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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattccaattcctctgtggattacagatgctagttatggatttgttatatgaatattgactcacactagtaagatgcgcagATTTCATGTCTTAGAGCAGAACAGACACAGCTGAGTAGGTCTCTAGAAAAGGAGAGACAGAGAGCAGCTGAAAATAGGCAGGAGTATCTAGCGGCAAAAG

Basic information

species Vitis vinifera
transcript Vv16s0098g00540.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os05g48620.1 (Oryza sativa), 3'ss of exon 12
----------------------------gtgatt-ccaattcctctgtggattacagatgctagttatggatttgttatatgaatattgactcacactagtaagatgc------gcagATTTCATGTCTTAGAGCAGAACAGACACAGCTGAGTAGGTCTCTAGAAAAGGAGAGACAGAGAGCAGCTGAAAATAGGCAGGAGTATCTAGCGGCAAAAG
                             | | |   ||     |  | | ||   |      |||  |  || || | |    |     || |||  | ||   ||       ||||||| ||  ||||||| |||| ||||||||||||||| | ||||| ||||| ||||| ||||||||| | |||| ||| |||||||| || ||    || |
gtttgtgcatcaagttattctgaaataaatcactattaacattaccataggtttatggccaaggtttagttttagtcagaaaggtgacttcttacaaaaatattttgttcttatgcagATTACAATTCTTAGAACAGAGCAGACACAGCTGAGTCGATCTCTTGAAAAAGAGAGGCAGAGAGCATCCGAAAGTAGACAGGAGTACCTGGCAATTAAGG

upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G168654_T01 (Zea mays), 3'ss of exon 21
-------------------gtgattccaattcctctgtgg-attac-----agatgctagttatggattt--gttatatgaatattgactcacactagtaagatgcgcagATTTCATGTCTTAGAGCAGAACAGACACAGCTGAGTAGGTCTCTAGAAAAGGAGAGACAGAGAGCAGCTGAAAATAGGCAGGAGTATCTAGCGGCAAAAG
                   |  |  | ||       || | ||||      |||   |  ||   |||||  || |  | | | |||      |||| |  | |  ||||||| ||  ||||||| |||| ||||||||||||||  | ||||| ||||||||||| ||||||||| |||||| ||| |||||||| |||||    ||||
gtttgtgcatcaatttctagcaaaacaaaaaatatggtagtattagtgttaagaccttgctttcagatttaagtcaagtaatttttggggtg-actattgggttatgcagATTACAATTCTTAGAACAGAGCAGACACAGCTGAGCCGATCTCTTGAAAAGGAGAGGCAGAGAGCATCTGAAAGTAGACAGGAGTACCTAGCAATCAAAG

upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G150257_T01 (Zea mays), 3'ss of exon 7
-----------------------gtgattccaattcctctgt--ggattacagatgctagttatggattt-gttatatgaatattgactcacactagtaagatgcgcagATTTCATGTCTTAGAGCAGAACAGACACAGCTGAGTAGGTCTCTAGAAAAGGAGAGACAGAGAGCAGCTGAAAATAGGCAGGAGTATCTAGCGGCAAAAG
                          |    ||| |   | |  || ||| |||    | ||   ||||| || |  | | | |||      |||| |  |    ||||||| ||  ||||||  |||| || |||||||||||  | ||||| ||||||||||| ||||||||| |||||| ||| |||||||| |||||    ||||
gtttgtgttcaatttctagcaaaagcaaaaaaatgctagtattagggtta-agacctcactttcagatttagtcaagtaatttttggggtg-actatttggtcatgcagATTACAATTCTTAGGACAGAGCAAACACAGCTGAGCCGATCTCTTGAAAAGGAGAGGCAGAGAGCATCTGAAAGTAGACAGGAGTACCTAGCAATTAAAG

upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA13G43330.1 (Glycine max), 3'ss of exon 15
gtgattccaattcctctgtggattacagatgctagttatggatttgttatatgaat-attgact---cacactagtaa-gatgcgcagATTTCATGTCTTAGAGCAGAACAGACACAGCTGAGTAGGTCTCTAGAAAAGGAGAGACAGAGAGCAGCTGAAAATAGGCAGGAGTATCTAGCGGCAAAAG
||  |   | |||    ||| | | ||  |  |   |    |||| || ||| ||| | | |||     |  ||  || ||    ||||||||||||||||||||||||||||| ||| | |||||| | || |||||||||||||| || ||||||||||  |||||||| ||||| || ||||| |
gttctgtaatttctcaagtgaaat-catgtctttaatggcaattttttgtataaatgacttactttgttctttaacaatgaattacagATTTCATGTCTTAGAGCAGAACAGACTCAGTTAAGTAGGACCCTTGAAAAGGAGAGACAAAGGGCAGCTGAAAGCAGGCAGGAATATCTTGCAGCAAAGG

upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA15G01980.1 (Glycine max), 3'ss of exon 13
gtgattccaattcctctgtggattacagatgctagttatggatttgt---tatatgaatattgactcacactagtaa-gatgcgcagATTTCATGTCTTAGAGCAGAACAGACACAGCTGAGTAGGTCTCTAGAAAAGGAGAGACAGAGAGCAGCTGAAAATAGGCAGGAGTATCTAGCGGCAAAAG
||  |   | |||    ||| | |   |    || |      |||||   || |||| |        ||  ||  || ||    |||||||||||||||||||| |||||||| ||| | |||||| | || |||||||||||||| || ||||||||||  |||||||| ||||| || ||||| |
gttctgtaatttctcaagtgaaattatgtctttaatggcaattttgtgtatacatgacttactttgtactttaacaatgaattacagATTTCATGTCTTAGAGCTGAACAGACTCAGTTAAGTAGGACCCTTGAAAAGGAGAGACAAAGGGCAGCTGAAAGCAGGCAGGAATATCTTGCAGCAAAGG

upper sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT1G79830.4 (Arabidopsis thaliana), 3'ss of exon 13
gtgattccaattcctctgtggattacagat-gctagttatggatttgttatatgaatattgactcacactagtaagatgcgcagATTTCATGTCTTAGAGCAGAACAGACACAGCTGAGTAGGTCTCTAGAAAAGGAGAGACAGAGAGCAGCTGAAAATAGGCAGGAGTATCTAGCGGCAAAAG
  | || | || | | |    | |     |    | || | |     || | | ||| ||  || || |   |    |   ||| |||||||||| ||||||||||||   ||| | || | ||| || || || ||||| ||||||||||| |||||||| ||||||||||| || || || |
--gttttctatgctttttgacactgttcttcatcaattttcgcagctttctctaaattttagcttacccagttctcctatccagCTTTCATGTCTCAGAGCAGAACAGGGCCAGTTAAGCAAGTCACTTGAGAAAGAGAGGCAGAGAGCAGCAGAAAATAGACAGGAGTATCTGGCAGCTAAGG

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|161717204|gb|FC068490.1|FC068490
EST:     ATGAACGCTTGTCGCAAACCTTATCTAGAGTAAATGTCCTTGAAGCACAG                         ATTTCATGTCTTAGAGCAGAACAGACACAGCTGAGTAGGTCTCTAGAAAAG
genomic: ATGAACGCTTGTCGCAAACCTTATCTAGAGTAAATGTCCTTGAAGCACAGgtgattccaa ... agatgcgcagATTTCATGTCTTAGAGCAGAACAGACACAGCTGAGTAGGTCTCTAGAAAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctagttatggatttgttatatgaatattgactcacactagtaagatgcgcagATTTCATGTCTTAGAGCAGAACAGACACAGCTGAGTAGGTCTCTAGAAAAGGAGAGACAGAGAGCAGCTGAAAATAGGCAGGAGTATCTAGCGGCAAAAG
                               gactcac  putative branch site (score: 2)
             atttgttatatgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattccaattcctctgtggattacagatgctagttatggatttgttatatgaatattgactcacactagtaagatgcgcagATTTCATGTCTTAGAGCAGAACAGACACAGCTGAGTAGGTCTCTAGAAAAGGAGAGACAGAGAGCAGCTGAAAATAGGCAGGAGTATCTAGCGGCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA