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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggttcaattcccttgcaagttgctgctatacttgcagtcatgctttctggtgcaattatgttgaaagcagatttttatgacacatgcatcttgctgcagTTGTGAGTGTTGGCGCAGCACTTTTCTTGTTCCAACAGTTGGCCGGCATAAATGCTGTGGTGTACTATTCAACATCTGTGTTCCGCAGTGCTGGAATTGC

Basic information

species Vitis vinifera
transcript Vv14s0006g02720.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g04190.4 (Oryza sativa), 3'ss of exon 9
---------------------------------------------------------------------aggttcaattcccttgcaagttgctgctatacttgcagtcatgctttctggtgcaattatgttgaaagcagatttttatgacacatgcatct-tgctgcagTTGTGAGTGTTGGCGCAGCACTTTTCTTGTTCCAACAGTTGGCCGGCATAAATGCTGTGGTGTACTATTCAACATCTGTGTTCCGCAGTGCTGGAATTGC
                                                                        |   ||| |||       || ||||| | |   |  |   | ||       ||      |      |  | ||  ||||| ||   |   | | |||||||| ||||| ||||||||  | ||||||||||||||| | ||||| ||||||||||| || || || || ||||| |||||||||||||| || |||||
gtagttttgttttctctgtttcagatctgactattttgattcctcaaattgcatcatgaaatcttccctgattgttatttcctactcttgtgttgctaaaataaaaacccaacatttaaccaaaacatcagtttggtgatttgttgctgacatattttttcataccgcagTTGTTAGTGTGGGCGCAGCTATGTTCTTGTTCCAACAGCTTGCCGGTATAAATGCTGTTGTATATTACTCTACATCGGTGTTCCGCAGTGCAGGCATTGC

upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G153704_T01 (Zea mays), 3'ss of exon 13
------aggttcaattcccttgcaagttgctgctatacttgcagtcatgctttctggtgcaattatgttgaaagcagatttttatgacacatgcatcttgctgcagTTGTGAGTGTTGGCGCAGCACTTTTCTTGTTCCAACAGTTGGCCGGCATAAATGCTGTGGTGTACTATTCAACATCTGTGTTCCGCAGTGCTGGAATTGC
      |  |   | |  | | |||  |    |   | | | |   || || |  |||| |   |   |  ||      |||| ||| | |||  || |  ||||||||||||||| || |||||||| || |||||||| ||| | || || ||||| ||||| || || || || ||||| |||||||| ||||| || |||||
gttttgatatgtgaattgcattcaacctaaaacgtcaat-gaatcgatactgt--ggtggag--accctacaatacatgttttctgatatatgtctcat-ttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAAACGCTGTTGTATATTACTCTACATCGGTGTTCCGTAGTGCAGGCATTGC

upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G098011_T02 (Zea mays), 3'ss of exon 9
aggttcaat---tcccttgcaagttgctgctatacttgcagtcatgctttctggtgcaattatgttgaaagcagatttttatgacacatgcatcttgctgcagTTGTGAGTGTTGGCGCAGCACTTTTCTTGTTCCAACAGTTGGCCGGCATAAATGCTGTGGTGTACTATTCAACATCTGTGTTCCGCAGTGCTGGAATTGC
 | ||  ||   |   ||||||    |    | || |  |   ||   | ||   |     | |    |||     |||| ||| | ||   || |  ||||||||||||||| || |||||||| || |||||||| ||| | || || ||||| ||||| || || || || ||||| |||||||| | ||| || ||| |
-gttttgatatgttgattgcaaacaacc-taaaacgtcaaagaattgatactatggtggagacgccacaagacatgttttctgatatatctttcat-ttgcagTTGTGAGTGTGGGGGCAGCACTGTTTTTGTTCCAGCAGCTTGCTGGTATAAACGCTGTTGTATATTACTCTACATCGGTGTTCCGTAATGCAGGCATTAC

upper sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G07780.1 (Glycine max), 3'ss of exon 9
aggttcaattcccttgcaagttgctgctatacttgcagtcatgctt-tctggtgcaattatgttgaaagcag------atttttatgacacatgcatcttgctgcagTTGTGAGTGTTGGCGCAGCACTTTTCTTGTTCCAACAGTTGGCCGGCATAAATGCTGTGGTGTACTATTCAACATCTGTGTTCCGCAGTGCTGGAATTGC
    | | ||| ||  ||| ||| |  |    || |  |   | |  |    || | |  | |   ||  ||      | ||   | | | ||||  |||| | ||||||| |||||||| |||||||||||||||||||| |||||||| || ||||||||||| ||||| |||||||| ||||||||||| ||||||||||||||
----taatttcactgacaacttgttttt-cgtttactatatagttgattaaatgaattcttatatgaaatagtatagcacttccttaaaatatgc--cttgtttcagTTGTCAGTGTTGGGGCAGCACTTTTCTTGTTCCAGCAGTTGGCTGGAATAAATGCTGTAGTGTATTATTCAACTTCTGTGTTCCGTAGTGCTGGAATTGC

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|110403571|gb|EC969185.1|EC969185
EST:     TGAACAGGAAGCTGGGTGGTTTGATCTATTTAGTGGCCGCTACTGGAAAG                         TTGTGAGTGTTGGCGCAGCACTTTTCTTGTTCCAACAGTTGGCCGGCATAA
genomic: TGAACAGGAAGCTGGGTGGTTTGATCTATTTAGTGGCCGCTACTGGAAAGgtataactga ... cttgctgcagTTGTGAGTGTTGGCGCAGCACTTTTCTTGTTCCAACAGTTGGCCGGCATAA
EST: gi|110370956|gb|EC934605.1|EC934605
EST:     TGAACAGGAAGCTGGGTGGTTTGATCTATTTAGTGGCCGCTACTGGAAAG                         TTGTGAGTGTTGGCGCAGCACTTTTCTTGTTCCAACAGTTGGCCGGCATAA
genomic: TGAACAGGAAGCTGGGTGGTTTGATCTATTTAGTGGCCGCTACTGGAAAGgtataactga ... cttgctgcagTTGTGAGTGTTGGCGCAGCACTTTTCTTGTTCCAACAGTTGGCCGGCATAA
EST: gi|110376760|gb|EC941834.1|EC941834
EST:     TGAACAGGAAGCTGGGTGGTTTGATCTATTTAGTGGCCGCTACTGAAAAG                         TTGTGAGTGTTGGCGCAGCACTTTTCTTGTTCCAACAGTTGGCCGGCATAA
genomic: TGAACAGGAAGCTGGGTGGTTTGATCTATTTAGTGGCCGCTACTGGAAAGgtataactga ... cttgctgcagTTGTGAGTGTTGGCGCAGCACTTTTCTTGTTCCAACAGTTGGCCGGCATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctggtgcaattatgttgaaagcagatttttatgacacatgcatcttgctgcagTTGTGAGTGTTGGCGCAGCACTTTTCTTGTTCCAACAGTTGGCCGGCATAAATGCTGTGGTGTACTATTCAACATCTGTGTTCCGCAGTGCTGGAATTGC
                                            tcttgct  CT-rich tract
                        agatttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggttcaattcccttgcaagttgctgctatacttgcagtcatgctttctggtgcaattatgttgaaagcagatttttatgacacatgcatcttgctgcagTTGTGAGTGTTGGCGCAGCACTTTTCTTGTTCCAACAGTTGGCCGGCATAAATGCTGTGGTGTACTATTCAACATCTGTGTTCCGCAGTGCTGGAATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - -ccttgca
- - - - - - - - - - - -ctgctat
- - - - - - - - - - - - - - - - - gcagtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatgc