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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgtgggatttttgtaagtgcaaatataacatcttttctgtatgatttctatgataccgaactgagatgtcaatgacactccaattctactctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT

Basic information

species Vitis vinifera
transcript Vv15s0046g02010.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------------------------actgtgggatttttgtaagtgcaaatata--acatcttttctgtat----gatttctatgataccg---aactgagatgtcaatgacactcca-attctactctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT
                                                                       ||  ||    ||| ||   |  |  | |    |||| | ||  |||    | ||   ||  |   |   | |||   |   ||| |||    | ||  |   |  |||||||||||||||| ||| || ||||||| || |||||||| ||||| |||||||||||||| |||||| ||||||| || |||||| | || ||||||||||
gtttgttgcttccagcttgtgctttgctgaaacattttgcttgcagaaaatctagacagagatttccatgcaccttgttcctttggtcgctatatgttttcttcatcctatccatatttcagcttaacattctcttgtttatctggtttaataatcacaagtgacatgttttgcattgcagTACTTCCTGTACCAGTTGCTACGAGGGCTAAAATATGTGCACTCGGCAAATGTCTTGCACCGTGATCTGAAGCCAAGCAATTTGTTCCTTAATGCAAATT

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 3
----actgtgggatttttgta-agtgcaaatataacatcttttctgtatgatttctatgataccgaactgagatgtcaatgacactccaattctactctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT
    |       ||||| |||  | |  | ||  | ||   |||   |  ||   |||  |    ||   | || || |||   | ||  ||    ||  ||||||||||| |||||||| |||||||||| || |||||||| |||||||||||| | ||||| || ||| |||||||||| |||||| | || ||||||||||
acaaagaactatattttggtacggagggagtaatatattgcttcacaacaatga-tatattctataatctatatttctatgttccccctttt----tccttgcagTACTTCTTGTATCAGTTGTTACGAGGGCTAAAATATGTGCACTCAGCAAATATATTGCACCGCGATCTGAAGCCGAGCAATTTGTTCCTAAATGCAAATT

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G39190.1 (Glycine max), 3'ss of exon 3
actgtgggatttttgtaagtgcaa-atataacat-cttttctgtatgatttctatgataccgaactgagatgtcaatgacactccaattctactctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT
 || |  | |||   | |   ||  |   | ||| | ||  | |||     | | ||||   |       |  || ||||     |  |  | | ||  ||||| || ||||||||| ||||||||||||| |||||||||||||||||||||||  |||| |||||| | ||||| || || ||||| |||||||| || |
cctttttgttttgaattaaaacagtactcagcatacattggtctatataaccaaagatatttatactgtcttacagtgactgataagatacattttc--cagTATTTTCTGTATCAGTTGTTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACT

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G07270.1 (Glycine max), 3'ss of exon 3
actgtgggatttttgtaagtgcaaatataacat-cttttctgtatgatttctatgataccgaactga--gatgtcaatgacactccaattctactctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT
    |||  ||  |||       ||     ||  |  |   | || |||  |||  |  |   || |  ||     || | |      || |  |  |  ||||| || ||||||||  |||||||||| || ||||||||||| ||||||||||| ||||| |||||| | ||||| |||||||||||  ||||||| ||||
--catggacttcatgtggtctttaaggcttcaggcactgtagcataattcttatattttctttcttacagacactcataagaactttttttttttgccc-cagTATTTTCTGTATCAATTGTTACGAGGGCTCAAATATGTACATTCAGCAAATGTTTTGCACCGTGATCTAAAGCCTAGTAATTTGCTATTGAATGCCAATT

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 3
actgtgggatttttgtaagtgcaaatataacat-cttttctgtatgatttctatgataccgaactgagatgtcaatgacactccaattctactctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT
    |||  ||  |||     | ||     ||  |  |   | || |||  |||  |  |   ||   | | || | | |      || |  |  |  ||||| || ||||||||  |||||||||| || ||||||||||| ||||||||||| ||||| || ||| | ||||| |||||||||||  ||||||| ||||
tgcatggatttcatgtggtctccaaggcttcaggcactgtagcataattcttatattttctttcttgca-gccactcataagaactttttttttgccccagTATTTTCTGTATCAATTGTTACGAGGGCTCAAATATGTACATTCAGCAAATGTTTTGCACCGAGATCTAAAGCCTAGTAATTTGCTATTGAATGCCAATT

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 3
actgtgggattt---ttgtaagtgcaaatataacatcttt-tctgtatgatttctatgataccgaactgagatgtcaatgacactccaattctactctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT-
 || |  | |||   ||  ||| | |   || | |  ||  | | ||| |   | | ||||   |       |  || ||||     |  |  | | ||  ||||| || || |||||| || |||||||||| |||||||||||||||||||||||  |||| |||||| | ||||| || || ||||| |||||||| || | 
-ctttttgttttgaattaaaagagtactcatcatacattggtttatataac--caaagatatttatactgtctcacagtgactgataagatacattttc--cagtATTTTCTTTATCAGTTGCTACGAGGACTCAAATATGTACACTCAGCAAATGTTCTGCACCGTGATCTAAAGCCTAGCAACTTGCTACTGAATGCCAACTG

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G01560.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------actgtgggatttt---tgtaagtgcaaat--ataac----atcttttctgtatgatttctatgataccgaactgagatgtcaatgacactccaattctac-tctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT
                                ||   | || ||   | || ||  || |  ||||     |||||||  ||  ||   ||||||    |   |  |||||  || || |   |||| ||  | | |||||| ||||||||||||| |||| ||||| || || ||||| || ||||| |||||  ||||||||||||| || |||||||| ||||| ||||||||||| |
gtacgcattaacctctcctgtgcttcttatagctcaagtatcttctgtttaggtcaaagtttataatcagaatctttttggttcgaaggctatgaagttggggtttgatgt--ataac-cataaattttatgtttttgcagTTCTTCCTGTATCAGTTGTTGCGAGGCCTCAAGTATGTGCATTCAGCCAATGTACTGCATCGTGATTTAAAACCGAGTAACTTGCTCCTGAATGCAAACT

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------------------------------------actgtgggat-ttttgtaagtgcaaatataacatcttttctgtatgattt-ctatgataccgaactgagatgtcaatgacactccaattctactctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT
                                                                                               | ||   |||  ||| ||||||  |   ||| |    ||  || || | | || |||    |   | ||   | | |     | | ||| |  | |  |||||  || ||||||||| |||| || || || |||||||| || ||||| ||||| |||||||| |||||||| || || |||||||| |||||||||||||
gtatgcatcaatctccatcttgcttatatctagcagctgaatcttctgtttctactttagaagcagctgttattgtgttagagcatctgatgagtattgcttgatactttataagtgagagc-taataaggatttcgtttgttatgctttgaagttgtgtttagtaattagt-----ttcgattatgtttt--gcagTTTTTTCTGTATCAGTTGTTGCGTGGGCTCAAATATGTTCATTCAGCTAATGTATTGCATCGAGATTTGAAACCTAGCAATTTGCTCCTGAATGCAAATT

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S59_325V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------actgtgggatttttgtaagtgcaaatataacatc--ttttctgtatgatttctatgataccgaactgagatgt--caatgacactccaatt------ctactctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT
                           | |    ||||| |   | |   |    | ||  ||||||  |  | |  | |  | |     |||  |||  || ||    |  |  |       |||| | ||||||||||  |||| ||| |  | || || || || ||  | ||||| || || ||  | || |||||||| |||||||| ||||||||||||||||||||||
gtgtgactgattgattttttttttttttttttttttttttttgctaccgtttcttcgtcgattttcttcactactgttgtttttcttg-ttgatgtgtggcagtggagtttgagatactgtgttactttgtgcagTACTTTTTGTACCAGCTACTTCGTGGGCTCAAGTACATTCACTCGGCGAAAGTTCTTCACCGTGATTTAAAGCCGAGCAATTTGCTTCTGAATGCAAATT

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|161717055|gb|FC068463.1|FC068463
EST:     TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGG                         TACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
genomic: TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGGgtttggcacc ... ctctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
EST: gi|351036505|gb|FQ457218.1|FQ457218
EST:     TGCGTCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGG                         TACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
genomic: TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGGgtttggcacc ... ctctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
EST: gi|110727011|gb|EE103312.1|EE103312
EST:     TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGG                         TACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
genomic: TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGGgtttggcacc ... ctctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
EST: gi|110686022|gb|EE063251.1|EE063251
EST:     TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGG                         TACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
genomic: TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGGgtttggcacc ... ctctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
EST: gi|351053736|gb|FQ441502.1|FQ441502
EST:     TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGG                         TACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
genomic: TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGGgtttggcacc ... ctctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
EST: gi|161706043|gb|FC054936.1|FC054936
EST:     TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGG                         TACTTCCTGTATCAGGT
genomic: TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGGgtttggcacc ... ctctctgcagTACTTCCTGTATCAGGT
EST: gi|27586442|gb|CB009137.1|CB009137
EST:     TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGG                         TACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
genomic: TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGGgtttggcacc ... ctctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
EST: gi|351046083|gb|FQ441466.1|FQ441466
EST:     TGCAACAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGG                         TACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
genomic: TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGGgtttggcacc ... ctctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
EST: gi|352786392|gb|FQ479001.1|FQ479001
EST:     TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGG                         TACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
genomic: TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGGgtttggcacc ... ctctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
EST: gi|26261816|gb|CA812879.1|CA812879
EST:     TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGG                         TACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGGCAAA
genomic: TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGGgtttggcacc ... ctctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAG-CAAA
EST: gi|351039574|gb|FQ461441.1|FQ461441
EST:     TGCAACAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGG                         TACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT
genomic: TGCATCAGATAATACGTTCCAACCAACCACTGAATGATGACCACTGCCGGgtttggcacc ... ctctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttctatgataccgaactgagatgtcaatgacactccaattctactctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT
                                        ttctactctct  CT-rich tract
     tatgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgtgggatttttgtaagtgcaaatataacatcttttctgtatgatttctatgataccgaactgagatgtcaatgacactccaattctactctctgcagTACTTCCTGTATCAGGTGTTACGAGGACTTAAATATGTACACTCAGCAAATGTCTTGCATCGTGATTTGAAGCCGAGTAATTTGCTTCTGAATGCAAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - aaatata
- - - - - - - - - - - - - - - - - - - ctgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - accgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactcca