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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggctttctttctctctcaatttctttggcttaggtttttattttttggaaaatggaaataatttacttcttttttctgtttgatttctgtgatttttggatatgggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCA

Basic information

species Vitis vinifera
transcript Vv05s0077g02110.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g15260.1 (Oryza sativa), 3'ss of exon 1
gttggctttctttctctctcaatttctttggcttaggtttttattttttggaaaatggaaataatttacttcttttttctgtttgatttctgtgatttttggatatgggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCA
||   |  ||  || | | ||  | | |   ||    |   |  ||    ||   |    ||   |   ||     |      || ||| |||| |||||||              |     |||| |  ||||| ||||   |||||||  |||| |||||||| ||||||||||||||||| ||||| || || ||||||||||| ||||| ||||| ||||
gtaaccactcgatcccccgcacctccctcctctcgattcccttgttccctga---ttcggattgctcggtttgcgatgtgaaatggtttttgtgttttttgg--------------ttcgctagGCGTTCGAGAAGCACACCATGGAGAAGGACATCGCGGAGTACATCAAGAAGGAGTTCGACAAGAACCACGGCCCTACCTGGCACTGCATCGTCGGCCGCA

upper sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os06g29690.1 (Oryza sativa), 3'ss of exon 1
gttggctttctttctctctcaatttctttggcttaggtttttattttttggaaaatggaaataatttacttcttttttctgtttgatttctgtgatttttggatatgggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCA---
||      ||  |  | | ||  | | |   || |  |   |  ||  ||    ||    ||   | ||   |||     | |||   | ||  ||  ||   | |   |||    ||| | |||| |  ||||| ||||   |||||||  |||| | |||||| || |||   |||||||| ||||| || || ||||||||||| ||||||||||| | ||   
gtaacgactcgattccccccacctccctcctctcaattccattcttcctg----attcggattgctcacgg-tttgggggggttgcgatttgaaatggttttttgtttttctttgttcagt-agGCGTTCGAGAAGCACACCATGGAGAAGGACATCGTGGAGTACATTAAG---GAGTTCGACAAGAACCACGGCCCTACCTGGCACTGCATTGTCGGCCACAACT

upper sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G472231_T01 (Zea mays), 3'ss of exon 1
----------------------gttggctttctttctctct-caatttctttggcttaggtttttattttttggaaaatggaaataatttacttcttttttctgtttgatttctgtgatttttggatatgggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCA
                       | |   | | ||||  || |  |   ||||| ||  ||   |     |||   |  ||   |   ||     |    | ||     ||   |   ||| ||   ||   |    | ||  |||||| |  ||||| |||||| |||||||  |||| |||||||| || |||||||||||||| ||||| || || || |||||||| ||||| ||||| ||||
gtaagaaccttatgcccttgctctcgctctgccttcttcctgcgctcgatttggtttccgtcgct-ccccttgttgaccggttcttcgttgggaatgggatttggccatttggggacttttctgtcgattccttctctgtcggtcagGCATTCGAGAAGCACAGTATGGAGAAGGACATCGCGGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCA

upper sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G146012_T01 (Zea mays), 3'ss of exon 1
gttggctttctttctctctcaatttctttggcttaggtttttattttttggaaaatggaaataatttacttcttttttctgtttgatttctgtgatttttggatat------gggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCA
                  | |    || | |||   | | |   || ||     |||  |   |||  |   | ||  | | ||| |   | | |||||  ||| |        |||   |     |||||| |  || || |||||  |||||||  |||| || ||||| || |||||||||||||| ||||| || || || |||||||| ||||| ||||| ||||
-----------------gtaagaacctctcgctctcgctctgccttcttc----atgcgatcgattcccccttgttgacgggttgttcgttataattttaagatttttttttctgtcgattgcttctcagGCGTTCGATAAGCACAGCATGGAGAAGGACATCGCTGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCAACCTGGCACTGCATCGTCGGCCGCA

upper sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G04830.1 (Glycine max), 3'ss of exon 1
gttggctttctttctctctcaatttctttggcttaggtttttattttttggaaaatggaaataa-tttacttcttttttctgtttgatttctgtgatttttggatatgggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCA
||| | | ||     || ||  | |||||   ||| | || |   |||||||   ||    |   |||  || |  || |||  |  | ||    | | |||    |    | |||   | |||||| |  |||||  ||| |||||||||| || |||||||| | || ||||||||||||||||||| ||||||||| || ||||||||||| || ||||| |
gttag-tctcaacaactttct-tctcttttttttatggttcttcgttttggattctgtttctgggtttggttgtgcttgctgcgttgtgtcgtaaagtcttgacctttttgcggatt--attcagGCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGACCCACTTGGCATTGCATCGTTGGTCGTA

upper sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA15G16050.1 (Glycine max), 3'ss of exon 1
gttggctttctttctctctcaatttctttggcttaggtttttattttttggaaaatggaaataa-tttacttcttttttctgtttgatttctgtgatttttggatatgggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCA
||| | ||||     || ||   || |||   ||  | ||     |||||||   ||    |   |||  || |  || |||  |  | ||    | | |||   ||    | |||   | |||||| |  |||||  ||| |||||||||| |  |||||||| | || ||||||||||||||||||| |||||| || || ||||||||||| || ||||| |
gttag-tttcgacaactttctcctttttt--tttgtggttcctcgttttggattctgtttctgggtttggttgtgcttgctgcgttgtgtcataaagtcttgaccattttgcggatt--attcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTA

