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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttttggctttgggatctggggccttattggctttcgttttcttggaagggtttgattatatattttgtctcatttagtgtcttttttatgtttcagATCTCGTGGGATTTGGACGTAGTCTTGACGGGAAACGAAGACAATGTTGCCTCAGAAGCAAGCAGAAGAAGCAATTGTCTCGAACATCAGCGAGGCAGAC

Basic information

species Vitis vinifera
transcript Vv08s0007g02030.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g02030.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G42640.1 (Glycine max), 3'ss of exon 1
atttttttggctttgggatctggggccttattggctttcgttttcttgga-agggtttgat----tatatattttgtctcatttagtgtctttttt----atgtttcagATCTCGTGGGATTTGGACGTAGTCTT-GACGGGAAACGAAGACAATGTTGCCTCAGAAGCAAGCAGAAGAAGCAATTGTCTCGA---ACATCAGCGAGGCAGAC
     | |||  |  |  | |     ||| |||||||||||||||| ||  || |||||||    | | | |||||||||||| |||||  |||||     |||||||||||   |    |||  |   |||    ||    ||| | | ||||||||||||||||| |||||||| |||||||| ||| | |    | | | |||| |||| 
-----tgtggtgtgtgttttt----tcttcttggctttcgttttctggggtagtgtttgatctttttttttttttgtctcattaagtgtacttttttcatgtgtttcagATCCATTT---TTTCAAGACAGTTGAAGAAAAAAAATGGAAACAATGTTGCCTCAGAACCAAGCAGAGGAAGCAATAGTCACAACAAGCCTTAACGAGACAGA-

upper sequence: Vv08s0007g02030.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G09100.1 (Glycine max), 3'ss of exon 1
atttttttggctttgggatctgggg-ccttattggctttcgttttcttgga--agggtttgattatata---ttttgtctcatttagtgtcttttttatgt--ttcagATCTCGTGGGATTTGGACGTAG--TCTTGACGGGAAACGA-AGACAATGTTGCCTCAGAAGCAAGCAGAAGAAGCAATTGTCTCGAACATCAGCGAGGCAGAC-
        |   |  |||||||||| | || |||||||||||||||| ||     | ||| ||   ||    ||||||||||||||||||| |||||||||  ||||||||       |||| |||   |  | |||  |  ||  || ||||||||||| |||||||||||||||| ||||| || ||| | |||   |  ||    ||  
--------gttatctggatctggggtctttcttggctttcgttttctggggctgcgtttttatatcatggttttttgtctcatttagtgtcctttttatgtatttcagATCC----ACATTTAGACACTGCTTTTTGTGGATAAGGGAGAGACAATGTTGTCTCAGAAGCAAGCAGAGGAAGCTATAGTCACAAACGAGACAGAACATGAAG

upper sequence: Vv08s0007g02030.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G09100.1 (Glycine max), 3'ss of exon 1
atttttttggctttgggatctgggg-ccttattggctttcgttttcttgga--agggtttgattatata---ttttgtctcatttagtgtcttttttatgt--ttcagATCTCGTGGGATTTGGACGTAG--TCTTGACGGGAAACGA-AGACAATGTTGCCTCAGAAGCAAGCAGAAGAAGCAATTGTCTCGAACATCAGCGAGGCAGAC-
        |   |  |||||||||| | || |||||||||||||||| ||     | ||| ||   ||    ||||||||||||||||||| |||||||||  ||||||||       |||| |||   |  | |||  |  ||  || ||||||||||| |||||||||||||||| ||||| || ||| | |||   |  ||    ||  
--------gttatctggatctggggtctttcttggctttcgttttctggggctgcgtttttatatcatggttttttgtctcatttagtgtcctttttatgtatttcagATCC----ACATTTAGACACTGCTTTTTGTGGATAAGGGAGAGACAATGTTGTCTCAGAAGCAAGCAGAGGAAGCTATAGTCACAAACGAGACAGAACATGAAG

upper sequence: Vv08s0007g02030.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G28310.1 (Glycine max), 3'ss of exon 1
atttttttggctttgggatctggggcctta-ttggctttcgttttcttgga--agggtttgattata----tattttgtctcatttagtgtcttttt---tatgtttcagATCTCGTGGGATTTGGACGTAGTCTTGACGGGAAACGAAGACAATGTTGCCTCAGAAGCAAGCAGAAGAAGCAATTGTCTCGAACATCAGCGAG-GCAGAC---
            |  |||||||||| |||  |||||||||||||||| ||     | ||| ||   |    | ||||||||||||||||||| ||||   | | |||||||||       |||| |||   |  ||   ||  ||   ||||||||||| |||||||||||||||| ||||| || ||| | |||   |  ||    | |    
----------tatctggatctggggtctttcttggctttcgttttctggggctgcgtttttatatcacggtttttttgtctcatttagtgtccttttttatgtatttcagATCC----ACATTTAGACACTGCTTTTGTGGATAAGAGAGACAATGTTGTCTCAGAAGCAAGCAGAGGAAGCCATAGTCACAAACGAGACAGAACATAAAGTTG

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|110359318|gb|EC920617.1|EC920617
EST:     CGAGTCTCTGATTTCTTCAATCTGCTAGCGAAAGAGACATCTCAAACAAG                         ATCTCGTGGGATTTGGACGTAGTCTTGACGGGAAACGAAGACAATGTTGCC
genomic: CGAGTCTCTGATTTCTTCAATCTGCTAGCGAAAGAGACATCTCAAACAAGgtattttact ... tatgtttcagATCTCGTGGGATTTGGACGTAGTCTTGACGGGAAACGAAGACAATGTTGCC
EST: gi|294966677|gb|GW839668.1|GW839668
EST:     CGAGTCTCTGATTTCTTCAATCTGCTGGCGAAAGAGACATCTCAAACAAG                         ATCTCGTGGGATTTGGACGTAGTCTTGACGGGAAACGAACACAATGTTGCC
genomic: CGAGTCTCTGATTTCTTCAATCTGCTAGCGAAAGAGACATCTCAAACAAGgtattttact ... tatgtttcagATCTCGTGGGATTTGGACGTAGTCTTGACGGGAAACGAAGACAATGTTGCC
EST: gi|161710741|gb|FC059078.1|FC059078
EST:     CGAGTCTCTGATTTCTTCAATCTGCTAGCGAAAGAGACATCTCAAACAAG                         ATCTCGTGGGATTTGGACGTAGTCTTGACGGGAAACGAAGACAATGTTGCC
genomic: CGAGTCTCTGATTTCTTCAATCTGCTAGCGAAAGAGACATCTCAAACAAGgtattttact ... tatgtttcagATCTCGTGGGATTTGGACGTAGTCTTGACGGGAAACGAAGACAATGTTGCC
EST: gi|22013976|gb|BQ799010.1|BQ799010
EST:     CGAGTCTCTGATTTCTTCAATCTGCTAGCGAAAGAGACATCTCAAACAAG                         ATCTCGTGGGATTTGGACGTAGTCTTGACGGGAAACGAAGACAATGTTGCC
genomic: CGAGTCTCTGATTTCTTCAATCTGCTAGCGAAAGAGACATCTCAAACAAGgtattttact ... tatgtttcagATCTCGTGGGATTTGGACGTAGTCTTGACGGGAAACGAAGACAATGTTGCC
EST: gi|110685103|gb|EE063138.1|EE063138
EST:     CGAGTCTCTGATTTCTTCAATCTGCTAGCGAAAGAGACATCTCAAACAAG                         ATCTCGTGGGATTTGGACGTAGTCTTGACGGGAAACGAAGACAATGTTGCC
genomic: CGAGTCTCTGATTTCTTCAATCTGCTAGCGAAAGAGACATCTCAAACAAGgtattttact ... tatgtttcagATCTCGTGGGATTTGGACGTAGTCTTGACGGGAAACGAAGACAATGTTGCC
EST: gi|110419696|gb|EC985944.1|EC985944
EST:     CGAGTCTCTGATTTCTTCAATCTGCTAGCGAAAGAGACATCTCAAACAAG                         ATCTCGTGGGATTTG
genomic: CGAGTCTCTGATTTCTTCAATCTGCTAGCGAAAGAGACATCTCAAACAAGgtattttact ... tatgtttcagATCTCGTGGGATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaagggtttgattatatattttgtctcatttagtgtcttttttatgtttcagATCTCGTGGGATTTGGACGTAGTCTTGACGGGAAACGAAGACAATGTTGCCTCAGAAGCAAGCAGAAGAAGCAATTGTCTCGAACATCAGCGAGGCAGAC
        gtttgat  putative branch site (score: 5)
                                      tcttttttatgtttc  putative PPT
             attatatattttgtct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttttggctttgggatctggggccttattggctttcgttttcttggaagggtttgattatatattttgtctcatttagtgtcttttttatgtttcagATCTCGTGGGATTTGGACGTAGTCTTGACGGGAAACGAAGACAATGTTGCCTCAGAAGCAAGCAGAAGAAGCAATTGTCTCGAACATCAGCGAGGCAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - -tggcttt
- - - - - - - - - - - - - - - - - - - - - ttcttgg
- - - - - - - - - - - - - - - - - - - - - - - - - -gggtttg