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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggtctgtgacatattaatcctgaacaaactaccttgtacttcatgccctaatatcaaatggagcctaataacaacccaggttcattcatcaatgtgcagGTTGAAGTTTTCCATCTCAAACAAAGGTTGCAGTCCATGGAGAATCGAGCGCCAACTCCCAGGAAACCTTTCCACGTGTAGTAGTATCAAGAAACATTTT

Basic information

species Vitis vinifera
transcript Vv05s0020g01740.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01740.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os12g35350.1 (Oryza sativa), 3'ss of exon 16
--cggtctgtgacatattaat---cctgaacaaactaccttgtacttcatgccctaatatcaaatggagcctaataacaacccaggttcattcatcaatgtgcagGTTGAAGTTTTCCATCTCAAACAAAGGTTGCAGTCCATGGAGAATCGAGCGCCAACTCCCAGGAAACCT----TTCCACGTGTAGTA-GTATCAAGAAACATTTT
     |   || ||  | | |   | | | ||    |  || |  |||||||    |   |||    |  |   | |||  |     || | | |  ||   ||||||||||| ||||||||||||||| ||||||||   |||||     |||||  ||| || | ||| |||    ||  |    ||||| | | |||  | ||    
aataattactggcacttaagttttcttcatcagcacaaattattgttcatgcatgcaacacaagaaaactcacctgacattctga--tcgtgctttgat---cagGTTGAAGTGTTCCATCTCAAACAACGGTTGCAG---ATGGAAGGAAGAGCGGGAACGCCAAAGAACCCTCCTGTTTAATCCATAGTAAGCAACAAAGAGCAAA--

upper sequence: Vv05s0020g01740.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os12g35350.2 (Oryza sativa), 3'ss of exon 16
--cggtctgtgacatattaat---cctgaacaaactaccttgtacttcatgccctaatatcaaatggagcctaataacaacccaggttcattcatcaatgtgcagGTTGAAGTTTTCCATCTCAAACAAAGGTTGCAGTCCATGGAGAATCGAGCGCCAACTCCCAGGAAACCTTTCCACGTGTAGTAGTATCAAGAAACATTTT
     |   || ||  | | |   | | | ||    |  || |  |||||||    |   |||    |  |   | |||  |     || | | |  ||   ||||||||||| ||||||||||||||| ||||||||   |||||     |||||  ||| || | ||| || | |    |  |    ||              
aataattactggcacttaagttttcttcatcagcacaaattattgttcatgcatgcaacacaagaaaactcacctgacattctga--tcgtgctttgat---cagGTTGAAGTGTTCCATCTCAAACAACGGTTGCAG---ATGGAAGGAAGAGCGGGAACGCCAAAGAA-CCCTCCTGTTTA-ATCCATA--------------

upper sequence: Vv05s0020g01740.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA13G28760.1 (Glycine max), 3'ss of exon 15
---------cggtctgtgacatattaatcctg-aacaaactaccttgtacttcatgccctaatatcaaatggagcctaataacaacccaggttcattcatcaatgtgcagGTTGAAGTTTTCCATCTCAAACAAAGGTTGCAGTCCATGGAGAATCGAGCGCCAACTCCCAGGAAACCTTTCCACGTGTAGTAGTATCAAGAAACATTTT
         || | |||| |   || ||  ||  | |||||   |  |   | |||  || |     ||       |  |  || |     ||  |   |   |    ||||||||||||||||||||||||| ||  | || || ||||| |||||||  || ||||||||||||||||| || |||||||  | | ||    ||  | 
gtttccactcgttgtgtgtcccgttcattatgtgataaactga-taatggctaatgttcttactcttaaca-----tgttgccatct----tttttgggtgcttacatagGTTGAAGTTTTCCATCTCAAACAGAGACTTCAATCAATGGAAAATCGAGTCCCTACTCCCAGGAAACCTTTTCAAGTGTAGTGTTTTGAAATGTCAAATA

upper sequence: Vv05s0020g01740.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA15G10310.2 (Glycine max), 3'ss of exon 9
cggtctgtgacatattaatcctgaacaaactaccttgtacttcatgccctaatatcaaatggagcctaataacaacc-caggtt--cat---tcatcaatgtgcagGTTGAAGTTTTCCATCTCAAACAAAGGTTGCAGTCCATGGAGAATCGAGCGCCAACTCCCAGGAAACCTTTCCACGTGTAGTAGTATCAAGAAACATTTT
         |  | |  |  |||      |       ||  | ||   || |||     |  |   |  | ||     || |||  |||   |  |   ||   ||||||||||||| ||||||||||| ||  | || || ||||| || ||||| || ||||||||||||||||| || |||||||  | | ||    || |  
------aatatgtttccactctgtgtgtcccgttcgttatgtgataaactgataatggttttaatgttcttactcttacatgttgccatgttttttgggtgcatagGTTGAAGTTTTTCATCTCAAACAGAGACTTCAATCAATGGAAAAACGAGCCCCTACTCCCAGGAAACCTTTTCAAGTGTAGTGTTTTGAAAGGCCAATGA

upper sequence: Vv05s0020g01740.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA07G38020.1 (Glycine max), 3'ss of exon 15
-----cggtctgtgacatattaatcctgaacaaactaccttgtacttcatgccctaatatcaaatggagcctaataacaacccaggttcattc-atcaatgtgcagGTTGAAGTTTTCCATCTCAAACAAAGGTTGCAGTCCATGGAGAATCGAGCGCCAACTCCCAGGAAACCTTTCCACGTGTAGTAGTATCAAGAAACATTTT---------------------------------------------------
        |  |      | | |||    |  |  |   || ||  |||  ||| | |||   |||    | | | |  | | |  ||||||| |||| ||| |    | |  || ||  | ||      |  ||  | |   | ||   | || ||     |      | || ||     |||| |||   |   |||   |||                                                    
gtacatatttggcttttaactgatctaacattatttgttttatatgtcaaacccca-tatatgatgtttac-atttatgatcta--ttcattcgatcattgttcctacttatcttatctgtgtccggttca--ttataatattttgaccgtagATCGTTGGATTTTGTCATACTTT---GGGTGTTGTACAGTTT-GAAGTTTTTCATCTCAAACAAAGATTGCAGTCAATGGAAAAAAATCGAGCATCTACTACTC

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|37188410|gb|CF607759.1|CF607759
EST:     CAACTAGAGGAGTGCTTGCAGGAGAGAGGGCAAGAGCATTCCAACTGCAG                         GTTGAAGTTTTCCATCTCAAACAAAGGTTGCAGTCCATGGAGAATCGAGCG
genomic: CAACTAGAGGAGTGCTTGCAGGAGAGAGGGCAAGAGCATTCCAACTGCAGgtatggtttt ... caatgtgcagGTTGAAGTTTTCCATCTCAAACAAAGGTTGCAGTCCATGGAGAATCGAGCG
EST: gi|110389348|gb|EC954177.1|EC954177
EST:     CAACTAGAGGAGTGCTTGCAGGAGAGAGGGCAAGAGCATTCCAACTGCAG                         GTTGAAGTTTTCCATCTCAAACAAAGGTTGCAGTCCATGGAGAATCGAGCG
genomic: CAACTAGAGGAGTGCTTGCAGGAGAGAGGGCAAGAGCATTCCAACTGCAGgtatggtttt ... caatgtgcagGTTGAAGTTTTCCATCTCAAACAAAGGTTGCAGTCCATGGAGAATCGAGCG
EST: gi|110698486|gb|EE076040.1|EE076040
EST:     CAACTANAGGAGTGCTTGCANGAGAGAGGGCAAGAGCATTCCAACTGCAA                         GTTGAAGTTTTC-ATCTCAA-CAAAGGTTGCAGTCCAGGGAGAATCGAGCG
genomic: CAACTAGAGGAGTGCTTGCAGGAGAGAGGGCAAGAGCATTCCAACTGCAGgtatggtttt ... caatgtgcagGTTGAAGTTTTCCATCTCAAACAAAGGTTGCAGTCCATGGAGAATCGAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccctaatatcaaatggagcctaataacaacccaggttcattcatcaatgtgcagGTTGAAGTTTTCCATCTCAAACAAAGGTTGCAGTCCATGGAGAATCGAGCGCCAACTCCCAGGAAACCTTTCCACGTGTAGTAGTATCAAGAAACATTTT
                     taataac  putative branch site (score: 1)
     aatatcaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cggtctgtgacatattaatcctgaacaaactaccttgtacttcatgccctaatatcaaatggagcctaataacaacccaggttcattcatcaatgtgcagGTTGAAGTTTTCCATCTCAAACAAAGGTTGCAGTCCATGGAGAATCGAGCGCCAACTCCCAGGAAACCTTTCCACGTGTAGTAGTATCAAGAAACATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - gaacaaa
- - - - - - - - - - - - - - - taccttg
- - - - - - - - - - - - - - - - - - - - -tcatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - -atcaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaccca