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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgtcagtaccattcttgcgattgtaaattgtaatatgcttatgtgcattccattccctgcctactggtagtctgatttgtagttgtgttttgttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACCCAAAATATTGATGACAGGGAAATGGAATGAGTCAATGAGTTACCAACCA

Basic information

species Vitis vinifera
transcript Vv06s0004g04930.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 7
gttgtcagtaccattcttgcgattgtaaattgtaatatgcttatgtgcattccattccctgcctactggtagtctgatttgtag--ttgtgttttgttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACCCAAAATATTGATGACAGGGAAATGGAATGAGTCAATGAGTTACCAACCA
  |   | ||    | ||   ||         |    |   || ||| || | |  |  |   | |     |  | |||| |    ||    ||  ||||||||||||||| ||||| |||||||| |||||||||| ||| |  || |||||||||||| |||| || || || |||||  |||| |||||||  || |||
-attcaaatatatatttttttatctcttgcctttgcctttgta-gtgtatccaaagctttaagttcataatgcttaatttctgagtttactcttcattgtagGGCTGGTCGGTACGAGGTGGATGGCTATGTGTATAGTGCAGCTGAAGAACCCAAAATAATGATAACTGGAAAGTGGAACCAGTCCATGAGTTGTCAGCCA

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 7
-----------------------------------------------gttgtcagtaccattcttgcgattgtaaattgt--aatatgcttatgtgcattccattcc-----ctgcctactggt------agtctgatttgtagttgtgttttgttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACCCAAAATATTGATGACAGGGAAATGGAATGAGTCAATGAGTTACCAACCA
                                                 | ||||||| ||   |  | ||   | |||    |   | |       |||| ||||       || ||  | ||      |||| | |||||| |||  ||   ||  |||||||| || || || || ||||| |||||||| | ||| | ||| |||||||||||| |||| ||||||||||||||  ||||| |||| | |||||||
gtatgatatttggccatcaatttattcttgcatttgttgactttttcagtttcagtactatatatttgcttactatttgctggaagcgttggcagttattcaattctttttattgtcttatagttcgctcagtccggtttgta-ttgc-ttacatttcagGGCTGGCCGGTATGAGGTAGATGGGTATGTGTACAGTGCAGCGGAAGAACCCAAAATAATGATTACAGGGAAATGGAACAAGTCACTGAGCTGCCAACCA

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 7
-gttgt-cagtaccattcttgcgattgtaaattgtaatatgcttatgtgcattccattccctgcctactgg--tagtctgatttgtagttgtgttt-tgttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACCCAAAATATTGATGACAGGGAAATGGAATGAGTCAATGAGTTACCAACCA
 ||||| ||||   | |      ||| ||  ||||  |||  || | | || |||| |   |      | |  ||| ||  | |  | ||    |    ||  |||||||| || ||||| |||||||| |||||||| | ||| | ||| |||||||||||  |||| |||||||| |||||  ||||  |||||| |||||||
ggttgtgcagt--taattcaaaaatttta--ttgtcttatagttctct-cagtccagtgtttattgctttgtctaggcttgtctcaatttaccctaacatttcagGGCTGGCCGTTACGAGGTGGATGGGTATGTGTACAGTGCAGCGGAAGAACCCAAAATCATGATTACAGGGAAGTGGAACAAGTCCCTGAGTTGCCAACCA

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 7
gttgtcagtaccattcttgcgattgtaaattgtaatatgcttatgtgcattccattccctgccta---ctggtagtctgatttgtagttgtgttttg-----ttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACCCAAAATATTGATGACAGGGAAATGGAATGAGTCAATGAGTTACCAACCA
        |   || ||| | |||    |||   || |  |||       |||||||      ||       || |  | ||| |   ||| |  ||     ||| |||||||||||||| ||||| ||||||||||| |||||| |||  ||||| || |||||||||||||| ||||| |||||||||||||||||||| ||||| 
--------ttaaatcctttccatttatgatttctatttctttaatctttctccattcaaatattagattctttaattagctttttgcgtgtttcctgatatcttgcagGGCTGGTCGCTATGAAGTAGATGGATATGTTTATAATTCTGCTGAGGAGCCTAAAATATTGATGACTGGGAAGTGGAATGAGTCAATGAGTTATCAACCT

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 7
gttgtcagtaccattcttgcgattgtaaattgta-atatgcttatgtgcattccattccctgcctactggt-agtctgatttgtagttgtgttttgttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACCCAAAATATTGATGACAGGGAAATGGAATGAGTCAATGAGTTACCAACCA
 |  |     || ||||      |||   ||  | || |   |||   || |  ||      |||     |  |    |||| |  |  || | |||||||| |||||||| || ||||||||||||||| | |||||| ||   ||||| || |||||||| ||||||||||| |||||||||||||||||||| ||||| 
-tctttctcccctttctccatcctgttttttagatatctaactattgtcaatatatctataacctttaatttggatctatttatt-tcctgatctgttgtagTGCTGGTCGATATGAAGTGGATGGATATATTTATAATTCTTCAGAGGAGCCTAAAATATTAATGACAGGGAAGTGGAATGAGTCAATGAGTTATCAACCC

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 7
gttgtcagtaccattcttgcgattgtaaattgtaatatgcttatgtgcattccattccctgcctactggtagt-ctgatttgtagttgtgttttgttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACCCAAAATATTGATGACAGGGAAATGGAATGAGTCAATGAGTTACCAACCA
  | |   | || ||  | |  |      ||   ||||  |  | |       ||  |   |||     |||  |  |||| |  |  || | |||||||| |||||||| || ||||||||||||||| | |||||| ||   ||||| || |||||||| ||||||||||| |||||||||||||||||||| || || 
catttttctcccctttatccattcagctttttagatatcttactattgtcaatatatctaacctttaattaggacctatttatt-tcctgatctgttgtagTGCTGGTCGATATGAAGTGGATGGATATATTTATAATTCTTCCGAGGAGCCTAAAATATTAATGACAGGGAAGTGGAATGAGTCAATGAGTTATCAGCCC

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 7
---gttgtcagtacca---ttcttgcgattgtaaattg-taatatgcttatgt------gcattccattccctgcctactggtagtctgatttgtagttgtgttttgttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACCCAAAATATTGATGACAGGGAAATGGAATGAGTCAATGAGTTACCAACCA
    ||| ||  ||     ||| |   |||||  |||| || | || | || |      |  ||  | ||||    | ||  ||   |||  | | | |    ||  | | ||  |||| ||||| ||||| ||||| || || || |  || |  || ||||| |||||  |||||||||| ||||||||||||  |||||| |||||||| 
gtaattgacaagacattgcttcatcttattgttcattgatactctgttcattttgtctcgtcttgtaatcccgatatgctattaaattgaaattt-gctac-cttgatcgcagTTCTGGCCGCTATGAAGTTGATGGCTACGTTTACAGCGCAGCTGAAGAACCGAAAATCATGATGACAGGAAAATGGAATGAGAAAATGAGCTACCAACCT

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|33405066|gb|CF210693.1|CF210693
EST:     ACAACCGGGGACAAGGCTGTGCTATATTTTCAACCATGTGGCTGGTTTGG                         GGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACC
genomic: ACAACCGGGGACAAGGCTGTGCTATATTTTCAACCATGTGGCTGGTTTGGgtatgtcaaa ... tttgttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACC
EST: gi|110688435|gb|EE066987.1|EE066987
EST:     ACAACCGGGGACAAGGCTGTGCTATATTTTCAACCATGTGGCTGGTTTGG                         GGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACC
genomic: ACAACCGGGGACAAGGCTGTGCTATATTTTCAACCATGTGGCTGGTTTGGgtatgtcaaa ... tttgttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACC
EST: gi|110378376|gb|EC943506.1|EC943506
EST:     ACAACCGGGGACAAGGCTGTGCTATATTTTCAACCATGTGGCTGGTTTGG                         GGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACC
genomic: ACAACCGGGGACAAGGCTGTGCTATATTTTCAACCATGTGGCTGGTTTGGgtatgtcaaa ... tttgttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACC
EST: gi|110705363|gb|EE082145.1|EE082145
EST:     ACAACCGGGGACAAGGCTGTGCTATATTTTCAACCATGTGGCTGGTTTGG                         GGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACC
genomic: ACAACCGGGGACAAGGCTGTGCTATATTTTCAACCATGTGGCTGGTTTGGgtatgtcaaa ... tttgttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACC
EST: gi|30252533|gb|CB970084.1|CB970084
EST:     ATTTTCAACCATGTGGCTGGTTTGG                         GGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACC
genomic: ATTTTCAACCATGTGGCTGGTTTGGgtatgtcaaa ... tttgttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACC
EST: gi|30252454|gb|CB970005.1|CB970005
EST:     ACAACCGGGGACAAGGCTGTGCTACATTTTCAACCATGTGGCTGGTTTGG                         GGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACC
genomic: ACAACCGGGGACAAGGCTGTGCTATATTTTCAACCATGTGGCTGGTTTGGgtatgtcaaa ... tttgttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcattccattccctgcctactggtagtctgatttgtagttgtgttttgttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACCCAAAATATTGATGACAGGGAAATGGAATGAGTCAATGAGTTACCAACCA
                          gtctgat  putative branch site (score: 4)
                                            ttttgtt  putative PPT
                               atttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtcagtaccattcttgcgattgtaaattgtaatatgcttatgtgcattccattccctgcctactggtagtctgatttgtagttgtgttttgttgtagGGCTGGTCGCTACGAAGTGGATGGATATGTGTATAATGCTGAGGAGGAACCCAAAATATTGATGACAGGGAAATGGAATGAGTCAATGAGTTACCAACCA

- - - - - ccattct
- - - - - - - - - - - - - - - - - - - - -tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggtag