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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatctgcttgcttaatatcttgttacagtgaatggtacttattctgactgaacctacttataaaaaaaaaaccttattctgaccgaacctatcatgctgcatgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCCTCTGCTCAACCAGTTACCAAGTTGGAATTTGAATTTGAGAGGAGAAGGA

Basic information

species Vitis vinifera
transcript Vv05s0020g02530.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 5
gtactatctgcttgcttaatatcttgttacagtgaatggtacttattctgactgaacctacttataaaaaaaaaaccttattctgaccgaacctatcatgctgcatgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCCTCTGCTCAACCAGTTACCAAGTTGGAATTTGAATTTGAGAGGAGAAGGA
                                |||||     |   ||||     | |||   | | |    |    |||   | |  |    |||  |||   || |  | ||||||| ||| |||||||||||||||| || |||||||||||||||||||| |||||||| |||||||||||| ||||||||||||| |||||  | ||||
------------------------------gttgaatttccatccatctgctgttaactatccacacatcgca---tttagctttaatgggaatattgtgcatgatataattagGCTCTAGCATATCCATATTTTAAAGGCTTGGCCAAGGTTGAGAGAGAACCTTCTGCTCAGCCAGTTACCAAGATGGAATTTGAATTCGAGAGACGTAGGA

upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G10940.3 (Glycine max), 3'ss of exon 6
gtactatctgcttgcttaatatcttgttacagtgaatggtacttattctgactgaacctacttataaaaaaaaaaccttattctgaccgaacctatcatgctgcatgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCCTCTGCTCAACCAGTTACCAAGTTGGAATTTGAATTTGAGAGGAGAAGGA
                         |||| |     || |    || ||  |||    |   | |       | | ||  ||   |  |    |    ||    ||  | | ||||||| || ||||||||||||||||| || || ||||||||||||||||| |||||||| |||||||||||| |||| ||||||||||||||  |  |||
-------------------------gttagatct--tgatgtccat-ctatctgttgttcactttctctgttacatctggtt--aataggttatcgtgtgtataataatgttagGCTCTAGCGGATCCATATTTTAAAGGCTTGGCAAAGGTTGAGAGAGAACCATCTGCTCAGCCAGTTACCAAGATGGAGTTTGAATTTGAGAGACGCCGGA

upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G28120.2 (Glycine max), 3'ss of exon 6
gtactatctgcttgcttaatatcttgttacagtgaatggtacttattctgactgaacctacttataaaaaaaaaaccttattctgaccgaacctatcatgctgcatgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCCTCTGCTCAACCAGTTACCAAGTTGGAATTTGAATTTGAGAGGAGAAGGA
                         |||| |     || |    || ||  ||| |  |     |       | | ||  || | |  |    |    ||    ||  | ||||||||| || |||||||||||||||||  | |||||||||||||||||||| |||||||| |||||||| ||| |||| ||||||||||||||  |  |||
-------------------------gttagatct--tgatgtccat-ctatctgtagttcacattctctgttatatctggttatta--ggttatcatgtgtataataatgtcagGCTCTAGCGGATCCATATTTTAAAGGCCTGGCCAAGGTTGAGAGAGAACCATCTGCTCAGCCAGTTACTAAGATGGAGTTTGAATTTGAGAGACGCCGGA

upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G02220.1 (Glycine max), 3'ss of exon 6
gtactatctgcttgcttaatatcttgttacagtgaatggtacttattctgactgaacctacttataaaaaaaaaaccttattctgaccgaacctatcatgctgcatgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCCTCTGCTCAACCAGTTACCAAGTTGGAATTTGAATTTGAGAGGAGAAGGA
                                |||||     |   ||||     |   ||||   | | |  |   ||| | | |  |    |||  ||    || |  | ||||||| |||||| | ||||||||||| || ||||||||||||||||| || ||||| || |||||||||||| | ||||||||||| |||||    ||||
------------------------------gttgaatttccatccatctgct---attgactttccacacatcatgtttagttttaatgggaatattgtgtatgatataattagGCTCTAGCAGATTCTTATTTTAAAGGCTTGGCCAAGGTTGAGAGAGAGCCTTCTGCCCAGCCAGTTACCAAGATAGAATTTGAATTCGAGAGACATAGGA

upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 6
gtactatctgcttgcttaatatcttgttacagtgaatggtacttattctgactgaacctacttataaaaaaaaaaccttattctgaccgaacctatcatgctgcatgtt--ttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCCTCTGCTCAACCAGTTACCAAGTTGGAATTTGAATTTGAGAGGAGAAGGA
                               |||  |  ||| | |  |   | |  || ||||| |   ||     |  || |  |  |    ||  |  |   ||||   |||||| |||||||||   || || || |||||||| |||||||| ||||| || ||||||||||| || || |||||||||||||| ||||| ||| | ||||
-------------------------------gtggttcatacatttcgttctttacactccttatgatgtaac--tttggttatagctaactaaatggttttatgtgttacctcagGCGCTTGCAGATGTGTACTTCAAGGGTTTAGCTAAGGTTGAAAGAGAGCCTTCTGCTCAACCTGTCACAAAGTTGGAATTTGAGTTTGAAAGGCGGAGGA

upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------gtac-tatctgcttgctt---aatatcttgttacagtga-----atggtacttattctgactgaa--cctacttataaaa--aaaaaaccttattctg-accgaacctatcatgctgcatgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCCTCTGCTCAACCAGTTACCAAGTTGGAATTTGAATTTGAGAGGAGAAGGA
                                          | | | | ||   | ||   ||  |||| | | |||        |  | |||| |   ||||||  ||| ||| |  |   | || |  |   | || | | || ||||  || ||  |||    ||||| | |||||||| ||||| |||||||| || || || || || |||||||||||||||||| |||| ||  |||| ||||| ||||| || || || |
gtacctcatggattgtacaacatgggatcgaatacagttaaatgcatgtttggacgattttgaagttcttttcaaagtcttttctgttattcttaatggaactgaattccttcttttgtagtcataatatgtcgctttgtatctaaactatattgatgggtgt----agGCTTTGGCAGATCCTTATTTCAAAGGTTTGGCAAAAGTGGATAGGGAACCCTCTGCTCAACCAATTACGAAAATGGAGTTTGAGTTTGAAAGAAGGAGAA

upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S80_71V6.2 (Physcomitrella patens), 3'ss of exon 6
-----------------gtactatctgctt---gcttaatatcttgttacagtgaatggta----cttattctgactgaaccta-------cttataaaaaaaaaaccttattctg-accgaacctatcatgctgcatgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCCTCTGCTCAACCAGTTACCAAGTTGGAATTTGAATTTGAGAGGAGAAGGA
                  |   || | |||   |     ||| ||||    ||  | |        ||  ||||   | | | |       |||  |    || ||  || |  || | | || ||||   | ||  |||    ||||  | |||||||| ||||| || ||||| || || || || || ||||| |||||||||||| |||| ||  ||||||| || |||||||||||||| |
gtaatccgcggtaactaatgtaatttacttcaggtgctttattttgtagtggttcacgtagatcttttgctctggacggaacaagtcctctcttgcatttgaacaatgttttaatgtatcaaaactatgtcgttgggtgt----agGCATTAGCAGATCCTTATTTCAAGGGTTTGGCGAAAGTGGATAGGGAACCTTCTGCTCAACCAATTACGAAAATGGAATTCGAGTTTGAGAGGAGAAGAA

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|71863134|gb|DT012189.1|DT012189
EST:     TGGAAAGAATGCTAGCATTTGAACCCAAGGATCGACCTTCCGCTGAAGAG                         GCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCC
genomic: TGGAAAGAATGCTAGCATTTGAACCCAAGGACCGACCTTCCGCTGAAGAGgtactatctg ... atgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCC
EST: gi|110690752|gb|EE068184.1|EE068184
EST:     TGGAAAGAATGCTAGCATTTGAACCCAAGGATCGACCTTCCGCTGAAGAG                         GCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCC
genomic: TGGAAAGAATGCTAGCATTTGAACCCAAGGACCGACCTTCCGCTGAAGAGgtactatctg ... atgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCC
EST: gi|161719505|gb|FC067398.1|FC067398
EST:     TGGAAAGAATGCTAGCATTTGAACCCAAGGATCGACCTTCCGCTGAAGAG                         GCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCC
genomic: TGGAAAGAATGCTAGCATTTGAACCCAAGGACCGACCTTCCGCTGAAGAGgtactatctg ... atgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCC
EST: gi|71860512|gb|DT009567.1|DT009567
EST:     TGGAAAGAATGCTAGCATTTGAACCCAAGGATCGACCTTCCGCTGAAGAG                         GCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCC
genomic: TGGAAAGAATGCTAGCATTTGAACCCAAGGACCGACCTTCCGCTGAAGAGgtactatctg ... atgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCC
EST: gi|37188545|gb|CF607894.1|CF607894
EST:     TGGAAAGAATGCTAGCATTTGAACCCAAGGATCGACCTTCCGCTGAAGAG                         GCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGCTGAGAGAGAACCC
genomic: TGGAAAGAATGCTAGCATTTGAACCCAAGGACCGACCTTCCGCTGAAGAGgtactatctg ... atgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCC
EST: gi|110730439|gb|EE107523.1|EE107523
EST:     TGGAAAGAATGCTAGCATTTGAACCCAAGGACCGACCTTCCGCTGAAGAG                         GCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCC
genomic: TGGAAAGAATGCTAGCATTTGAACCCAAGGACCGACCTTCCGCTGAAGAGgtactatctg ... atgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttataaaaaaaaaaccttattctgaccgaacctatcatgctgcatgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCCTCTGCTCAACCAGTTACCAAGTTGGAATTTGAATTTGAGAGGAGAAGGA
                     ttctgac  putative branch site (score: 2)
                                              tgttttc  putative PPT
     taaaaaaaaaacctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactatctgcttgcttaatatcttgttacagtgaatggtacttattctgactgaacctacttataaaaaaaaaaccttattctgaccgaacctatcatgctgcatgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCCTCTGCTCAACCAGTTACCAAGTTGGAATTTGAATTTGAGAGGAGAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA