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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attggattacatatattacagcgttatgtttttaatgttgttgaggctacatttgacaaattccatttttttggttctgcttgttgattgttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCATCTATACATTGGTGATATATTTCTCGTCAACTCCAAGGAGATCATTAGAC

Basic information

species Vitis vinifera
transcript Vv07s0031g02010.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------attggattacatatattacag-cgttatgtttttaatgttgttgaggctacatttgacaaattccatttttttggttctgcttgttgattgttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCATCTATACATTGGTGATATATTTCTCGTCAACTCCAAGGAGATCATTAGAC
                                                          ||||   | | |   | | || | |    |      | |  |      ||  |   ||        || || || |  | ||||||  |  |  |  | |||  || || |  ||||||||  ||||||| |||| ||| || ||||| ||||| ||||||||||| |||||||| || |||||  ||||||| || ||||
gtaattcatgtagggttctatatggaataaatatgagttagattaacaaaaatctgttattgaggtgctt-cgtcatagacatgccatgccatgtatgatccgtaataggtgcaactgtgcttgttcttatgttagt-cttgtttgtgttctatggcagACTGACAAAGGCGACGAAGAACTGTGCAGCGTTTATGTGCCAACAAATCATCTTTACATTGGTGACATATTTCTGGTGAACTCTGAGGAGATAATAAGAC

upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G149662_T01 (Zea mays), 3'ss of exon 5
attggattacatatattacagcgttatgtttttaa-tgttgttgaggctacatttgacaaattccatttttttggttctgcttgttgattgttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCATCTATACATTGGTGATATATTTCTCGTCAACTCCAAGGAGATCATTAGAC
  |  || | | |||  || ||   ||| | |||  | ||| |   |  |      |||    |  |   ||| | | ||  |||   ||  |    | |||  || || |  || |||||  |||| ||||| | ||| || ||||| ||||||||||| ||||| |||||||| || |||||  |||||||||| ||||
gctttataaaaaataa-actgctacatgctattagcttttgattttgtcatgccctacatgcacgctcccttttgatgtggatgtacctttctttttgcagACTGACAAAGGCGATGAAGAACTGTGTAGTGTGTATGTGCCAACAAATCATCTATACATCGGTGACATATTTCTGGTGAACTCTGAGGAGATCATAAGAC

upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G15360.2 (Glycine max), 3'ss of exon 5
-----attggattacatatattacagcgttatgtttttaatgttgttgaggctacatttgacaaattccatttttttggttctgcttgttgattgttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCATCTATACATTGGTGATATATTTCTCGTCAACTCCAAGGAGATCATTAGAC
     | || |||   | | |||     | | |   | | |  | |    | |   ||||| | |||  |   ||  | || |   | ||  |  |  | || ||||||| || ||||| |||||| | || ||||||||||| || || ||||||||||| ||||||||||||||| | || || ||||| || || || ||||
cctccaatgaatttt-tgtgttattttctgaggaact-actagtttctctgttttgtttgatatatttaaccatt--gattatatcttttt-tcctccatcgcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTACCTACGAACCATCTATATATTGGTGATATATTTTTGGTTAATTCCAAAGATATTATAAGAC

upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 5
---attggattacatatattacagcgttatgtttttaatgttgttgaggctacatttgacaaattccatttttttggttctgcttgttgattgttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCATCTATACATTGGTGATATATTTCTCGTCAACTCCAAGGAGATCATTAGAC
    |||   |   | |          |  ||   || |  | |     ||   ||||| | |||  |   ||  | || |   | ||  |  |  |    ||||||| || ||||| |||||| | || |||||||||||||| || || |||||||| ||||||||||||||| | || || ||||| || || || ||||
tttgttgttgtttttttcccctccttctgagtaactactaatttctcttctttgtttgatatatttaaccatt--gattatatcttttt-tcctccatttcagAAAGATAATGAAGATGAAGAGCTTTGTAGTGTTTTTGTCCCTACGAATCATCTATATATTGGTGATATATTTTTGGTTAATTCCAAAGATATTATAAGAC

upper sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ37288 (Selaginella moellendorffii), 3'ss of exon 6
attggattacatatattacagcgttatgtttttaatgttgttgaggctacatttgacaaattccatttttttg--gttctgcttgttgattgttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCATCTATACATTGGTGATATATTTCTCGTCAACTCCAAGGAGATCATTAGAC
                           |||  | | |   |  | ||| || | |     || |||  |      ||     ||||||  || |   |  |||| ||    |  ||||| ||  | |||||  | |  || || ||||||||||| |||||||| ||||| |||||||| |||||   |||  | || || |
---------------------------gttgatcaagc--tcaaagctccaat-gcttcgtttcatcgtcccattgtctcatttgttgcgtgatcttc-cagAATGAATCTGGCGACGAGGAACTTTGCAGCATCTACGTTCCCACAAACCATCTCTACATTGGAGATATCTTTCTCGTGAACTCGCGGGACGTGATCAGGC

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|22014341|gb|BQ799375.1|BQ799375
EST:     GTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG                         AAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCAT
genomic: GTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAGgtacttttag ... ttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCAT
EST: gi|110712883|gb|EE088318.1|EE088318
EST:     GTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCNG                         AAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCC
genomic: GTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAGgtacttttag ... ttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCC
EST: gi|110700237|gb|EE078049.1|EE078049
EST:     TGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTTC-G                         AGAGAGAACGAAGACGATGAGTTGTGCAGTGTCTTTGTCCCGACAAACCA
genomic: TGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTT-CAGgtacttttag ... ttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCA
EST: gi|110365975|gb|EC929565.1|EC929565
EST:     GTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG                         AAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCAT
genomic: GTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAGgtacttttag ... ttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCAT
EST: gi|161713089|gb|FC062465.1|FC062465
EST:     GTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG                         AAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAA-CCAT
genomic: GTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAGgtacttttag ... ttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCAT
EST: gi|110425265|gb|EC991647.1|EC991647
EST:     GTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG                         AAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCAT
genomic: GTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAGgtacttttag ... ttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCAT
EST: gi|110398629|gb|EC965098.1|EC965098
EST:     GTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG                         AAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCAT
genomic: GTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAGgtacttttag ... ttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctacatttgacaaattccatttttttggttctgcttgttgattgttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCATCTATACATTGGTGATATATTTCTCGTCAACTCCAAGGAGATCATTAGAC
                                           tgttgac  putative branch site (score: 3)
            aaattccattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attggattacatatattacagcgttatgtttttaatgttgttgaggctacatttgacaaattccatttttttggttctgcttgttgattgttgaccgtagAAAGAGAACGAAGACGAAGAGTTGTGCAGTGTTTTTGTCCCGACAAACCATCTATACATTGGTGATATATTTCTCGTCAACTCCAAGGAGATCATTAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgt