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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgttgcatatagttttcagatttctcatacttctgaaacaccgagtttgtgtatctccgcttgcaaatttctgaatgtggtcatcatgaaatgtgcagGCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAGAGTTGTTGACGGGAAGGAAGTCAGTTGACAAGACCCGACCTAGCAAGGA

Basic information

species Vitis vinifera
transcript Vv08s0056g00150.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 5
catgttgcatatagttttcagatttctcatacttctgaaacaccgagtttg---tgtatctccgcttgcaaatttctg---aatgtggt-catcatgaaatgtgcagGCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAGAGTTGTTGACGGGAAGGAAGTCAGTTGACAAGACCCGACCTAGCAAGGA
    ||   ||| |  ||  | |||    | | ||||   ||  |  | |    || |  |    | |||| | |||    ||  |||    |  | | |||  ||||||||||||| || ||||| ||||| || |||||||| ||||||||| | ||  | || ||||| ||||| || |||||||||||| ||||| | |||| 
----ttagttatggccttt-gttttgcattccctctggtgcat-gcttctacattgaaaatgtattggcaagtgtctactaaacttggcatgtgttaatatggccaGGCCACCTGACGGCTAGGAGTGATGTCTATAGCTTTGGCGTTGTTCTTTTGGAACTTTTAACGGGGAGGAAATCTGTTGACAAGACCAGACCTGGAAAGG-

upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G40650.1 (Glycine max), 3'ss of exon 5
---catgttgcatatagttttcagatttctcatacttctgaaacaccgagtttgtgtatctccgcttgcaaatttctgaatgtggt-catcatgaaatgtgcagGCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAGAGTTGTTGACGGGAAGGAAGTCAGTTGACAAGACCCGACCTAGCAAGGA
   | ||||  |||   | ||   ||| |   || | |   |   |    | | || |  |    | |||| | ||| ||  |||    |  | | |||  ||||||||||||| || ||||| || || || |||||||| ||||||||| | ||| | || || || ||||| || |||||||||||| ||||| | |||||
gagcttgttatataatatatt---attccctctagtgc-atacttctacatgtttgaacatgtattggcaagtatctaaacttggcatgtactaatatggccagGCCACCTGACGGCTAGGAGTGACGTCTATAGCTTTGGCGTTGTTCTTTTGGAGCTTTTAACAGGGAGGAAATCTGTTGACAAGACCAGACCTGGAAAGGA

upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G01020.1 (Arabidopsis thaliana), 3'ss of exon 4
catgttgcatatagttttcagatttctcatacttctgaaacaccgagtttgtgtatctccgcttgcaaatttctgaatgtggtcatcatga-aatgtgc-agGCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAGAGTTGTTGACGGGAAGGAAGTCAGTTGACAAGACCCGACCTAGCAAGGA
 |  |    |  || |      | |||| |  ||     |||   |||   |  | |    |    | |      ||  ||    | ||   ||||  | ||| ||| |||| ||||| || ||||| ||||||||||||||||||||||||||| ||||||| ||||| || ||||| || |||||  |||||||||| ||
-acatcatttcgagctacatagtctctctt-tttgcatgacaataagtgcttagaccattacacaaataaacactaacttgactctaatactaatgcactagGACACTTGACGGCCAGAAGTGATGTATACAGCTTTGGAGTTGTTCTTCTAGAGATGTTGACAGGAAGAAAATCAGTGGATAAGACAAGACCTAGCAAAGA

upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ22709 (Selaginella moellendorffii), 3'ss of exon 5
catgttgcatatagttttcagatttctcatacttctgaaacaccgagtttgtgtatctccgcttgcaaatttctgaatgtggtcatcatgaaatgtgcagGCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAGAGTTGTTGACGGGAAGGAAGTCAGTTGACAAGACCCGACCTAGCAAGGA
                              | |||  ||| |  ||       | |    | |    || ||   |   | ||     ||     | |||| ||| |||| |||||||||||||| |||||||||||||||||  | || ||| || | || || ||    ||  | |||||| |  |||| |     ||
---------------------------gtaagttcacaaagaaagaaaaaaaat-tgagagttcttgaacttaaaaggatcgtacctttgtttcctccagGTCACTTGACAGCCAGGAGCGATGTTTACAGCTTTGGAGTTGTCTTCCTGGAGATGCTAACTGGCAGACGATCCATGGACAAGTCTAGACCCACTGGCGA

upper sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ19239 (Selaginella moellendorffii), 3'ss of exon 5
catgttgcatatagttttcagatttctcatacttctgaaacaccgagtttgtgtatctccgcttgcaaatttctgaatgtggtcatcatgaaatgtgcagGCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAGAGTTGTTGACGGGAAGGAAGTCAGTTGACAAGACCCGACCTAGCAAGGA
                             ||  |    ||               |    | |    || ||   |   | ||     ||     | |||| ||| |||| |||||||||||||| |||||||||||||||||  | || ||| || | || || ||    ||  | |||||| |  |||| |     ||
----------------------------gtaagttcacaaggaaagaaaaaaacttgagagttcttgaacttaaaaggatcgtacctttgtttcctccagGTCACTTGACAGCCAGGAGCGATGTTTACAGCTTTGGAGTTGTCTTCCTGGAGATGCTAACTGGCAGACGATCCATGGACAAGTCTAGACCCACTGGAGA

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|110370255|gb|EC929228.1|EC929228
EST:     TCGTGTAATGGGTACCTATGGTTATGCTGCACCCGAATATGTAATGACTG                         GCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAG
genomic: TCGTGTAATGGGTACCTATGGTTATGCTGCACCCGAATATGTAATGACTGgtaaggcctc ... aaatgtgcagGCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAG
EST: gi|110382258|gb|EC938997.1|EC938997
EST:     TCGTGTAATGGGTACCTATGGTTATGCTGCACCCGAATATGTAATGACTG                         GCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAG
genomic: TCGTGTAATGGGTACCTATGGTTATGCTGCACCCGAATATGTAATGACTGgtaaggcctc ... aaatgtgcagGCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAG
EST: gi|351019747|gb|FQ439564.1|FQ439564
EST:     TCGTGTAATGGGTACCTATGGTTATGCTGCACCCGAATATGTAATGACTG                         GCCACCTGACTGCCAGGACCGATGTGTA
genomic: TCGTGTAATGGGTACCTATGGTTATGCTGCACCCGAATATGTAATGACTGgtaaggcctc ... aaatgtgcagGCCACCTGACTGCCAGGAGCGATGTGTA
EST: gi|33410518|gb|CF216145.1|CF216145
EST:     CGTGTAATGGGTACCTATGG-GATCGATGCACCCGAATATGTAATGACTG                         GCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAG
genomic: CGTGTAATGGGTACCTATGGTTAT-GCTGCACCCGAATATGTAATGACTGgtaaggcctc ... aaatgtgcagGCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAG
EST: gi|110696363|gb|EE072413.1|EE072413
EST:     TCGTGTAATGGGTACCTATGGTTATGCTGCACCCGAATATGTAATGACTG                         GCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAG
genomic: TCGTGTAATGGGTACCTATGGTTATGCTGCACCCGAATATGTAATGACTGgtaaggcctc ... aaatgtgcagGCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttgtgtatctccgcttgcaaatttctgaatgtggtcatcatgaaatgtgcagGCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAGAGTTGTTGACGGGAAGGAAGTCAGTTGACAAGACCCGACCTAGCAAGGA
                     aaatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgttgcatatagttttcagatttctcatacttctgaaacaccgagtttgtgtatctccgcttgcaaatttctgaatgtggtcatcatgaaatgtgcagGCCACCTGACTGCCAGGAGCGATGTGTACAGCTTTGGAGTTGTTCTTCTAGAGTTGTTGACGGGAAGGAAGTCAGTTGACAAGACCCGACCTAGCAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
catgttg
- - - - - - - - - - - - - - - - - - gaaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcatg