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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaataccacctaaaagagtttgtatgttaccattagagcttctctcgagttacctattatgattcattacttgaaaaaaatttaaacccaattttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCACTTGCATATGCCCGCATACAGGGAAAGGCTGCTCTCATTGCCCATTTCC

Basic information

species Vitis vinifera
transcript Vv01s0150g00090.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0150g00090.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 13
--aaataccacctaaaagagtttgtatgttaccattagagcttctctcgagttacctattatgattcattacttgaaaaaaatttaaacccaattttg--gcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCACTTGCATATGCCCGCATACAGGGAAAGGCTGCTCTCATTGCCCATTTCC
  ||| |  |  |         ||||   |||    ||   | | || |  ||  ||| |   |   ||  | |   |  ||||  |    |  ||||  |||| |||| ||||| |||||||||||||| |||||||| ||||||||||| || || ||||| ||||| || || |||| |  |||| | ||||| ||||| |
ttaaaaagtatttctgc---cctgtagagtactgccagttttcccctggcattttctaattgaaagtat-gcataggattaattggacttgacatttgctgcagACATTTAATGGCAAGAAATGGGAGAAATTCAATAGTGAAAAGGTGGCGTCGCTCGCATACGCCCGGATTCAAGGAAGGAGTGCTTTGATTGCTCATTTTC

upper sequence: Vv01s0150g00090.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
--aaatacc---acctaaaagagtttgtatgttaccattagagcttctctcgagttacctattatgattcattacttgaaaaaaatttaaacccaat---tttg-gcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCACTTGCATATGCCCGCATACAGGGAAAGGCTGCTCTCATTGCCCATTTCC
  |  | ||    || | |      |   ||  |  |   ||   | | || ||||       |  |||   |    ||| |  |  || | |  ||   | || |||| ||||||| || ||||||||||||||||||||||| || || |||||||||||||| || ||| | || ||||||| |   ||| | ||||| |||||||
gtatgttcctgtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaagattaactatagctgatacttctgtgcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC

upper sequence: Vv01s0150g00090.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------------aaataccacctaaaag-agtttgtatg--ttacc--attagagcttctctcgagt---tacct--attatgatt---cattacttgaaaaaaatttaaacccaattttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCACTTGCATATGCCCGCATACAGGGAAAGGCTGCTCTCATTGCCCATTTCC
                                                  | |   || |   |  |  || ||||  || ||  ||| |  ||||  |  | |    | ||  |  |||  |      ||     |   | |||     |  ||||  |||   || ||||| || || ||||||||||| || || || ||||||||||||||||| |||||| | || || || ||  | || || ||||| |||||||
gtgagaattattcaattaaataagtgctactgtatcgtgcagttatggctattttgacttttgatcaacttatatggcttgccaaatttgtacttcgataaaatatccatctggaacatggatgtgtgctatcctgagctattttttcatcgttttt--cagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCCAGAATCCAAGGGAAAACAGCCCTGATTGCTCATTTCC

upper sequence: Vv01s0150g00090.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
aaataccacctaaaagagtttgtatgttaccattagagcttctctcgagttacctattatgattcattacttgaaaaaaatttaaacccaattttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCACTTGCATATGCCCGCATACAGGGAAAGGCTGCTCTCATTGCCCATTTCC
                                                |||    |   |  ||  ||  | |     | | | |  |    | |  ||| | |||||||||||||| |||||||||||||| ||||| ||||| || || || || || || || ||||| || |||| ||| ||| | || |||||||
------------------------------------------------gtttgacaccgttgtt--ttcttcgtgcgcattctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC

upper sequence: Vv01s0150g00090.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
aaataccacctaaaagagtttgtatgttaccattagagcttctctcgagttacctattatgattcattacttgaaaaaaatttaaacccaattttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCACTTGCATATGCCCGCATACAGGGAAAGGCTGCTCTCATTGCCCATTTCC
                   || | ||| |  |  ||||        ||| |   |  || || |   | ||  ||||    | |  |    ||||  ||| | |||||||| ||||||||||||||||| || ||||| ||||||||||| || || || || || || || || ||||| || || || || || ||||
------------------gttctctgtgaaaaagagagag------gagat-tttcctacgacttggttct--aaaacttgtcattctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC

upper sequence: Vv01s0150g00090.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: EFJ29693 (Selaginella moellendorffii), 3'ss of exon 10
aaataccacctaaaagagtttgtatgttaccattagagcttctctcgagttacctattatgattcattacttgaaaaaaatttaaacccaattttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCACTTGCATATGCCCGCATACAGGGAAAGGCTGCTCTCATTGCCCATTTCC
                                                |||    |   |  ||  ||  | |     | | | |  |    | |  ||| | |||||||||||||| |||||||| ||||| ||||| ||||| || || || || || || || ||||| || |||| ||| ||| | || |||||||
------------------------------------------------gtttgacaccgttgtt--ttcttcgtgcgcattctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAATTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC

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|83274793|gb|DV938889.1|DV938889
EST:     ATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAG                         GCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCA
genomic: ATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAGgtttgtttct ... attttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCA
EST: gi|46910430|gb|CN545805.1|CN545805
EST:     ATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAG                         GCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCA
genomic: ATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAGgtttgtttct ... attttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCA
EST: gi|32245817|gb|CD711636.1|CD711636
EST:     ATGCCTTTATCAACAGGACCGATCCTTGCCAGATTATTCCATTCTATCAG                         GCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGAGAAAAGGTGGCATCA
genomic: ATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAGgtttgtttct ... attttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCA
EST: gi|110732197|gb|EE107275.1|EE107275
EST:     ATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAG                         GCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCA
genomic: ATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAGgtttgtttct ... attttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCA
EST: gi|110429936|gb|EC996451.1|EC996451
EST:     ATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAG                         GCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCA
genomic: ATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAGgtttgtttct ... attttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCA
EST: gi|110379026|gb|EC944195.1|EC944195
EST:     ATGCCCTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAG                         GCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCA
genomic: ATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAGgtttgtttct ... attttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCA
EST: gi|110389267|gb|EC954091.1|EC954091
EST:     ATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAG                         GCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCA
genomic: ATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAGgtttgtttct ... attttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCA
EST: gi|32245389|gb|CD711208.1|CD711208
EST:     ATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAG                         GCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCA
genomic: ATGCCTTTATCAACATGACCGATCCTTGCCAGATTATTCCATTCTATCAGgtttgtttct ... attttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagttacctattatgattcattacttgaaaaaaatttaaacccaattttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCACTTGCATATGCCCGCATACAGGGAAAGGCTGCTCTCATTGCCCATTTCC
         tattatgattcattac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaataccacctaaaagagtttgtatgttaccattagagcttctctcgagttacctattatgattcattacttgaaaaaaatttaaacccaattttggcagGCATTCAATGGAAAGAAATGGGAGAAGTTCAATAGCGAAAAGGTGGCATCACTTGCATATGCCCGCATACAGGGAAAGGCTGCTCTCATTGCCCATTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - -ccaccta
- - - - - - aaagagt
- - - - - - - - - - tgtatgt
- - - - - - - - - - - - - - -ccattag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaccca