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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatgtgatgatattttcaatttggttctgtcaggggcatgtatcattcagagcatatcctacattcaaacgcttccctgtattggcttaattttacttcaattactgtaactgaatagcatctgtttcatttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTTAAGCCATCGAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGA

Basic information

species Vitis vinifera
transcript Vv16s0100g00650.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g00650.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os07g12250.1 (Oryza sativa), 3'ss of exon 3
gtaaaatgtgatgatattttcaatttggttctgtcaggggcatgtatcattcagagcatatcctacattcaaacgcttccctgtattggcttaattttacttcaattactgtaactgaatagcatctgtt-tcatttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTTAAGCCATCGAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGA
                                                     | |  ||   |      |        | ||| | ||   ||   ||    | ||       ||||  |   ||| |  | |  |||||||||| || || ||| | || || || |||||| | |||||||||||||| || |||||| | ||||||||||||||||||||||||||||||||||||||||
-----------------------------------------------------gtgagtactttggcaagatggatacacatgtgtaggacaaaagctaacctattt-------ctgatcaatttctttggtaaactatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTGAAGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGA

upper sequence: Vv16s0100g00650.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g59990.2 (Oryza sativa), 3'ss of exon 3
gtaaaatgtgatgatattttcaatttggttctgtcaggggcatgtatcattcagagcatatcctacattcaaacgcttccctgt-attggcttaattttacttcaattactgtaactgaatagcatctgtttcatttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTTAAGCCATCGAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGA
                                           ||| |  ||   |   ||   |  || |||  |    || | |||   |||      |||   || |    |   |||  ||  ||||   ||     ||||||||||| |||||||| || ||||||||| | |||||||||||||| || |||||  | |||||||| |||||||| |||||||| |||||||||||||
-------------------------------------------gtaaccctctttgtccattgaagtttgaaagtccaatctatgattaagttagggggtctt---ttgc----atacaatttcaagtgttctcttctg--cagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCCAAGCTTACCTGGACAGCTATGTACAGGAAGCAGCACAAGA

upper sequence: Vv16s0100g00650.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 3
gtaaaatgtgatgatattttcaatttggttctgtcaggggcatgtatcattcagagcatatcctacattcaaacgcttccctgtattggcttaattttacttcaattactgtaactgaatagcatctgtttcatttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTTAAGCCATCGAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGA
                                                  ||||    |       ||   |  ||||   |||   |   |   | | |||  |    |||     ||  | ||  || |  | ||   ||||| || || ||||| || || ||||||||| | |||||||||||||| || |||||  | |||||||| ||||||||||||||||| |||||||||||||
-------------------------------------------------gtcaggctgttcatcgaat--gattgctttaatgtcaggatatttctctgcttagaaggttgttgt--aaacgtattggtatattgta---cagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGA

upper sequence: Vv16s0100g00650.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G110328_T04 (Zea mays), 3'ss of exon 3
gtaaaatgtgatgatattttcaatttggttctgtcaggggcatgtatcattcagagcatatcctacattcaaacgcttccctgtattggcttaattttacttcaattactgtaactgaatagcatctgtttcatttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTTAAGCCATCGAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGA
                                                               |||   | | |   |   ||||   | |   |   | |  ||   ||     || | || | ||   |   || ||| ||||||| || |||||||| || ||||||||| | |||||||||||||| || |||||  | |||||||| |||||||| |||||||| |||||||||||||
-------------------------------------------------------------gttactagctatcatatttttgtaagagatgtctaagattataaaatcttcttatggaaagaaactacatatgttttat-agGTTTTCCTTTTTGCCAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCAATGTACAGGAAGCAGCACAAGA

upper sequence: Vv16s0100g00650.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G074898_T01 (Zea mays), 3'ss of exon 3
gtaaaatgtgatgatattttcaatttggttctgtcaggggcatgtatcattcagagcatatcctacattcaaacgcttccctgtattggcttaattttacttcaattactgtaactgaatagcatctgtttcatttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTTAAGCCATCGAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGA
                                              | | |    |  ||   |   |  ||  | ||     | |  |||| || |  | | |  |  ||  |  |||   |||||||||   || ||   |||||| || |||||||| || ||||||||| | |||||||||||||| || |||||  | |||||||| |||||||| |||||||| |||||||||||||
---------------------------------------------gttacttgctgt-tacattttttgtaataggtt-----tgtaagctttatatagcatgatcttatggcaaggaaatacatctgttt---ttgta---gGTTTTCCTTTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCAATGTACAGGAAGCAGCACAAGA

upper sequence: Vv16s0100g00650.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G142640_T03 (Zea mays), 3'ss of exon 2
gtaaaatgtgatgatattttcaatttggttctgtcaggggcatgtatcattcagagcatatcctacattcaaacgcttccctgtattggct-taattttacttcaattactgtaactgaatagcatctgtttcatttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTTAAGCCATCGAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGA
                                                            |    |  |   ||  ||   |        | |||  |||    || |  |     || | || |  |   |   || ||| |||| || || |||||||| || ||||||||| | |||||||||||||| || |||||  | |||||||| |||||||| |||||||| |||||||||||||
-----------------------------------------------------------gttactcgctgttacatttttataagagatttataagcttatagaaaatgtttgttatggaaagaacttacatttgttctat-agGTCTTCCTTTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCAATGTACAGGAAGCAGCACAAGA

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|71867502|gb|DT016557.1|DT016557
EST:     CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAG                         GTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT
genomic: CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAGgtaaaatgtg ... tttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT
EST: gi|110394381|gb|EC959247.1|EC959247
EST:     CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAG                         GTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT
genomic: CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAGgtaaaatgtg ... tttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT
EST: gi|110389669|gb|EC954526.1|EC954526
EST:     CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAG                         GTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT
genomic: CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAGgtaaaatgtg ... tttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT
EST: gi|351021758|gb|FQ437143.1|FQ437143
EST:     CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAG                         GTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT
genomic: CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAGgtaaaatgtg ... tttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT
EST: gi|71865895|gb|DT014950.1|DT014950
EST:     CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAG                         GTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT
genomic: CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAGgtaaaatgtg ... tttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT
EST: gi|77586726|gb|DV222495.1|DV222495
EST:     CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAG                         GTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT
genomic: CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAGgtaaaatgtg ... tttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT
EST: gi|110385691|gb|EC950237.1|EC950237
EST:     CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAG                         GTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT
genomic: CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAGgtaaaatgtg ... tttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT
EST: gi|71890456|gb|DT039511.1|DT039511
EST:     CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAG                         GTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT
genomic: CCAAGATATACCCTGGTAAGGGTATCAGATTTGTTCGGTCTGATTCCCAGgtaaaatgtg ... tttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttaattttacttcaattactgtaactgaatagcatctgtttcatttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTTAAGCCATCGAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGA
                    ctgtaac  putative branch site (score: 3)
                                        tttcattt  putative PPT
     attttacttcaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatgtgatgatattttcaatttggttctgtcaggggcatgtatcattcagagcatatcctacattcaaacgcttccctgtattggcttaattttacttcaattactgtaactgaatagcatctgtttcatttatatcagGTTTTTCTCTTTGCCAATTCTAAATGCAAGAGGTACTTCCACAACCGGCTTAAGCCATCGAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA