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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctggtgagttttttaatgtttggtagtactcagatttcaattggtcttgcatatgtgtatttaaagaaggtagatatattccacttctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAA

Basic information

species Vitis vinifera
transcript Vv18s0001g12780.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g47590.1 (Oryza sativa), 3'ss of exon 2
---gtatgctggtgagttttttaatgtttggtagtactcagatttcaattggtcttgcatatgtgtatttaaagaaggtagatatattccacttctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAA
    |    |  ||      |  ||   | |||| | ||| | |  |  || |    |  | |  |  | | |        | |  ||  | |  | |||||||||||| | ||  |||| || |||||| ||||||||||||| |||||||| || |||||||| ||||| ||||| |||||||||||||| || || ||  
ttattcccattctgcacccatgcattgctcgtagaattca-actgaaggtgattccac-caagcattctcatatcttcctaacaacttata-tgatcttgcagGACATTTTGGACTTGGCAAAGTATGCAGCTGTACCTGTCATAAATGGCCTTACGGACTACAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGC

upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G046748_T02 (Zea mays), 3'ss of exon 3
gtatgctggtgagttttttaatgtttggtagt---actcagatttcaattggtcttgcatatgtgtatttaaagaaggtagatatattccacttctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAA
    | | ||   | |||| || ||  |||||    ||| |  || |     | |||  |   |  |   |          |  | |   |    | |  ||||| ||||| ||  |||| ||||||||| ||||||||||||| ||||| || || ||||| || ||||| ||||| |||||||||||||| || || ||  
---cgtttgtccttgttttgatcttgcgtagttccgctcggtgttgatccttttttgtttccatccaagcactatctcctaacttctcatatggttttgacagGATATTCTGGACTTGGCAAAATATGCAGCTGTACCTGTCATAAATGGTCTCACCGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGC

upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G050371_T01 (Zea mays), 3'ss of exon 2
-gtatgctggtgagttttttaatgtttggtagtactca--gatttcaattggtcttgcatatgtgtatttaaagaaggtagatatattccacttctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAA
  | | ||  | |   | || ||||| |||||| |     | |||  |||  | |||  |   |  |   |  |       |  | |   |    | | | |||| ||||| ||  |||| ||||||||| ||||||||||||| ||||| || || ||||| || ||||| ||||| |||||||||||||| || || ||  
tttgtccttctca---tattgatgttaggtagttccagttggttttgattccttttgtttccatccaaacattgtctcctaacttctcatatggttttggtagGATATTCTGGACTTGGCAAAATATGCATCTGTACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGC

upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G157210_T01 (Zea mays), 3'ss of exon 5
-gtatgctggtgagttttttaatgtttggtagtactca--gatttcaattggtcttgcatatgtgtatttaaagaaggtagatatattccacttctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAA
  | | ||  | |   | || ||||| |||||| |     | |||  |||  | |||  |   |  |   |  |       |  | |   |    | | | |||| ||| | ||  |||| |||||||||  |||||||||||| ||||| || || ||||| || ||||| ||||| |||||||||||||| || || ||  
tttgtccttctca---tattgatgttaggtagttccagttggttttgattccttttgtttccatccaaacattgtctcctaacttctcatatggttttggtagGATATTTTGGACTTGGCAAAATATGCATATGTACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGC

upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G349547_T01 (Zea mays), 3'ss of exon 2
gtatgctggtgagttttttaatgtttggtagtactca--gatttcaattggtcttgcatatgtgtatttaaagaaggtagatatattccacttctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAA
 | || |  |     | || ||||| |||||| |     | |||  |||  | |||  |   |  |   |  |       |  | |   |    | | | |||| ||| |  |  |||| ||||||||| || |||||||||| ||||| || || ||||| || ||||| ||||| |||||||||||||| || || ||  
-tttgttcttct-catattgatgttaggtagttccagttggttttgattccttttgtttccatccaaacattgtctcctaacttctcatatggttttggtagGATATTTTGTACTTGGCAAAATATGCATCTCTACCTGTCATAAATGGTCTCACTGACTATAACCATCCATGCCAGATAATGGCTGATGCACTTACTATGC

upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G03280.1 (Glycine max), 3'ss of exon 2
gtatgctggtgagttttttaatgtttggtagtactcagatt--tcaattggtcttgcatatgtgtatttaaagaaggtagatatattccacttct----gttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAA
      |||   |  |||| || |     ||   |  |||   ||| |  |      | ||| | | ||   |        | | ||    ||       ||| ||||||| |||||||| || |||||||||||||| || |||||||||||  ||||||||||||| ||||||||||| ||||||||||||||||| || ||  
------tgggaggaatttttatctgctccagagatgtgatcaatcattatgaaagaaaaatgagcactttttgcttacctttttttttgtgttgaaaaaattgtagGACATACTTGATCTTGCAAAATATGCAACTGTGCCAGTCATCAATGGGTTGACAGACTACAACCATCCCTGCCAGATAATGGCTGATGCCCTTACCATGG

upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G03360.1 (Glycine max), 3'ss of exon 2
-gtatgctggtgagttttttaatgtttggtagtactcagatttcaattggtcttgcatatgtgtatttaaagaa--ggtagatatattccacttctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAA
  |    |||   |  |||| |||| |   |  | |  ||    ||  |       ||  |    |||     |    |   | | |   |       || ||||||| |||||||| || |||||||| ||||| || |||||||||||  ||||||||||||| ||||||||||| ||||||||||||||||| || ||  
attggtttgggaggaatttttatgtgttcaatcattatgacagaaaacgaa---aaatgagcacttttgggttaccattttttttgtgttaaaaaaactgtagGACATACTTGATCTTGCAAAATATGCTACTGTGCCAGTCATCAATGGGTTGACAGACTACAACCATCCCTGCCAGATAATGGCTGATGCCCTTACCATGG

upper sequence: Vv18s0001g12780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G75330.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgctggtgagttttttaatgtttggtagtactcagattt-caattggtcttgcatatgtgtatttaaagaaggtagatatattccacttctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAA
  |||    |  |||||| ||   ||     | || |  ||| ||  |  |      |      |  | ||  |   |  |  | ||||||||  |||||||||||||||||| ||||||| ||  | | |||||| ||  ||||||| ||||| ||  | || ||||| |||||||| ||||| |||||||||||||| |
-catggatatttgtttttcaactcttttctatgcttaagtttgcacgtctttccaatttcagaaagatgaatgaacaaacttgaatccacttcatttgcagGACATTCTTGATTTGGCTAACTACTCGAGTGTACCAGTTGTCAATGGTCTGACTGATCATAACCATCCTTGCCAAATCATGGCCGATGCCCTCACAATGA

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|351056870|gb|FQ443497.1|FQ443497
EST:     TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCGCATCAG                         GACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
genomic: TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAGgtatgctggt ... tctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
EST: gi|110713639|gb|EE089746.1|EE089746
EST:     TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTCTTTGCTCATCAG                         GACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
genomic: TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAGgtatgctggt ... tctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
EST: gi|110718848|gb|EE096153.1|EE096153
EST:     TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAG                         GACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
genomic: TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAGgtatgctggt ... tctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
EST: gi|351041613|gb|FQ455829.1|FQ455829
EST:     TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAG                         GACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
genomic: TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAGgtatgctggt ... tctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
EST: gi|110723485|gb|EE100851.1|EE100851
EST:     TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAG                         GACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
genomic: TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAGgtatgctggt ... tctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
EST: gi|349824294|gb|FQ417705.1|FQ417705
EST:     TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAG                         GACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
genomic: TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAGgtatgctggt ... tctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
EST: gi|351030940|gb|FQ438976.1|FQ438976
EST:     TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAN                         GACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
genomic: TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAGgtatgctggt ... tctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
EST: gi|351036443|gb|FQ457156.1|FQ457156
EST:     TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAG                         GACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
genomic: TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAGgtatgctggt ... tctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
EST: gi|351034924|gb|FQ458281.1|FQ458281
EST:     TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAG                         GACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGACCTG
genomic: TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAGgtatgctggt ... tctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
EST: gi|351035513|gb|FQ463358.1|FQ463358
EST:     TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAG                         GACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
genomic: TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAGgtatgctggt ... tctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
EST: gi|351048346|gb|FQ449438.1|FQ449438
EST:     TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAN                         GACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
genomic: TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAGgtatgctggt ... tctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
EST: gi|351034882|gb|FQ458239.1|FQ458239
EST:     TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAG                         GACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
genomic: TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAGgtatgctggt ... tctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
EST: gi|351035222|gb|FQ458579.1|FQ458579
EST:     TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAG                         GACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
genomic: TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAGgtatgctggt ... tctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
EST: gi|351032125|gb|FQ460382.1|FQ460382
EST:     TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAG                         GACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG
genomic: TGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAGgtatgctggt ... tctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtcttgcatatgtgtatttaaagaaggtagatatattccacttctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAA
                                      ttccacttct  CT-rich tract
          atatgtgtatttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctggtgagttttttaatgtttggtagtactcagatttcaattggtcttgcatatgtgtatttaaagaaggtagatatattccacttctgttgcagGACATTCTTGATCTGGCTAAATATGCAACTGTACCTGTCATCAATGGCCTGACAGACTACAATCATCCCTGCCAAATAATGGCTGATGCCCTCACAATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT