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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacaacattttgggctggctgacttgagtctctttatttttaggaaataaaaacaatgtaaagcataaaccattctgataattgttatcaagtcttgcagTGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTGCCTAAACCGGGAATTCGAACGAAAGGCTCCTTGTGTTTCTGCCATGGAT

Basic information

species Vitis vinifera
transcript Vv01s0011g03620.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g03620.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G25020.2 (Glycine max), 3'ss of exon 1
-tacaacattttgggctggc---tgacttgagtctctttatttttaggaaataaaaacaatgtaaagcata-aaccattctgataattgttatcaagtcttgcagTGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTGCCTAAACCGGGAATTCGAACGAAAGGCTCCTTGTGTTTCTGCCATGGAT
  | | |   |  ||||  |   ||  ||    | | | || |||      |        ||  ||  |||  |  | | || | ||| || | || |     || ||||||||| |||||| ||||| |||||||||||| ||||| ||||| ||||| || ||||  | | |   || |   | ||||||||||||||||| |
tcatacccgatgtggctcacacttgtatttcaacacatgatatttttcttttcttggttttgcgaaaaatatgatgaatttggttatttttgttaatt-----agGGGTATGAAAGGAATTCCAGGGGATTGGAAATTTTCTGCAAAAGCTGGATGCCTGAATCGGGCGTCCCACTCAAGGCTGCTTTGTGTTTCTGCCATGGTT

upper sequence: Vv01s0011g03620.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G19820.1 (Glycine max), 3'ss of exon 2
-------------------tacaacattttgggctg-gctga----cttgagtctctttatttt---taggaaataaaaacaatgtaaagcataaaccattctgataattgttatcaagtcttgcagTGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTGCCTAAACCGGGAATTCGAACGAAAGGCTCCTTGTGTTTCTGCCATGGAT
                      |  || | ||  || | |||    ||  ||| | |||| |||   |||    | |      || |||| ||||   ||| | ||| || ||  ||| |     ||||||| |||| |||||| ||||| |||||||||||| ||||| ||||| |||| || || || |||| ||  || | |||  |||||||||| |||||||
gtaagattttctgctttaccttattatctgggagtgtgttgatgttctgaagtttttttactttgactagtttgttaccttggtgcaaagtataatttatttt-atattttttgacaact-----agTGGTACGAAAGGAATTCTAGGGGATTGGAAATTTTCTGCAAAAGCTGGATGCCAAAGCCTGGCATTCCAATCAAGGCCTCTGTGTGTTTCTGTCATGGAT
















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|71864904|gb|DT013959.1|DT013959
EST:     ATCGCTCCTACTGGGATCAGAACTGAGGAG                         TGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
genomic: ATCGCTCCTACTGGGATCAGAACTGAGGAGgtaagcaatg ... agtcttgcagTGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
EST: gi|71870300|gb|DT019355.1|DT019355
EST:     ATCGCTCCTACTGGGATCAGAACTGAGGAG                         TGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
genomic: ATCGCTCCTACTGGGATCAGAACTGAGGAGgtaagcaatg ... agtcttgcagTGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
EST: gi|71863380|gb|DT012435.1|DT012435
EST:     ATCGCTCCTACTGGGATCAGAACTGAGGAG                         TGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
genomic: ATCGCTCCTACTGGGATCAGAACTGAGGAGgtaagcaatg ... agtcttgcagTGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
EST: gi|71863974|gb|DT013029.1|DT013029
EST:     ATCGCTCCTACTGGGATCAGAACTGAGGAG                         TGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
genomic: ATCGCTCCTACTGGGATCAGAACTGAGGAGgtaagcaatg ... agtcttgcagTGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
EST: gi|71866817|gb|DT015872.1|DT015872
EST:     ATCGCTCCTACTGGGATCAGAACTGAGGAG                         TGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
genomic: ATCGCTCCTACTGGGATCAGAACTGAGGAGgtaagcaatg ... agtcttgcagTGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
EST: gi|71861822|gb|DT010877.1|DT010877
EST:     ATCGCTCCTACTGGGATCAGAACTGAGGAG                         TGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
genomic: ATCGCTCCTACTGGGATCAGAACTGAGGAGgtaagcaatg ... agtcttgcagTGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
EST: gi|71861840|gb|DT010895.1|DT010895
EST:     ATCGCTCCTACTGGGATCAGAACTGAGGAG                         TGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
genomic: ATCGCTCCTACTGGGATCAGAACTGAGGAGgtaagcaatg ... agtcttgcagTGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
EST: gi|161707839|gb|FC055239.1|FC055239
EST:     ATCGCTCCTACTGGGATCAGAACTGAGGAG                         TGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
genomic: ATCGCTCCTACTGGGATCAGAACTGAGGAGgtaagcaatg ... agtcttgcagTGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
EST: gi|71863921|gb|DT012976.1|DT012976
EST:     ATCGCTCCTACTGGGATCAGAACTGAGGAG                         TGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG
genomic: ATCGCTCCTACTGGGATCAGAACTGAGGAGgtaagcaatg ... agtcttgcagTGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataaaaacaatgtaaagcataaaccattctgataattgttatcaagtcttgcagTGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTGCCTAAACCGGGAATTCGAACGAAAGGCTCCTTGTGTTTCTGCCATGGAT
                           ttctgat  putative branch site (score: 3)
                                ataattgttatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacaacattttgggctggctgacttgagtctctttatttttaggaaataaaaacaatgtaaagcataaaccattctgataattgttatcaagtcttgcagTGGTATGAAAAGAATTCAAGGGGCTTGGAAATTTTCAGCAAATGCTGGTTGCCTAAACCGGGAATTCGAACGAAAGGCTCCTTGTGTTTCTGCCATGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - ggctggc
- - - - - - - - - -tgacttg
- - - - - - - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -caatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagcataa