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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtttctttctttatgaatgctctatttactacacttgaatgatgaatcctaaatttttatagctgtgagttgtgaggtctttcaacaaatcttcaaaatctatggttgcagATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCATTGGAGATCCCCCTGAGGAACGATTTGATTTGGCATTTTGCGGAAGCCTT

Basic information

species Vitis vinifera
transcript Vv17s0000g09910.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09910.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA06G18320.1 (Glycine max), 3'ss of exon 8
gtaagttgtttctttctttatgaatg--ctctatttactacacttgaatgatgaatcctaaatttttatagctgtgagttgtgaggt--ctttcaacaaatcttcaaaatctatggttgcagATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCATTGGAGATCCCCCTGAGGAACGATTTGATTTGGCATTTTGCGGAAGCCTT
              |   ||  ||||  || || || || || |   ||  | ||    |||||  |||   |||||    ||||||  |||||  |  |  ||   |  | |    ||||| |||||||| |||||||| ||||| ||||| ||||| || |||||||||||||| ||||| ||||||||  ||||||||||||| || ||||||||||||
--------------ttgctagcaatgatctttactttct-cagtaacattcttaaatgcaaattggtat---tgtgaac-atgaggtagctttctgctgacattttcatccaaa---tgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCATTGGTGATCCTCCTGAGGAGAGATTTGATTTGGCTTTCTGCGGAAGCCTT

upper sequence: Vv17s0000g09910.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA04G36600.1 (Glycine max), 3'ss of exon 7
gtaagttgtttctttctttatgaatgctctatttactacacttgaatgatgaatcctaaatttttatag---ctgtgagttgtgaggt--ctttcaacaaatcttcaaaatctatggttgcagATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCATTGGAGATCCCCCTGAGGAACGATTTGATTTGGCATTTTGCGGAAGCCTT
                   ||||| ||  | ||||||     | | | |  | || |||||    || |    |||||    ||||||  ||||| ||  |  ||   |  | |    ||||| |||||||| |||||||| ||||| ||||| ||||| || |||||||||||||| ||||| ||||||||  ||||||| |||||||| || |||||||||
----------------agaatgaaagccatctttacttt--ctcagtaac-attcttaaatgcaaattggttttgtgaac-atgaggttgctttccactgacattttcatccaaa---tgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCATTGGTGATCCTCCTGAGGAGAGATTTGACTTGGCATTCTGTGGAAGCCTT

upper sequence: Vv17s0000g09910.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT3G48420.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagttgtttctttctttatgaatgctctatttactacacttgaatgatgaatcctaaatttttatagctgtgagttgtgaggtctttcaacaaatcttcaaaatctatggttgcagATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCATTGGAGATCCCCCTGAGGAACGATTTGATTTGGCATTTTGCGGAAGCCTT
                     |   | | || |  ||  | |   |     | || |||  ||  ||| |  | ||   |||  |  | ||     ||||  |  | |    ||| ||||| || ||||||||||| |||  ||| || ||||| ||||| |||||||||||||| || || || ||  |||||||||||||||| || ||||| |||
---------------------gtgagttttagt--ctgaaatcagaatcctattcataa--ttccataacaatcagaattgaaatgat-cattcgttctttcatctttggaattgtagATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCATTGGAGACCCTCCAGAAGAGAGATTTGATTTGGCATTCTGTGGAAGTCTT

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|110366041|gb|EC929676.1|EC929676
EST:     CTTGCAGCTGCCAAGTCTGCTGGAATGAAGTGTATTGTAACAAAGAGCGG                         ATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCAT
genomic: CTTGCAGCTGCCAAGGCTGCTGGAATGAAGTGTATTGTAACAAAGAGCGGgtaagttgtt ... atggttgcagATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCAT
EST: gi|110357588|gb|EC921779.1|EC921779
EST:     CTTGCAGCTGCCAAGGCTGCTGGAATGAAGTGTATTGTAACAAAGAGCGG                         ATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCAT
genomic: CTTGCAGCTGCCAAGGCTGCTGGAATGAAGTGTATTGTAACAAAGAGCGGgtaagttgtt ... atggttgcagATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCAT
EST: gi|110376295|gb|EC941348.1|EC941348
EST:     CTTGCAGCTGCCAAGGCTGCTGGAATGAAGTGTATTGTAACAAAGAGCGG                         ATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCAT
genomic: CTTGCAGCTGCCAAGGCTGCTGGAATGAAGTGTATTGTAACAAAGAGCGGgtaagttgtt ... atggttgcagATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCAT
EST: gi|110383854|gb|EC948256.1|EC948256
EST:     CTTGCAGCTGCCAAGGCTGCTGGAATGAAGTGTATTGTAACAAAGAGCGG                         ATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCAT
genomic: CTTGCAGCTGCCAAGGCTGCTGGAATGAAGTGTATTGTAACAAAGAGCGGgtaagttgtt ... atggttgcagATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCAT
EST: gi|110376164|gb|EC941208.1|EC941208
EST:     CTTGCAGCTGCCAAGGCTGCTGGAATGAAGTGTATTGTAACAAAGAGCGG                         ATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCAT
genomic: CTTGCAGCTGCCAAGGCTGCTGGAATGAAGTGTATTGTAACAAAGAGCGGgtaagttgtt ... atggttgcagATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCAT
EST: gi|18459790|gb|BM438068.1|BM438068
EST:     CTTGCAGCTGCCAAGGCTGCTGGAATGAAGTGTATTGTAACAAAGAGCGG                         ATATACGGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCAT
genomic: CTTGCAGCTGCCAAGGCTGCTGGAATGAAGTGTATTGTAACAAAGAGCGGgtaagttgtt ... atggttgcagATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCAT
EST: gi|110361698|gb|EC925191.1|EC925191
EST:     CTTGCAGCTGCCAAGGCTGCTGGAATGAAGTGTATTGTAACAAAGAGCGG                         ATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCAT
genomic: CTTGCAGCTGCCAAGGCTGCTGGAATGAAGTGTATTGTAACAAAGAGCGGgtaagttgtt ... atggttgcagATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatagctgtgagttgtgaggtctttcaacaaatcttcaaaatctatggttgcagATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCATTGGAGATCCCCCTGAGGAACGATTTGATTTGGCATTTTGCGGAAGCCTT
                                      aaaatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtttctttctttatgaatgctctatttactacacttgaatgatgaatcctaaatttttatagctgtgagttgtgaggtctttcaacaaatcttcaaaatctatggttgcagATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCATTGGAGATCCCCCTGAGGAACGATTTGATTTGGCATTTTGCGGAAGCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC