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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactgtgcatttgtggtgctgaaataatttcagaatctcatgtgtgactgcctttccttatatacgtgtatttgttttcactttgatgtactaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGAACCACACATCAAAAGTTTATATTCCGGAATGTAATTTG

Basic information

species Vitis vinifera
transcript Vv13s0067g03320.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g03320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G55000.1 (Arabidopsis thaliana), 3'ss of exon 2
-----tactgtgcatttgtggtgctgaaataatttcagaa-tctcatgtgtgactgcctt--tccttatatacgtgtatttgttttcactttgatgtactaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGAACCACACATCAAAAGTTTATATTCCGGAATGTAATTTG
     | ||   ||  | |  ||||   ||  ||| | |  | || | | ||| ||  ||  | || |    | | | || ||||  | |||  |||   ||||||||||||||| ||| ||||  | || |||||||||||||||||||||||| | || |||||    | |||||||   || ||| | ||||||
gttttttcttcacaagtttt-tgcttttatccttttaaatctttcctctatgaatggtttggttctaaatggcatctcttggtttgaaatttt-tgt-tgaaatgcagGAAGGTTACTATCTGCGTTGATTTGTGAATACTTGGACTGGGCACAACTTAATCACACGCTCATAGTTTATCAACCTGAAAGCAATTTG

upper sequence: Vv13s0067g03320.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G55005.1 (Arabidopsis thaliana), 3'ss of exon 2
----tactgtgcat-ttgtggtgctgaaataatttcagaatctcatgtgtgactgcctttccttatatacgtgtatttgttttcactttgatgtactaaa-tgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGAACCACACATCAAAAGTTTATATTCCGGAATGTAATTTG
     ||| ||| |  |    | || |    || | |  ||      || || |   | |  ||   || ||    ||| |  |  | | |  |  |||| |||||| ||||||||| ||||| | || |||||||| ||||||||||| ||||| || |||||    |||||||||   || ||||| |||| |
gtgaaactttgcttgcttctattcttaggcgatatgaacat------tgagattttgtgtagttgagtaggtcatcttgatcactttataaaatgttaaaatgcagGCAGGTTGCTATCTGCATTGATTTGTGAATATTTGGACTGGGCGCAATTAAATCACACGCTTAAAGTTTATCAACCAGAATGCAATTCG
















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|110423901|gb|EC990254.1|EC990254
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGCGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|110699314|gb|EE076202.1|EE076202
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|351043024|gb|FQ443866.1|FQ443866
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|110730208|gb|EE107028.1|EE107028
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGCGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|351029495|gb|FQ436889.1|FQ436889
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCCTCAG                         GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|349829621|gb|FQ421139.1|FQ421139
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|110410730|gb|EC976422.1|EC976422
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGCGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|110732400|gb|EE107653.1|EE107653
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGCGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|349827978|gb|FQ422846.1|FQ422846
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGTAAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|30301939|gb|CB978733.1|CB978733
EST:     GGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
genomic: GGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|110685295|gb|EE063554.1|EE063554
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|349825323|gb|FQ418055.1|FQ418055
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|349817511|gb|FQ407301.1|FQ407301
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|18458749|gb|BM437027.1|BM437027
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|110381982|gb|EC938169.1|EC938169
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|30301871|gb|CB978665.1|CB978665
EST:     GGGTAGCTGC-ATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
genomic: GGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|351014234|gb|FQ434823.1|FQ434823
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|351016330|gb|FQ446190.1|FQ446190
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|110727163|gb|EE103612.1|EE103612
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGCGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|349827894|gb|FQ422762.1|FQ422762
EST:     ATTGGGTAGCTGCAACGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAACTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|294965188|gb|GW837019.1|GW837019
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATCTGTGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|110710077|gb|EE086097.1|EE086097
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGCGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
EST: gi|349824073|gb|FQ417460.1|FQ417460
EST:     ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAG                         GAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA
genomic: ATTGGGTAGCTGCAATGATAGGGCAAAACAACTTCATGCTTCTCCTTCAGgtcctctccc ... ctaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactgcctttccttatatacgtgtatttgttttcactttgatgtactaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGAACCACACATCAAAAGTTTATATTCCGGAATGTAATTTG
                                           tactaaa  putative branch site (score: 1)
                       tatttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactgtgcatttgtggtgctgaaataatttcagaatctcatgtgtgactgcctttccttatatacgtgtatttgttttcactttgatgtactaaatgcagGAAGGTTGCTAGCTGCACTAATATGTGAATACTTGGACTGGGCACAATTGAACCACACATCAAAAGTTTATATTCCGGAATGTAATTTG

- - - gcatttg
- - - - - - -tggtgct
- - - - - - - - - - gaaataa
- - - - - - - - - - - - - - - - - - - catgtgt