCAGTTTGCAACCAACCATTTAG
        |   |||  ||  ||  ||  | ||| | ||| |||   |   |   |  || |||||||| || |   |    ||  ||||| |||  || ||||||||||||||||||| ||||| |||||||||   |||||||| ||||| || ||  ||||||| |||||||| |||||||
atgtgttgattgcaga-ttcctcatttgaagttgaa-acaaataatatt--ccttttctttttttgaaagttgaaagaaataatactctttctttcctttgaagTAACAATGCAGGGGTGATGGCGACTCCATTCACACTTTCCCAAGACAATATTGAATTGCAGTTCGCAACCAATCATTTAG
















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|110369965|gb|EC934139.1|EC934139
EST:     AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCAT                         TAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
genomic: AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCATgtatgaaaac ... tatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
EST: gi|161715967|gb|FC068756.1|FC068756
EST:     AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCAT                         TAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
genomic: AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCATgtatgaaaac ... tatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
EST: gi|110373040|gb|EC937247.1|EC937247
EST:     AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCAT                         TAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
genomic: AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCATgtatgaaaac ... tatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
EST: gi|71857391|gb|DT006446.1|DT006446
EST:     AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCAT                         TAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
genomic: AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCATgtatgaaaac ... tatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
EST: gi|110395392|gb|EC961055.1|EC961055
EST:     AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCAT                         TAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
genomic: AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCATgtatgaaaac ... tatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
EST: gi|110394584|gb|EC959749.1|EC959749
EST:     AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCAT                         TAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
genomic: AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCATgtatgaaaac ... tatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
EST: gi|71868300|gb|DT017355.1|DT017355
EST:     AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCAT                         TAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
genomic: AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCATgtatgaaaac ... tatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
EST: gi|110361021|gb|EC924471.1|EC924471
EST:     AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCGTGAACCTTCTCAT                         TAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
genomic: AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCATgtatgaaaac ... tatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
EST: gi|110417605|gb|EC983675.1|EC983675
EST:     AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCAT                         TAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
genomic: AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCATgtatgaaaac ... tatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
EST: gi|110712661|gb|EE087900.1|EE087900
EST:     AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCAT                         TAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
genomic: AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCATgtatgaaaac ... tatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
EST: gi|161706209|gb|FC055419.1|FC055419
EST:     AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCAT                         TAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT
genomic: AAATTTGCATCTGAATATAAGTCCTTGGGTCTTCCCCTGAACCTTCTCATgtatgaaaac ... tatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctcctctttcttttgaaaattcaggaatgacattgtctttttttatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACATAGAGCTGCAGTTTGCAACCAACCATTTAG
                                  ttgtctttttttattt  CT-rich tract
                                 attgtctttttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccctaccacaggctttttctcttacacttgcacacacatagcttctgctcctctttcttttgaaaattcaggaatgacattgtctttttttatttggaagTAACAATGCAGGGGTTATGGCCACTCCATTCCTGCTTTCCCATGACAACATAGAGCTGCAGTTTGCAACCAACCATTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
ccctacc
- - - - - - - - - - - - cacttgc
- - - - - - - - - - - - - - - -acacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattgtc