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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgttgctattatctttttacatgtatttaattactatttgttacttttctaattattttatcttgtggctgatgtaatttttctcaaatcatttcagATCCCTTTCCAGCTGGGATTGTCAAAAATGGATCTTCGGAAGATGTTGAAATCCAGTTTATCTGGG

Basic information

species Vitis vinifera
transcript Vv18s0001g11700.t01
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA14G08570.1 (Glycine max), 3'ss of exon 3
-tattgt-tgctattatctttttacatgtatttaattactatttgttacttttctaattattttatcttgtggctgatgtaatttttctcaaatcatttcagATCCCTTTCCAGCTGGGATTGTCAAAAATGGATCTTCGGAAGATGTTGAAATCCAGTTTATCTGGG
  ||||  ||| |    | || || ||  | |   |    |  | | || ||     | | |||      |  |  |  |   | || |  |  |||||||||| ||||| ||||| ||| |||||||||||||||||||||||||||| ||||||||||||||||||
agattgagtgcca--gacattataaattaaatagttagacaaatttcacattgaatttgactttgaacattcacaaacttccatgttttgcatccatttcagATTCCTTTTCAGCTTGGACTGTCAAAAATGGATCTTCGGAAGATGTTAAAATCCAGTTTATCTGGG

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 22
tattgttgctattatctttttacatgtatttaattactatttgttacttttctaattattttatcttgtggctgatgtaatttttctcaaatcatttcagATCCCTTTCCAGCTGGGATTGTCAAAAATGGATCTTCGGAAGATGTTGAAATCCAGTTTATCTGGG
|         | |     | |  ||  | |   |    |  | | || ||     | | |||      |  |  |  |   | || |  |  |||||||||| ||||| ||||| ||| |||||||||||||||||||||||||||| ||||||||||||||||||
ttcctggatgaatgaaactgtgaattaaatagttagacaaatttcacattgaatttgactttgaacattcacaaacttccatgttttgcatccatttcagATTCCTTTTCAGCTTGGACTGTCAAAAATGGATCTTCGGAAGATGTTAAAATCCAGTTTATCTGGG

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 22
tattgttgctattatctttttacatgtatttaattactatttgttacttttctaatt--attttatcttgtg-gctgatgtaattt----ttctcaaatcatttcagATCCCTTTCCAGCTGGGATTGTCAAAAATGGATCTTCGGAAGATGTTGAAATCCAGTTTATCTGGG
     || ||     | |   ||    | |||| ||   ||||  |  ||||  |||  |||| |  |||     | |   ||||     || |  |  |||||||||| ||||| ||||| ||| |||||||||||||||||||||||||||| ||||||||||||||||||
-----ttcctggatgcatgaaactgtgaattaaata--gtttgacaaatttcacattgaatttgactttgaacattcacaaaattccatgttttgcatccatttcagATTCCTTTTCAGCTTGGACTGTCAAAAATGGATCTTCGGAAGATGTTAAAATCCAGTTTATCTGGG

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|30305681|gb|CB982475.1|CB982475
EST:     AGTTTGCTCGAAGAGCTGAGGATTTGATGTTCACCATCTCACCAGAAGAG                         ATCCCTTTCCAGCTGGGATTGTCAAAAATGGATCTTCGGAAGATGTTGAAA
genomic: AGTTTGCTCGAAGAGCTGAGGATTTGATGTTCACCATCTCACCAGAAGAGgttagcatat ... atcatttcagATCCCTTTCCAGCTGGGATTGTCAAAAATGGATCTTCGGAAGATGTTGAAA
EST: gi|110385940|gb|EC950502.1|EC950502
EST:     AGTTTGCTCGAAGAGCTGAGGATTTGATGTTCACCATCTCACCAGAAGAG                         ATCCCTTTCCAGCTGGGATTGTCAAAAATGGATCTTCGGAAGATGTTGAAA
genomic: AGTTTGCTCGAAGAGCTGAGGATTTGATGTTCACCATCTCACCAGAAGAGgttagcatat ... atcatttcagATCCCTTTCCAGCTGGGATTGTCAAAAATGGATCTTCGGAAGATGTTGAAA
EST: gi|30134416|gb|CB919754.1|CB919754
EST:     AGTTTGCTCGAAGAGCTGAGGATTTGATGTTCACCATCTCACCAGAAGAG                         ATCCCTTTCCAGCTGGGATTGTCAAAAATGGATCTTCGGAAGATGTTGAAA
genomic: AGTTTGCTCGAAGAGCTGAGGATTTGATGTTCACCATCTCACCAGAAGAGgttagcatat ... atcatttcagATCCCTTTCCAGCTGGGATTGTCAAAAATGGATCTTCGGAAGATGTTGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttctaattattttatcttgtggctgatgtaatttttctcaaatcatttcagATCCCTTTCCAGCTGGGATTGTCAAAAATGGATCTTCGGAAGATGTTGAAATCCAGTTTATCTGGG
                                              tcatttc  CT-rich tract
     tctaattattttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattgttgctattatctttttacatgtatttaattactatttgttacttttctaattattttatcttgtggctgatgtaatttttctcaaatcatttcagATCCCTTTCCAGCTGGGATTGTCAAAAATGGATCTTCGGAAGATGTTGAAATCCAGTTTATCTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- -tgttgct
- - - - - - - - - - - catgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctga