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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttagggtacttatctttttgggaaaattgctgcaactcacctttattttttgggtcatcatggtcaactgaatcttaattggttgttttgattgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAG

Basic information

species Vitis vinifera
transcript Vv02s0012g01170.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 6
gttagggtacttatctttttgggaaaattgctgcaactcaccttt--attttttgggtcatcatggtcaactgaatcttaat--tggttgttttgat---tgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAG
       |  ||   ||| |   |    || |     |   | ||  || ||||      || |       |    ||  ||  ||  | | |  |    | | ||||| ||||| ||| | ||||||||||| ||||||||||||||||||||||| |||||  |||||
-------tgttttcttttgttctatttctggtttcgtttgtccttgaatgttttacaatttcgtaactgcttagtgctagatactgaatctctgaaaatgtttgtagGCGATGGTGGCAAGAGGGGATCTTGGTGCTGAACTTCCAATTGAGGAAGTTCCTTTGCTGCAG

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G144730_T01 (Zea mays), 3'ss of exon 6
-gttagggtacttatctttttgggaaaattgctgcaactcacctttattttt---tgggtcatcatggtcaactgaatcttaattggttgttttgattgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAG
   |||  |   ||       ||||||||  |  || ||     ||| || |   |     ||  | |||  ||  |   |||  | |||   |   | |  |||||||||| |||||||| || ||||| ||||||||||| |||||||| || |||||  | |||
ctctagttttgataaacaaaagggaaaatatcaccatcttgtacttagttataattctactattctagtctgctagacactaa--gcttgaaat--cttttcagGCAATGGTGGCACGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G033526_T02 (Zea mays), 3'ss of exon 6
gttagggtacttatctttttgggaaaattgctgcaactcacctttattttttgggtcatcatggtcaactgaatcttaattggttgttttga---ttgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAG
 |   |||     | |  |    |||| ||     | |  || | || |  |   |  | ||  |     |  || ||     |    ||||    | |  |||||||||| || ||||| || ||||| ||||||||||| |||||||| || |||||  | |||
-tacaggtctaggtttgataaacaaaaatgaaaataat-gccatcatgtactccttagttataattc-tagtctcctagacactgaacttgaaatcttttcagGCAATGGTGGCGCGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAG

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G40860.1 (Glycine max), 3'ss of exon 5
---gttagggtacttatctttttgggaaaattgctgcaactcacctttattttttgggtcatcatggtcaactgaatcttaattggttgttttgattgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAG
    |    ||  ||   | ||    || ||    | | |  | |   || |||      |       || | |  || |  |  ||| | || ||| |  |||| ||||| || ||||||||||||||||||||||||||||| |||||||| ||||||||||||
ttgatggaagtctttgaatgttattcaatatcaagg-atcgaagcaagatcttt--atctacaggtagcatccggttcatcttgagttttatttattttgcagGCCATGGTCGCTCGTGGGGATCTTGGAGCTGAACTTCCAATAGAGGAAGTTCCTTTATTGCAG

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G04490.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------gttagggtacttatctttttgggaaaattgctgcaactcacctttattttttgggtcat-catggtcaact---gaatctta-attggttgttttg---attgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAG
                                                  || | | | | || |||||   |  | |  ||  | || |  || | |||      ||  |||      |   |||  | | ||||   |||||    ||| | ||||| |||||| |  |||||||||||||||||||||||||||| |||||||| ||||||||||||
gttaattggtaaatgtaaactttttattctgttgagaagttttatattgatttgtgaagtaattttttttaaattactcttgttattctctattttatttcactatatatatgtctggatagagaacgtcacattgagagttttatttattttgtagGCCATGGTTACTTGTGGGGATCTTGGAGCTGAACTTCCAATAGAGGAAGTTCCTTTATTGCAG

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G32440.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagggtacttatctttttgggaaaattgctgcaactcacctttattttttgggtcatcatggtcaactgaatcttaattggttgttt-tgattgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAG
               ||  |   ||| |   | |        ||||| | |||   | |   |   | |   | ||||  |  || |   || || |  ||||||||||||| ||||| |||||||||||||||||||| ||||| || ||||| || || |||
--------------gttggtttcaaagtcttttctgtcagagtttatatgttgatacttagcgcagagccttagcttatataattatcaatgctttttcagGCAATGGTTGCTCGTGGAGATCTTGGAGCTGAACTTCCCATTGAAGAGGTCCCGTTGTTACAG

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S318_21V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------gttagggtacttatct-ttttgggaaaattg--ctgcaactcacctttattttttgggtcatcatggtcaact------gaatcttaattggttgttttgattgt-----atagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAG
                                                                                    |||   || |||   | ||||  |||   ||   | | | | |    | |    ||| |||   |||| || |         || |  ||   ||||  | || |       |||| |||||||| ||||| ||||||||||| || || ||||||||||| || ||| |  | |||
gtgagtttctattaacctggtttatactgtgtgtgtggtcctttcggccaactaattctgtgccaaagtttttgggtaggatgggttcaagtgcttgcatgttttatgaattgtggatttctatttattcctctcggctggctcaatctggttaaattgcaaaagttcctctttaagtgttcagctttttgtttgcagGCTATGGTTGCCCGTGGTGATCTTGGAGCCGAGCTGCCAATTGAGGAGGTGCCTCTTCTCCAG

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S205_25V6.1 (Physcomitrella patens), 3'ss of exon 5
-------gttagggtacttatctttttgggaaaattgctgcaactcacctttattttttgggtcatcatggtcaactgaatcttaattggttgttttgattgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAG
       |   | |||    || | ||  | | ||     | |  | | |||   |   | || | |    |  | | ||  ||  |    ||||||  ||    |||| |||||||| || || |||||||||||||| || |||||||||||||| ||  |  |||||
actttatgcatgtgtaag-gtcatgttttgcacatcatcacgaaacgcattttggtacagtgtgagcgccat--attaaaattt--tcaactgttttcctttc--agGCTATGGTTGCTCGAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAG

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|110711036|gb|EE087773.1|EE087773
EST:     GTGCAGATTCCATACCAAATCTTCATTCCATTATTTCTGCTTCTGATGGG                         GCAATGGTTGCACGTGGGGATCTCGGAGCTGAACTTCCAATTGAGGAAGTC
genomic: GTGCAGATTCCATACCAAATCTTCATTCCATTATTTCTGCTTCTGATGGGgttagttttc ... gattgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTC
EST: gi|27586266|gb|CB008961.1|CB008961
EST:     GTGCAGATTCCATACCAAATCTTCATTCCATTATTTCTGCTTCTGATGGG                         GCAATGGTTGCACGTGGGGATCTCGGAGCTGAACTTCCAATTGAGGAAGTC
genomic: GTGCAGATTCCATACCAAATCTTCATTCCATTATTTCTGCTTCTGATGGGgttagttttc ... gattgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTC
EST: gi|351025070|gb|FQ433487.1|FQ433487
EST:     GTGCAGATTCCATACCAAATCTTCATTCCATTATTTCTGCTTCTGATGGG                         GCAATGGTTGCACGTGGGGATCTCGGAGCTAAACTTCCAATTGAGGAAGTC
genomic: GTGCAGATTCCATACCAAATCTTCATTCCATTATTTCTGCTTCTGATGGGgttagttttc ... gattgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTC
EST: gi|351014767|gb|FQ437967.1|FQ437967
EST:     GTGCAGATTCCATACCAAATCTTCATTCCATTATTTCTGCTTCTGATGGG                         GCAATGGTTGCACGTGGGGATCTCGGAGCTAAACTTTCCAATTGAGGAAGT
genomic: GTGCAGATTCCATACCAAATCTTCATTCCATTATTTCTGCTTCTGATGGGgttagttttc ... gattgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTT-CCAATTGAGGAAGT
EST: gi|110388166|gb|EC952886.1|EC952886
EST:     GTGCAGATTCCATACCAAATCTTCATTCCATTATTTCTGCTTCTGATGGG                         GCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTC
genomic: GTGCAGATTCCATACCAAATCTTCATTCCATTATTTCTGCTTCTGATGGGgttagttttc ... gattgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTC
EST: gi|351030123|gb|FQ430865.1|FQ430865
EST:     GTGCAGATTCCATACCAAATCTTCATTCCATTATTTCTGCTTCTGATGGG                         GCAATGGTTGCACGTGGGGATCTCGGAGCTAAACTTCCAATTGAGGAAGTC
genomic: GTGCAGATTCCATACCAAATCTTCATTCCATTATTTCTGCTTCTGATGGGgttagttttc ... gattgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTC
EST: gi|351027131|gb|FQ439993.1|FQ439993
EST:     GTGCAGATTCCATACCAAATCTTCATTCCATTATTTCTGCTTCTGATGGG                         GCAATGGTTGCACGTGGGGATCTCGGAGCTAAACTTCCAATTGAGGAAGTC
genomic: GTGCAGATTCCATACCAAATCTTCATTCCATTATTTCTGCTTCTGATGGGgttagttttc ... gattgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttttgggtcatcatggtcaactgaatcttaattggttgttttgattgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAG
                          aatcttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagggtacttatctttttgggaaaattgctgcaactcacctttattttttgggtcatcatggtcaactgaatcttaattggttgttttgattgtatagGCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - -ggaaaat
- - - - - - - - - - - - - - - - -caactca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggttgt