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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgcattaaaaaagttgcatgttgaatttccttggggtttgcataatgggtcaatgatagtttgaagctttattaatatgttactggtgatttgtacagATTATGGGACGTAAGAAGTGGTAAAATAGTCCAGACACTTGAGACTAACTCTTCTGTAACCAGTGCTGAAGTGAGTCAAGATGGCCGTTATATCATAACT

Basic information

species Vitis vinifera
transcript Vv11s0016g04710.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G08200.1 (Glycine max), 3'ss of exon 4
---catgcattaaaaaagttgcatgttgaatttccttggggtttgcataatgggtcaatgatagtttgaagctttattaatatgttactggtgatttgtacagATTATGGGACGTAAGAAGTGGTAAAATAGTCCAGACACTTGAGACTAACTCTTCTGTAACCAGTGCTGAAGTGAGTCAAGATGGCCGTTATATCATAACT
    ||  ||  | | |  |  || |  |  |   |     | |  |||      || ||     |  |   |  | | | || |   || || ||   |||| |||||||| |||||||||||||||||||||||||||||||| ||||| || ||||| || ||||||||||||||||| |||||||||||||| |  |||
atatatatatatatatatatatatatatatatatatatatatatatatatatcagcattggatactatatattgcactga-atctagttgatgtttc--acagGTTATGGGATGTAAGAAGTGGTAAAATAGTCCAGACACTTGAAACTAAGTCATCTGTGACAAGTGCTGAAGTGAGTCAGGATGGCCGTTATATAACCACT

upper sequence: Vv11s0016g04710.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G12770.2 (Glycine max), 3'ss of exon 4
------------------------------------catgcattaaaaaagttgcatgttgaatttcct---tggggtttgcata-atgggtcaatgatagtttgaagctttattaatatgttactggtgatttgtacagATTATGGGACGTAAGAAGTGGTAAAATAGTCCAGACACTTGAGACTAACTCTTCTGTAACCAGTGCTGAAGTGAGTCAAGATGGCCGTTATATCATAACT
                                      |   |     || | |  || |   |||| |   |    | |  ||| ||    || ||     |  |   |  | | | || |   || || ||   |||| |||||||| ||||||||||||||||||||||||||||| || || || || ||||| || ||||||||||||||||| |||||||||||||| | ||||
gtatatcctccattaagccatttgatactgaaagcttgtctgtgttgtaaatcgtgtgctagctttcttgtttttaatatatatatatatagcattggatactatatattgcactga-atctagttgatgtttc--acagGTTATGGGATGTAAGAAGTGGTAAAATAGTCCAGACACTGGAAACCAAGTCATCTGTGACAAGTGCTGAAGTGAGTCAGGATGGCCGTTATATAACAACT
















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|161716787|gb|FC069173.1|FC069173
EST:     CATAGTGATCAAACAATATTAAGTTCGTGTACAGATATTGGGGGTGTAAG                         ATTATGGGACGTAAGAAGTGGTAAAATAGTCCAGACACTTGAGACTAACTC
genomic: CATAGTGATCAAACAATATTAAGTTCGTGTACAGATATTGGGGGTGTAAGgtagcatttc ... atttgtacagATTATGGGACGTAAGAAGTGGTAAAATAGTCCAGACACTTGAGACTAACTC
EST: gi|110702782|gb|EE079052.1|EE079052
EST:     CATAGTGATCAAACAATATTAAGTTCGTGTACAGATATTGGGGGTGTAAG                         ATTATGGGATGTAAGAAGTGGTAAAATAGTCCAGACACTTGAGACTAACTC
genomic: CATAGTGATCAAACAATATTAAGTTCGTGTACAGATATTGGGGGTGTAAGgtagcatttc ... atttgtacagATTATGGGACGTAAGAAGTGGTAAAATAGTCCAGACACTTGAGACTAACTC
EST: gi|161718203|gb|FC065673.1|FC065673
EST:     CATAGTGATCAAACAATATTAAGTTCGTGTACAGATATTGGGGGTGTAAG                         ATTATGGGACGTAAGAAGTGGTAAAATAGTCCAGACACTTGAGACTAACTC
genomic: CATAGTGATCAAACAATATTAAGTTCGTGTACAGATATTGGGGGTGTAAGgtagcatttc ... atttgtacagATTATGGGACGTAAGAAGTGGTAAAATAGTCCAGACACTTGAGACTAACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgggtcaatgatagtttgaagctttattaatatgttactggtgatttgtacagATTATGGGACGTAAGAAGTGGTAAAATAGTCCAGACACTTGAGACTAACTCTTCTGTAACCAGTGCTGAAGTGAGTCAAGATGGCCGTTATATCATAACT
                          tattaat  putative branch site (score: 2)
                        tttattaatatgttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgcattaaaaaagttgcatgttgaatttccttggggtttgcataatgggtcaatgatagtttgaagctttattaatatgttactggtgatttgtacagATTATGGGACGTAAGAAGTGGTAAAATAGTCCAGACACTTGAGACTAACTCTTCTGTAACCAGTGCTGAAGTGAGTCAAGATGGCCGTTATATCATAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
catgcat
- - - -taaaaaa
- - - - - - - - -gcatgtt
- - - - - - - - - - - - - - ttccttg
- - - - - - - - - - - - - - - - - -gggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttactgg