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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttgataattacagtatgttttgacccttatttgttgagtaagagtatactgtagagcagacatttaaaattgttaccttatcagttgcattctcacagGTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTTGATACAACTGATAGAAAGATCCAGAAAAAG

Basic information

species Vitis vinifera
transcript Vv19s0015g00470.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g00470.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA01G03930.1 (Glycine max), 3'ss of exon 16
atttgataattacagtatgttttgacccttat-ttgttgagtaagagtatactgtagagcagacattta---aaattgttaccttatca-gttgcattctcacagGTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTTGATACAACTGATAGAAAGATCCAGAAAAAG
     || | ||   | ||||  ||  ||| |  |  |   | |   |||  || | ||||     ||    |   ||| || || |     |||| | |   ||||  | |||||||| || ||||| || ||| | ||||||| ||||||||||||||| ||||| |||||||||
----cattactaatttttgttaggatacttgtactactatattatgatatg-tgaaaagcaagggcttgttgattgtgtaacattcttgcactgcaattttctagGTGCGAGATCAGATCCACCAAGCAGGGTATCACGTTGATGCTGATACAACTGATAGGAAGATTCAGAAAAAG

upper sequence: Vv19s0015g00470.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA02G03750.1 (Glycine max), 3'ss of exon 16
-atttgataattacagtatgttttgacccttatttgttgagtaagagtatactgtagagcagacatttaaaattgttaccttatca-gttgcattctcacagGTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTTGATACAACTGATAGAAAGATCCAGAAAAAG
  ||  || | ||   | ||||  |   ||  | |  ||| || | | | |     |   ||   ||||   | || || || |     |||| | |   ||||  | |||||||| || ||||| || ||||| ||||||| ||||||||||||||| ||||| || || |||
tgttccattactaatttgtgttagggtactagtattatga-tatgtgaaaagcaagggctagttgtttattgt-gtaacattcttgcactgcaattttctagGTGCGAGATCAGATCCACCAAGCAGGGTATTACGTTGATGCTGATACAACTGATAGGAAGATTCAAAAGAAG

upper sequence: Vv19s0015g00470.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT1G18130.1 (Arabidopsis thaliana), 3'ss of exon 2
atttgataattacagtatgttttgaccctta-tttgttgagtaagagtatactgtagagcagacatttaaaattgttaccttatcagt-tgcattctcacagGTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTTGATACAACTGATAGAAAGATCCAGAAAAAG
      | ||      |||  |  || ||||    ||| | |   ||  |  | |          ||   ||||  | | || |  |  |  ||||  |||||| || ||||| |||||  ||||||| || |||||||||||||| ||||| ||||||||  ||    | |||
-----gttatacattcatgactgtactcttaacgagtttacttgcagagtcttattatatctctcttcctaatt--tcctttgtttgcgtatattcaaacagGTGAGAGATCAAATTCACGAAGCTGGCTACTATGTTGATGTTGACACAACGGATAGAAACGTCAGTGACAAG

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|30330560|gb|CD013822.1|CD013822
EST:     AAGCAATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTCAG                         GTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTTGATACAACT
genomic: AAGCAATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTCAGgtagtttgct ... attctcacagGTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTTGATACAACT
EST: gi|110694684|gb|EE072006.1|EE072006
EST:     AAGCAATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTCAG                         GTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTTGATACAACT
genomic: AAGCAATTGTTTGCCCTGTGTCAGAGAAATCTCAGCCATATGCACTTCAGgtagtttgct ... attctcacagGTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTTGATACAACT
EST: gi|32460758|gb|CD801932.1|CD801932
EST:     CAGCCATATGCACTTCAG                         GTATAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTTGATACAA
genomic: CAGCCATATGCACTTCAGgtagtttgct ... attctcacagG--TAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTTGATACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatactgtagagcagacatttaaaattgttaccttatcagttgcattctcacagGTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTTGATACAACTGATAGAAAGATCCAGAAAAAG
                                            cattctc  CT-rich tract
                acatttaaaattgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttgataattacagtatgttttgacccttatttgttgagtaagagtatactgtagagcagacatttaaaattgttaccttatcagttgcattctcacagGTAAGGGATCAGATTCATCAAGCTGGTTATTATGTTGATGTTGATACAACTGATAGAAAGATCCAGAAAAAG

- - - - - - cagtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcagaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagttgc