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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggaccatccttcctttcattatctgattccacatttagcttacttggaaaaaaaaaaggttgctgaatactatgatattttctcag

Basic information

species Vitis vinifera
transcript Vv06s0061g01120.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 6
CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagt------ggaccatccttcctttcatta-tctgattccacatttagcttacttggaaaaaaaaaaggt-tgctgaatactatgatattttctcag
 || || ||||  ||||| || || ||||| ||||||||||| ||||||||||| ||||||||||| |||||||| |||||||| ||    |||||||||||  ||       |   ||| || ||| | ||  ||| || | | ||||| |||  | |   ||   ||| || | ||  ||   |  |           
TCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGATTgtatgttttctctgtttatctttacttcctttgctcttatgctagatttaccttgttagttgaactgaaatgtgtactttatgtcaaaag----------

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 6
CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggaccatccttcctttcattatctgattccacat-ttagcttacttggaaaaaaaaaaggttgctgaatactatgatattttctcag
 || || ||    |||||  | |||||||| ||||| || || || |||||||||||||| ||||| ||||||||||| ||||| ||  || ||||||||||  || |       |  || |   |   || ||  |     ||    | |  |    ||     ||||   | | | |              
TCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgctgcgtttatctctggctccttgtttttatgcactaatccaatgaggctgaactcttgttgtcaattgcaaaag-----------

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G167872_T02 (Zea mays), 5'ss of exon 4
CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggaccatccttcctttcattatc--tgattccacatt-tagcttacttggaaaaaaaaaaggttgctgaatactatgatattttctcag------------------
 || || || |  |||||  | |||||||| ||||| ||||| || |||||||||||||| ||||| |||||||| || ||||| ||  || ||||||||||  ||  ||   |   | ||| || |||  ||  |||   || |    | |     |   |   ||| ||   |||  | |  | || | || |                  
TCTGCTCCGCCGAGAGCCTTTGAAGCTTGTCGATGGGGGCCAGTCTCAGAGAACCTTTGTATACATCAAGGATGCCATCGAAGCTGTTGTGCTGATGATTgtatgtt-actgcctgcctttttatcatctctgcctccttgttctcatatgcccctgattcatcgaggctg--aaatcgtgtttt-ttctgtctgttgtgaactgcggaaaag

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G08930.1 (Glycine max), 5'ss of exon 6
CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtg-----gaccatccttcctttc---attatctgatt--------cca--------catttagcttacttggaaaaaaaaaaggttg------------ctgaatactatgatattttctcag
 |||||  |    ||||| |||||||||||||| |||||||| ||||||||||||||||||||||| || |||||||||||||| |||||| ||||||||||  ||      | | ||| ||  |||    | | | || ||        |||        ||| |   ||  ||   ||   |||   |||            |||| |  |||||  | ||  |||
TCTTCTCAGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTTGTTTACATTAAAGATGCTATTGAAGCTGTCTTGCTGATGATTgtacgttctaatgtctatctttatttttgggactgtttgttttttaaataccatacaggtccatgtgatttttttttcaagtcaaattattgttggctggtccactgagtgttatgacctgttaacag

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G30490.1 (Glycine max), 5'ss of exon 6
CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggaccatccttcctttcattatctgattccacatttagcttacttggaaaaaaaaaaggttgctgaatactatgatattttctcag-----------------------------------
 || || |||   ||||| |||||||||||||||||||||||||||||||| || ||||| || || ||||||||||||||||| ||||| |||||||||||  ||   ||||      | |  ||||   | |  | || |       |  ||    | ||      ||  | ||||| ||  ||  |                                      
TCTCCTCCGTGGAGAGCCCCTCAAGCTTGTGGATGGTGGCCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCTGTCTTATTGATGATTgtaggttc-ccatatccaatctttttatgcaactttatatattttaagttctgattgtagaatttcatctttaaactattattcttgttggatggttcaactaaatgtgaacgataatttttaacag

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA11G19550.2 (Glycine max), 5'ss of exon 6
CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtgg-accatccttcctttcattatctgattccacatttagcttacttggaaaaaaaaaaggttgctgaatactatgatatt----ttctcag---
 ||||| ||    ||||| |||||||||||||| |||||||| ||||||||||||||  ||||||| || |||||||||||||| |||||||||||||||||  ||   |   ||||  ||||  || |  || |     | |     |    ||   |    |  ||  |  ||  |    ||||    || ||||   
TCTTCTCCGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttctaatgtcctatctttatttttgggactgtttgtgttttaaatacagattcatgtgatattttttcatgttcaattattgttgttgtcagctg

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 6
CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtgg-accatccttcctttcattatctgattccacatttagcttacttggaaaaaaaaaaggttgctgaatactatgatatt----ttctcag--------------------------------
 ||||| ||    ||||| |||||||||||||| |||||||| ||||||||||||||  ||||||| || |||||||||||||| |||||||||||||||||  ||   |   ||||  ||||  || |  || |     | |     |    ||   |    |  ||  |  ||  |    ||||    || ||||                                
TCTTCTCCGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttctaatgtcctatctttatttttgggactgtttgtgttttaaatacagattcatgtgatattttttcatgttcaattattgttgttgtcagctggtccactgagtgttatgacctgttaacag

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA17G05440.1 (Glycine max), 5'ss of exon 4
CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggaccatccttcctttcattatctgattccacatttagcttacttggaaaaaaaaaaggttgctgaatactatgatattttctcag--------------------------------
 || || ||    ||||| |||||||||||||||||||| ||||||||||| || ||||| || || ||||||||||||||||| ||||| |||||||||||  ||       | |      | |||| |  ||  |    |    |  ||| | ||    |   ||  ||| || |||  |  ||||   |                                
TCTCCTCCGCGGAGAGCCCCTCAAGCTTGTGGATGGTGGTCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCCGTCTTATTGATGATTgtaggt----tcccatatgaaactttatatattttaagtactgatctgattgtagaagttcatcttt--tgactattattcttgtttcatggttcaactaaatgtgaacgataatttttaacag

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 6
CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgt-tagtggaccatccttcctttcattatctgattccacatttagcttacttggaaaaaaaaaaggtt---gctgaatactatgatattttctcag-------------
 ||||| |||| |||||| ||||||||||| ||||||||  |||| |||||||| || || ||||| || |||||||||||||| ||| | |||||||||||    |  |    |     | |   | | || || || | |     |  | | |     ||   |||    || ||  |||| ||    |   |              
TCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttccattgcctgatatatagctttttgtttacaaactgttaatgttagaagttcgaagtagtttcaactaaaacctataatgacattgtatgtttgtggttcag

upper sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 6
CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggaccatccttcctttcattatctgattccacatttagctt-acttggaaaaaaaaaaggttgctgaatactatg----atattttctcag
 ||||| || |  ||||| ||||||||||||||||||||  |||| |||||||||||  | ||||| || |||||||| ||||| ||| | |||||||| || |||   |  || || |||        ||||    | |||   || |  |    ||| ||   |   ||||||    ||    ||  |||  |||
TCTTCTGCGACGGGAGCCTCTCAAGCTTGTGGATGGTGGAGAATCACAGAGAACCTTCATCTACATCAAAGATGCTATCGAAGCTGTCCTTTTGATGATCgtgagttt-cattcattgcttatccctggtgatatatcgtttgtttttatattattaaagaagttgcatctgaattgcttgcggaattctttaccag

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|110405386|gb|EC970927.1|EC970927
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
EST: gi|30298239|gb|CB975033.1|CB975033
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACACCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
EST: gi|71884664|gb|DT033719.1|DT033719
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
EST: gi|33401793|gb|CF207420.1|CF207420
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
EST: gi|71882410|gb|DT031465.1|DT031465
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCC
EST: gi|33402259|gb|CF207886.1|CF207886
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
EST: gi|71868252|gb|DT017307.1|DT017307
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
EST: gi|349828491|gb|FQ417233.1|FQ417233
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
EST: gi|71884313|gb|DT033368.1|DT033368
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
EST: gi|22007527|gb|BQ792561.1|BQ792561
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
EST: gi|33404942|gb|CF210569.1|CF210569
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
EST: gi|110397475|gb|EC963215.1|EC963215
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
EST: gi|110420047|gb|EC986308.1|EC986308
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
EST: gi|71890357|gb|DT039412.1|DT039412
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
EST: gi|110396028|gb|EC961702.1|EC961702
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
EST: gi|110371215|gb|EC935056.1|EC935056
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
EST: gi|71888796|gb|DT037851.1|DT037851
EST:     GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATT                         GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC
genomic: GAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggac ... attttctcagGATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgttagtggaccatccttcctttcattatctgattccacatttagcttacttggaaaaaaaaaaggttgctgaatactatgatattttctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC