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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttacgtatcaaaaaaaaaagaaaaagaaaaaaaaagggggaacaggaaaatgagattctgctttctgttatactaaatttcttatttcctttcctcagGACAGATAAATGGGCTGAGACTGAACTAGGAACCAAATGGGGTGACAAGTGGGAAGAGAAATTCTTTGCTGGCATAGGTTCACGTCAAGGGGAGACTTGG

Basic information

species Vitis vinifera
transcript Vv18s0001g00110.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g00110.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os03g04100.1 (Oryza sativa), 3'ss of exon 7
-atttacgtatcaaaaaaaaaagaaaaagaaaaaaaaagggggaacaggaaaatgagat-tctgctttctgttatactaaatttcttatttcctttcctcagGACAGATAAATGGGCTGAGACTGAACTAGGAACCAAATGGGGTGACAAGTGGGAAGAGAAATTCTTTGCTGGCATAGGTTCACGTCAAGGGGAGACTTGG
 |        | | |     ||   |           |      |  |||| ||  ||| | || |   || ||  |        | ||||   || |  ||||||||||| ||||| ||||| ||  |||| ||||||||||| ||||| ||||||||||||||||||||||| || ||||| || ||||||||||| |||
cacaagttctttatacttttaatttatttgcctgttcaatcatgattggaacatccgatgtatgttaattggtaaccactgcaattcatttgtattac--agGACAGATAAGTGGGCAGAGACAGACTTAGGCACCAAATGGGGGGACAAATGGGAAGAGAAATTCTTTGCTGGAATTGGTTCTCGACAAGGGGAGACATGG

upper sequence: Vv18s0001g00110.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G126812_T01 (Zea mays), 3'ss of exon 7
-atttacgtatcaaaaaaaaaagaaaaagaaaaaaaaagggggaacaggaaaatgagattctgctttctgttatactaaatttcttatttcctttcctcagGACAGATAAATGGGCTGAGACTGAACTAGGAACCAAATGGGGTGACAAGTGGGAAGAGAAATTCTTTGCTGGCATAGGTTCACGTCAAGGGGAGACTTGG
  || |   ||   |||               | | |    |       ||       |  || ||  |   |  ||  ||| | |   |  | |   |||||||||||| ||||| ||||| ||  |||| ||||||||||| ||||||||||| |||||||||||||| || || ||||| || ||||||||||| |||
agttcagacattggaaagctgttttggtttgcatatactttgtctgctcaactgccagtggtggttgataacac-ctgcattgcatgaatgttcttaacagGACAGATAAGTGGGCAGAGACAGACTTAGGCACCAAATGGGGGGACAAGTGGGAGGAGAAATTCTTTGCAGGAATTGGTTCTCGACAAGGGGAGACATGG

upper sequence: Vv18s0001g00110.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G110345_T01 (Zea mays), 3'ss of exon 7
atttacgtatcaaaaaaaaaagaaaaagaaaaaaaaagggggaacaggaaaatga-gattctgctttctgttatactaaatttcttatttcctttcctcagGACAGATAAATGGGCTGAGACTGAACTAGGAACCAAATGGGGTGACAAGTGGGAAGAGAAATTCTTTGCTGGCATAGGTTCACGTCAAGGGGAGACTTGG
 || |   ||   |||                | | |             | |||   |  || ||  |   || ||  ||| | |   |  | |   |||||||||||| ||||| ||||| ||  |||| ||||||||||| ||||||||||| |||||||||||||| || || ||||| || ||||||||||| |||
gttcagacattggaaagctgtttttggtttgcatatactttatctgctcgactgacagtggtggttgatagcat-ctgcattgcattaatgttcttaacagGACAGATAAGTGGGCAGAGACAGACTTAGGCACCAAATGGGGGGACAAGTGGGAGGAGAAATTCTTTGCAGGAATTGGTTCTCGACAAGGGGAGACATGG

upper sequence: Vv18s0001g00110.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G42430.2 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------------------------------------------atttacgtatcaaaaaaaaaagaaaaagaaaaaaaaagggggaacaggaaaatgagattctgctttctgttat-actaaatttcttatttcctttcctcagGACAGATAAATGGGCTGAGACTGAACTAGGAACCAAATGGGGTGACAAGTGGGAAGAGAAATTCTTTGCTGGCATAGGTTCACGTCAAGGGGAGACTTGG
                                                                ||      || |   |   ||| |  ||      |        ||   ||  ||||| || |     || | | | | ||  |  |   |  ||| ||||||||| || ||||||||||| ||  | || ||||||||||| |||||||||||||||||||| ||   ||| || ||||||||||| |||||||| |||
gttttctattctaactactctctagtcctcaattttttccttactggtttatatataaggctccttgttagccagagttacttgaacattaatttgtgaaattcttgagatcaaaaagattgtgttaatgattttgatttagttgttggtgaacaatccacagGACAGACAAGTGGGCTGAGACAGAGTTGGGGACCAAATGGGGAGACAAGTGGGAAGAGAAATTTTTCAGTGGGATTGGTTCACGTCAGGGGGAGACATGG

upper sequence: Vv18s0001g00110.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S138_38V6.1 (Physcomitrella patens), 3'ss of exon 8
atttacgtatcaaaaaaaaaagaaaaagaaaaaaaaagggggaacaggaaaatgagattctgctttctgttatactaaatttcttatttcctttcct-cagGACAGATAAATGGGCTGAGACTGAACTAGGAACCAAATGGGGTGACAAGTGGGAAGAGAAATTCTTTGCTGGCATAGGTTCACGTCAAGGGGAGACTTGG
  | |  | |||| | |         |      | |     |   | ||   |   ||      |   | || | |  ||   |  || |   || | |||||| || || ||||| ||||  |     || || ||||||||||| ||||||||||||||||||     |||  | ||  || | ||||| || || |||
tatcaaatctcaatatatgctcgttgaagtgtgagattttaggttatgagtgttc-atgagaactctggataaatttgatcgttctttacacatcatgcagGACGGACAAGTGGGCAGAGAACGGCACGGGTACGAAATGGGGTGATAAGTGGGAAGAGAAATTCAACCATGGTGTTGGAACAAGACAAGGCGAAACATGG

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|26267104|gb|CA818167.1|CA818167
EST:     GGGAGAGCATTATGATGGAAGAGGATCCGTTCTAAAATG                         GACAGATAAATGGGCTGAGACTGAACTAGGAACCAAATGGGGTGACAAGTG
genomic: GGGAGAGCATTATGATGGAAGAGGATCCGTTCTAAAATGgttttctcta ... ctttcctcagGACAGATAAATGGGCTGAGACTGAACTAGGAACCAAATGGGGTGACAAGTG
EST: gi|26265169|gb|CA816232.1|CA816232
EST:     GGGAGAAGTGGGGAGAGCATTATGATGGAAGAGGATCCGTTCTAAAATG                         GACAGATAAATGGGCTGAGACTGAACTAGGAACCAAATGGGGTGACAAGTG
genomic: GGGAGAAGTGGGGAGAGCATTATGATGGAAGAGGATCCGTTCTAAAATGgttttctcta ... ctttcctcagGACAGATAAATGGGCTGAGACTGAACTAGGAACCAAATGGGGTGACAAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggaaaatgagattctgctttctgttatactaaatttcttatttcctttcctcagGACAGATAAATGGGCTGAGACTGAACTAGGAACCAAATGGGGTGACAAGTGGGAAGAGAAATTCTTTGCTGGCATAGGTTCACGTCAAGGGGAGACTTGG
                           tactaaa  putative branch site (score: 1)
                                  tttcttatttcctttc  CT-rich tract
                      tgttatactaaatttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttacgtatcaaaaaaaaaagaaaaagaaaaaaaaagggggaacaggaaaatgagattctgctttctgttatactaaatttcttatttcctttcctcagGACAGATAAATGGGCTGAGACTGAACTAGGAACCAAATGGGGTGACAAGTGGGAAGAGAAATTCTTTGCTGGCATAGGTTCACGTCAAGGGGAGACTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - -aaaaaaa
- - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - -gggggaa
- - - - - - - - - - - - - - - - - - - - - - - ggaaaat