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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacctccacagatcacatatgaggaatttgtttggtgaaccttttgataccatctctcattattatgtctgggttcataaacattggtggttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCACTATTCTACTCCTGTTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGA

Basic information

species Vitis vinifera
transcript Vv15s0045g00310.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------------tacctccacagat-cacatatgaggaatttgtttggtg-aaccttttgataccatctctcatt--attatgtctgggttcataaacattggtggttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCACTATTCTACTCCTGTTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGA
                                                                             |     |  ||| | || |      |   |  |   | ||||||||| |      |||  |   ||||  ||   || ||||   || ||  ||  |   ||||| |||||  | ||||||||||| || ||||| ||||||||| | || || ||||| || || |||||||||||||||||||||||||| ||||| || |
gtacatttgttatgctctaacttgagaaagggagtctgaattgtcctgttagggaaaaaaatattgtgagggatgccaaagttatggattcccacaatttttacccgaataacgtaaccttttgctgtatattctagtcacattaattcacagtacatatctat-ggaagtatttttcagGTAGTGACATTATGGTACAGAGCTCCAGAAATTCTGCTTGGAGCGCGGCAGTATTCCACACCAGTTGATGTGTGGTCTGTGGGCTGTATCTTTGCGGAAA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 4
tacctccacagatcacatatgaggaatttgtttggtgaaccttttgataccatct----ctcattattatgtctgggttcataaacattggtggttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCACTATTCTACTCCTGTTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGA
    |      |    ||    | |   || ||| |||   |||| |    || |     | |||   || |||| ||| ||||  ||||||| || |    ||||||||||  | ||||||||||| || |||||| |||||||||| || || |||||||| || |||||||| ||||| ||||| ||||||||||| ||||
--ttttgtggaaaggtattgtggtaggctggttgatga--tttttaacgtaatttaatatttattcccatttctgtgtttataataattggtgattgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCATTATTCTACGCCAGTTGATGTTTGGTCAGTGGGATGTATATTTGCAGAGA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 4
tacctccacagatca-catatgaggaatttgtttggtgaaccttttgataccatctctcattattatgtctgggttcataaacattggtggttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCACTATTCTACTCCTGTTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGA
 |  | ||  ||     ||    | |   || ||| |||   ||   |    |    | |||   || |||| ||| ||||  ||||||| || |    ||||||||||  | ||||||||||| || |||||| |||||||||| || || |||||||| || |||||||| ||||| ||||| || |||||||| ||||
-aatttcatggaaaggtattgtggtaggctggttgatgatttttaacagtttaatatttattcccatttctgtgtttataataattggtgattgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCATTATTCTACGCCAGTTGATGTTTGGTCAGTGGGATGCATATTTGCAGAGA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G25320.1 (Glycine max), 3'ss of exon 3
---tacctccacagatcacatatgaggaatttgtttggtgaaccttttgataccatctctcattattatgtctgggttcataaacattggtggttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCACTATTCTACTCCTGTTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGA
    |     | | |||   | | | |   |  |  |||  |      |  |  |  ||  |||||  | |   |  | |||||  |||| | || |    ||||||| || |||||||||||||| || |||||  |||||||||| || || |||||||| || |||||| | ||||| ||||| || |||||||| ||||
cttaaaaaatataaatcttttgtaaaggtataat--ggtagatggacagtaaaaacatcaaattatctttttctgagttataaat-ttggcgattgtttgtagGTGGTAACACTGTGGTACAGAGCTCCGGAAATTTTGCTTGGATCCCGTCAGTATTCTACCCCAGTTGATATTTGGTCAGTGGGATGCATATTTGCAGAGA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G08330.1 (Glycine max), 3'ss of exon 4
-tacctccacagatcacatatgaggaatttgtttggtgaaccttttgataccatctctcattattatgtctgggttcataaacattggtggttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCACTATTCTACTCCTGTTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGA
 |      | | |   | | |||  |  |    ||||  |      |  |  |  ||  |||||  | |   |  | ||| |  |||| | || |    ||||||| || |||||||||||||| || |||||  |||||||||| |  || |||||||| || |||||| | ||||| ||||| || |||||||| ||||
cttaaaaaatataattcttgtgaaaaggtacaatggtagagggacagtaaaaacatcaaattatctttttctgagttatagat-ttggcgattgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCATTATTCTACCCCAGTTGATATTTGGTCAGTGGGATGCATATTTGCAGAGA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 5
tacctccacagatcac-atatgaggaatttgtttggtga-accttttgataccatctctcattattatgtctgggttcataaacattggtggttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCACTATTCTACTCCTGTTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGA
 |       || |||  |||     || |  ||   ||  || |   |||  ||  |||| |  |  |   |      ||         | |||| |   |||| || || || |||||| ||||||| || ||||| || ||||| |  || || ||||| ||||||||| | ||||||||||| || |||||||||||||
-agtaagctagttcaagatactgtaaaatatttcaatgctacatccagatttcagatctcttcctggttattcacacaatttttgcatattgttc-ctttagGTTGTTACTCTCTGGTACCGAGCACCAGAGATACTCCTAGGATCTCATCATTACTCTACACCTGTTGATATTTGGTCTGTGGGGTGCATATTTGCTGAGA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S25_198V6.6 (Physcomitrella patens), 3'ss of exon 6
tacctccacagatcacatatgaggaat-ttgtttggtga--accttttgataccatctctcatta--ttatgtctgggttcataaacattggtggttctccc-----cagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCACTATTCTACTCCTGTTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGA
          ||||  |       ||| ||||| | |||  || ||||   | |||       |   ||  |||   ||||||     |   ||  |  |       |||||||| ||  |||||||||||||||| ||||| ||  | || || |||||||| ||||| ||||| |||||||||||||| || || || || |||||||
----------gatcttacgattcaaatgttgttagctgataacttttttgcatcataaacagctcatttgggtcgtagttcatgggtttcattgtctggcttaaatgcagGTGGTAACATTGTGGTACAGAGCACCAGAAATTCTCTTAGGTTCTCGCCACTACTCTACACCTGTAGATGTGTGGTCTGTAGGATGCATTTTCGCTGAGA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ15022 (Selaginella moellendorffii), 3'ss of exon 4
tacctccacagatcacatatgaggaatttgtttggtgaaccttttgataccatctctcattattatgtctgggttcataaacattggtggttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCACTATTCTACTCCTGTTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGA
            |  |  |  |  ||    ||      | ||  | || |  | |||  |  ||   |||  ||   |  |   |  || |||  ||||||| || ||| |||||||| | || || ||||| || ||||| || ||||||||||||||||| || ||  |||||||||| || || || || || ||||
-----------gtagccaaccaaaaacactttc-----atctcgtcattcgctgtcttgtagtt---tctaagtatttctatgatt-tgcttcgacccagGTTGTCACCTTGTGGTACCGTGCTCCAGAAATCCTACTTGGCTCGCGCCACTATTCTACTCCCGTAGACATGTGGTCTGTCGGGTGCATTTTCGCCGAGA

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|30132539|gb|CB917878.1|CB917878
EST:     TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAG                         GTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
genomic: TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgt ... ttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
EST: gi|22013045|gb|BQ798079.1|BQ798079
EST:     TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACA-TTACACATGAG                         GTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
genomic: TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgt ... ttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
EST: gi|110732023|gb|EE106947.1|EE106947
EST:     TTGGATTGGCAAGAGCATTTGGTATTCCTGTTANGACATTTACACATGAG                         GTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
genomic: TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgt ... ttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
EST: gi|71875892|gb|DT024947.1|DT024947
EST:     TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAG                         GTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
genomic: TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgt ... ttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
EST: gi|110376567|gb|EC941627.1|EC941627
EST:     TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAG                         GTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
genomic: TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgt ... ttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
EST: gi|110360550|gb|EC923749.1|EC923749
EST:     TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAG                         GTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
genomic: TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgt ... ttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
EST: gi|110716217|gb|EE091004.1|EE091004
EST:     TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAG                         GTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
genomic: TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgt ... ttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
EST: gi|29781538|gb|CB346072.2|CB346072
EST:     TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAG                         GTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
genomic: TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgt ... ttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
EST: gi|30126104|gb|CB911443.1|CB911443
EST:     TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAG                         GTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
genomic: TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgt ... ttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
EST: gi|71889466|gb|DT038521.1|DT038521
EST:     TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAG                         GTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
genomic: TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgt ... ttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
EST: gi|110702955|gb|EE079378.1|EE079378
EST:     TTGGATTGGCAAGAGCATTTGGTATTCCTGTTANGACATTTACACATGAG                         GTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
genomic: TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgt ... ttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
EST: gi|30126370|gb|CB911709.1|CB911709
EST:     TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAG                         GTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
genomic: TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgt ... ttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
EST: gi|110422498|gb|EC988823.1|EC988823
EST:     GGTATTCCTGTTAGGACATTTACACATGAG                         GTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
genomic: GGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgt ... ttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
EST: gi|110427638|gb|EC994087.1|EC994087
EST:     TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAG                         GTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
genomic: TTGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgt ... ttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
EST: gi|28967267|gb|CB346300.1|CB346300
EST:     TGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAG                         GTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC
genomic: TGGATTGGCAAGAGCATTTGGTATTCCTGTTAGGACATTTACACATGAGgtatcaatgt ... ttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataccatctctcattattatgtctgggttcataaacattggtggttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCACTATTCTACTCCTGTTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGA
 ttttgat  putative branch site (score: 4)
                                             ttctcccc  putative PPT
           tcattattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacctccacagatcacatatgaggaatttgtttggtgaaccttttgataccatctctcattattatgtctgggttcataaacattggtggttctccccagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCACTATTCTACTCCTGTTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGA

-acctcca
- - - - - - - - - - - - - - tgtttgg
- - - - - - - - - - - - - - - - - - - -ccttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cataaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttggtgg