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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtttaatttggcatctggatagattatatagtttattgttcttgccagcttcaatgatactgaaatctaagaacttcttactgtttgtgcatctgcagGATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAATGCCTATCACACAAAGTATCGAGGAATGATTTATGCCCAGAACTTCTCC

Basic information

species Vitis vinifera
transcript Vv01s0011g03560.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g03560.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G20230.1 (Glycine max), 3'ss of exon 2
-----ctgtttaatttggcatctggatagattatatagtttattgttcttgccagcttcaatgatactgaaatctaagaacttcttactgtttgtgcatctgcagGATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAATGCCTATCACACAAAGTATCGAGGAATGATTTATGCCCAGAACTTCTCC
      || ||  | ||| ||||| | |||| ||  |    |      |  |   | | ||| ||  |||| |  |        ||  | | | |||||   |||| | ||||||||||| |||||| ||||  | || ||||||||||||||||||||||||||||| || || || |||||||||||||| ||||||||||| 
accacatgattgttgtgg-atctgtaaagatcattcatgccacaccgttcacacccgtgaatcat--tgaatttcatttgtacatt--tttctatgcattcccagGGTCACTTTTCTGGTAGCAGAATCATGCTTGATAGCAGGTGCAACCAAGAATGCCTATCACACCAAATACCGTGGAATGATTTATGCTCAGAACTTCTCA

upper sequence: Vv01s0011g03560.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G31000.1 (Glycine max), 3'ss of exon 2
--ctgtttaatttg-gcatctggatagattatatagtttattgttcttgccagcttcaatgatactgaaatctaagaacttctt----actgtttgtgcatctgcagGATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAATGCCTATCACACAAAGTATCGAGGAATGATTTATGCCCAGAACTTCTCC
   | | |  |||     |||  ||  ||  || || || ||| ||  | || ||      | | |||| |||  ||  ||| |    ||  ||  ||| |   |||| | ||||||||||| |||||||| ||  | || ||||||||||||||||||||||| ||||| || || || |||||||||||||| || |||||||| 
caatatgtggtttttatgtctttattcatgtta-agcttcttggtcccgacaactc-----acattgaa-tctttgagtttcatgtgtacatttaatgctttcccagGGTCACTTTTCTGGTAGCAGAAGCTTGCTTGATAGCAGGTGCAACCAAGAATGCCTACCACACCAAATACCGTGGAATGATTTATGCTCATAACTTCTCA

upper sequence: Vv01s0011g03560.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G13380.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------------ctgtttaatttggcatctg--gataga---ttatatagtttattgttcttgccagcttcaatgatac----------------tgaaatctaag--aacttcttactgtttgtg-----catctgcagGATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAATGCCTATCACACAAAGTATCGAGG--AATGATTTATGCCCAGAACTTCTCC
                                                            | || |   ||  || |   || |||   ||| || | ||  |||| |||  |||||  |  |||                 |||  ||| |   ||  | ||  | ||         ||  | ||||||||| |||||||| |||||||| ||| |||| ||||| || |||||||| || || |||||||||||   | |      |    |  |  |  | ||   
gtgagtccctttatcttaaacatctctaaagcaatgtatatatcttcaagtttagcttcatcttgagagtgatatatattgaaagagctttagattgatttctgtttttga-agctttgaacatatcaatggattagtagtttgatttctcaaccaatattttgatattcaaatttgacaatttcagGATGACATTTCTGGTAGCAGAAGCTTGTGTAATAGCAGGAGCGACCAAGAACGCATACCACACAAAGTACTTAAGTTCGCAAACCTTTTCGTGTGCATCA--

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|110356770|gb|EC919841.1|EC919841
EST:     GCTCCTGGTGGAAATCGGGCTTGGTCCATCATCTATTTTGTCTCATCATG                         GATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAA
genomic: GCTCCTGGTGGAAATCGGGCTTGGTCCATCATCTATTTTGTCTCATCGTGgtgagaaatc ... gcatctgcagGATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAA
EST: gi|161712668|gb|FC062240.1|FC062240
EST:     GCTCCTGGTGGAAATCGGGCTTGGTCCATCATCTATTTTGTCTCATCATG                         GATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAA
genomic: GCTCCTGGTGGAAATCGGGCTTGGTCCATCATCTATTTTGTCTCATCGTGgtgagaaatc ... gcatctgcagGATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAA
EST: gi|110703227|gb|EE079888.1|EE079888
EST:     GCTCCTGGTGGAAATCGGGCTTGGTCCATCATCTATTTTGTCTCATCATG                         GATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAA
genomic: GCTCCTGGTGGAAATCGGGCTTGGTCCATCATCTATTTTGTCTCATCGTGgtgagaaatc ... gcatctgcagGATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAA
EST: gi|110412485|gb|EC978235.1|EC978235
EST:     GCTCCTGGTGGAAATCGGGCTTGGTCCATCATCTATTTTGTCTCATCATG                         GATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAA
genomic: GCTCCTGGTGGAAATCGGGCTTGGTCCATCATCTATTTTGTCTCATCGTGgtgagaaatc ... gcatctgcagGATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAA
EST: gi|110385297|gb|EC949807.1|EC949807
EST:     GCTCCTGGTGGAAATCGGGCTTGGTCCATCATCTATTTTGTCTCATCATG                         GATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAA
genomic: GCTCCTGGTGGAAATCGGGCTTGGTCCATCATCTATTTTGTCTCATCGTGgtgagaaatc ... gcatctgcagGATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAA
EST: gi|110373094|gb|EC937304.1|EC937304
EST:     GCTCCTGGTGGAAATCGGGCTTGGTCCATCATCTATTTTGTCTCATCATG                         GATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAA
genomic: GCTCCTGGTGGAAATCGGGCTTGGTCCATCATCTATTTTGTCTCATCGTGgtgagaaatc ... gcatctgcagGATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccagcttcaatgatactgaaatctaagaacttcttactgtttgtgcatctgcagGATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAATGCCTATCACACAAAGTATCGAGGAATGATTTATGCCCAGAACTTCTCC
                               ttcttac  putative branch site (score: 2)
                   aaatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtttaatttggcatctggatagattatatagtttattgttcttgccagcttcaatgatactgaaatctaagaacttcttactgtttgtgcatctgcagGATGACTTTTCTGGTTGCAGAAGCATGTCTAATTGCAGGTGCAACCAAGAATGCCTATCACACAAAGTATCGAGGAATGATTTATGCCCAGAACTTCTCC

- - - - - - gcatctg
- - - - - - - - - - - - - - - - - - - - - cttgcca