upper sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G04820.1 (Glycine max), 3'ss of exon 1
gttggcttt-----ctttctctctcaatttctttggctt---aggtttttattttttggaaaatggaaataa-tttacttcttttttctgtttgatttctgtgatttttggatatgggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCA
||| | |||     || |||||||| || ||| |  |||   | | ||     |||||||   ||    |   |||  || |  || |||| |  | ||    | | |||    |    | |||     |||||| |  |||||  ||| |||||||||| || |||||||| | || ||||||||||||||||||| |||||| || || |||||||| || || || || |
gttagttttaacgactctctctctctatatctctctctttttatggttcctcgttttggattctgtttctgggtttggttgtacttgctgtgttgtgtcgtaaagtcttgacctttttgcggattgt--tcagGCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACGTGGCATTGTATCGTTGGACGTA

upper sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA15G16060.1 (Glycine max), 3'ss of exon 1
------gttggctttctttctctctcaatttctttggcttaggtttttattttttggaaaatggaaataa-tttacttcttttttctgtttgatttctgtgatttttggatatgggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCA
       |   |    ||  ||||||  | |||||   ||| | ||   |  ||||||   ||    |   |||  || |  || |||| |  | ||    | | |||    |    | |||   | |||||| |  ||||   ||| |||||||||| || | |||||  | || ||||||||||||||||||| |||||| || || ||||||||||| || ||||| |
gttagtttcaacaactttcttctctctctctcttttttttatggttccttggtttggattctgtttctgggttttgttgtgcttgctgtgttgtgtcataaagtcttgacctttttgcggatt--attcagGCGTTTGAGAGGTACAATGTGGAGAAAGACGTCGCGGAACAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTA

upper sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G15930.1 (Arabidopsis thaliana), 3'ss of exon 1
gttggctttctttctctctcaatttctttggcttaggtttttattttttggaaaatggaaataatttacttcttttttctgtttgatttctgtgatttttggatatgggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCA
                  ||||||  ||   || ||  | |  |   |||   | ||||   |  |||  | | |  |||| | |||      |||||         | | || | |    ||||| |  |||||  |||||||||||||  | || || ||| |||| ||||||||||| || ||||| |||||  |||| |||||||||||||| |||||||
----------------aatcaattggttcaactaagagtctggtgaattgtcta-tggagtga--ttatatgtgtactctgatagata---aggatttgcattctgagatttgcttttg--cagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCA

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|110415832|gb|EC981770.1|EC981770
EST:     CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCC                         GCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
genomic: CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCCgttggctttc ... tctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
EST: gi|349822936|gb|FQ399915.1|FQ399915
EST:     CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCC                         GCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
genomic: CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCCgttggctttc ... tctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
EST: gi|110705677|gb|EE082803.1|EE082803
EST:     CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCC                         GCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
genomic: CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCCgttggctttc ... tctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
EST: gi|110365922|gb|EC929475.1|EC929475
EST:     CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCC                         GCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
genomic: CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCCgttggctttc ... tctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
EST: gi|30136271|gb|CB921609.1|CB921609
EST:     CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCC                         GCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
genomic: CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCCgttggctttc ... tctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
EST: gi|34544540|gb|CF512772.1|CF512772
EST:     CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCC                         GCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
genomic: CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCCgttggctttc ... tctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
EST: gi|34543853|gb|CF512085.1|CF512085
EST:     CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCC                         GCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
genomic: CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCCgttggctttc ... tctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
EST: gi|110702866|gb|EE079212.1|EE079212
EST:     CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCG-C                         GCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
genomic: CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCCgttggctttc ... tctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
EST: gi|34362768|gb|CF404353.1|CF404353
EST:     CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCC                         GCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGATTATATCAAGAAG
genomic: CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCCgttggctttc ... tctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
EST: gi|110376712|gb|EC941782.1|EC941782
EST:     CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCC                         GCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
genomic: CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCCgttggctttc ... tctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
EST: gi|30131911|gb|CB917250.1|CB917250
EST:     CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCC                         GCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
genomic: CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCCgttggctttc ... tctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
EST: gi|34416663|gb|CF415417.1|CF415417
EST:     AGGAGGCCATCGATATAGCCATCGCC                         GCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
genomic: AGGAGGCCATCGATATAGCCATCGCCgttggctttc ... tctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
EST: gi|110384168|gb|EC948587.1|EC948587
EST:     CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCC                         GCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
genomic: CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCCgttggctttc ... tctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
EST: gi|110691067|gb|EE068745.1|EE068745
EST:     CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCC                         GCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG
genomic: CCGATATGAAGGATGACATGCAGAAGGAGGCCATCGATATAGCCATCGCCgttggctttc ... tctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttttttctgtttgatttctgtgatttttggatatgggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCA
                                       gtctgat  putative branch site (score: 4)
            tttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggctttctttctctctcaatttctttggcttaggtttttattttttggaaaatggaaataatttacttcttttttctgtttgatttctgtgatttttggatatgggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA