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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaaatgattgtaaatgctctaggatggtaatattttgtgcatcacatgaactgatgtcactgctttatcctttttaattttggctattttctcaaacagGGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTACATTGGATTCTGATGTTGGATATTTTGAACTTGTTATAAAG

Basic information

species Vitis vinifera
transcript Vv08s0056g01150.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g59930.2 (Oryza sativa), 3'ss of exon 2
ccaaatgattgtaaatgctctaggatggtaatattttgtgcatcacatgaactgatgtcactgctttatcctttttaattttggctattttctcaaacagGGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTACATTGGATTCTGATGTTGGATATTTTGAACTTGTTATAAAG
         | |  || |      |||    | |||      |    |   ||  | |   | | | |        ||| |  |   | ||||     || ||  | |||| |   ||  ||||| | |||||||| |||||||| |||||||||||||||||| | ||  ||||||| |||||||| |||
--------gtttggattccgccttatgcctttctttatgaagtttgctacccttttttttttacataaattggaaaaatgtatgtgctattcttt--tagAGGACAAGATGCTACAGGCGAAGAAGTAATCAAACCTTATACCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAG

upper sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G133213_T01 (Zea mays), 3'ss of exon 2
ccaaatgattgtaaatgctctaggatggtaatattttgtgcatcacatgaactgatgtcactgctttatcctttttaattttggctattttctcaaacagGGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTACATTGGATTCTGATGTTGGATATTTTGAACTTGTTATAAAG
                | | |  |||  |    |||     |     ||   | |  ||| | ||||| |  | |   | ||  || | || | |  ||| ||  | || | |   ||| ||||| | ||||| || |||||||| |||||||||||||||||| ||||||||||||| ||||| ||||||
----------------gtttt--gattctgccttttcccttaattt-tgcttttacatcatttctttaactatatctgtgttctct-tgtttttatgcagAGGACAAGACGCTACAGGTGAAGAAGTAATCAAGCCTTATACCCCTACTACATTGGATTCTGATCTTGGATATTTTGAGCTTGTCATAAAG

upper sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G157263_T01 (Zea mays), 3'ss of exon 2
---ccaaatgattgtaaatgctctaggatggtaatattttgtgcatcacatgaactgatgtcactgctttatcctttttaattttggctattttctcaaacagGGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTACATTGGATTCTGATGTTGGATATTTTGAACTTGTTATAAAG
        |  | || |   || | | | |    |       |||   |    |||  ||    |  || |  |||  |   | |  ||           ||| ||  |||||| |   ||  | ||| | ||||| || ||||| ||||||||  |||| ||||||||||||| |||||| ||||||||||||
gtttgggctcttcgttaccacttttgaaagtgggttcgaaaggcacagccgttactc-tgaatttctttcagtcttactgtgtctacctcccaatcgttccagAGGACAGGATGCTTCTGGCGAGGAAGTGATCAAGCCTTATACTCCAACTACTCTGGACTCTGATGTTGGATCTTTTGAGCTTGTTATAAAG

upper sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G29720.1 (Glycine max), 3'ss of exon 2
ccaaatgattgtaaatgctctaggatggtaatattttgtgcatcacatgaactgatgtcactgctttatc--ctttttaattttggctattttctcaaacagGGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTACATTGGATTCTGATGTTGGATATTTTGAACTTGTTATAAAG
   ||||||    ||||   ||  |  | |||  |||     |   |    ||  | ||| || ||| |   | | ||     |    |  ||||||||||||||||| |||| | | ||| ||||  ||||||||||||||||||| |||||||||||||| ||||||||| |||||||||| ||||| |||
tataatgataactaatgag-tataacaggaattgtttccattttttagtttctt-tatcaatgtttttttgtcatcttgtgaataaacaacttctcaaacagGGGTAAAGATGCTCAAGGTGAAGACGTTATCAAACCATATACCCCTACTACATTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG

upper sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 2
ccaaatgattgtaaatgctctaggatggtaatattttgtgcatcacatgaactgatgtcactgctttatccttt--ttaattttggctattttctcaaacagGGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTACATTGGATTCTGATGTTGGATATTTTGAACTTGTTATAAAG
   | ||||    |||    ||  |  | |||  |||     |   |    ||  | | | || ||| || |    ||     |    |  ||||||||||||||||| |||| | | ||| ||||  |||||||||||||||| || ||||| |||||||| ||||||||| |||||||||| ||||| |||
tatagtgataactaataag-tataacaggaattatttccattttttagtttctt-tattaatgttttgtcgtcacattgtgaataaacaacttctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG

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|33406972|gb|CF212599.1|CF212599
EST:     ACTCCCACATCAGTGTTGGGCCTCCCAATTGGACAACATATAAGTTGCAA                         GGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTAC
genomic: ACTCCCACATCAGTGTTGGGCCTCCCAATTGGACAACATATAAGTTGCAAgtacggttgg ... tctcaaacagGGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTAC
EST: gi|351024116|gb|FQ423539.1|FQ423539
EST:     ACTCCCACATCAGTGTTGGGCCTCCCAATTGGACAACATATAAGTTGCAA                         GGGTAAGGATGGTGAGGGTCAAGAAATTATCAAGCCATATACCCCAACTAC
genomic: ACTCCCACATCAGTGTTGGGCCTCCCAATTGGACAACATATAAGTTGCAAgtacggttgg ... tctcaaacagGGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTAC
EST: gi|110397391|gb|EC963126.1|EC963126
EST:     CCCAATTTGACAACATATAAGTTGCAA                         GGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTAC
genomic: CCCAATTGGACAACATATAAGTTGCAAgtacggttgg ... tctcaaacagGGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTAC
EST: gi|33406880|gb|CF212507.1|CF212507
EST:     ATCAGTGTTGGGCCTCCCAATTGGACAACATATAAGTTGCAA                         GGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTAC
genomic: ATCAGTGTTGGGCCTCCCAATTGGACAACATATAAGTTGCAAgtacggttgg ... tctcaaacagGGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTAC
EST: gi|294965698|gb|GW839153.1|GW839153
EST:     ACTCCCACATCAGTGTTGGGCCTCCCAATTGGACAACATATAAGTTGCAA                         GGGTAAGGATGGTGAGGGTCAAG
genomic: ACTCCCACATCAGTGTTGGGCCTCCCAATTGGACAACATATAAGTTGCAAgtacggttgg ... tctcaaacagGGGTAAGGATGGTGAGGGTCAAG
EST: gi|351015566|gb|FQ426808.1|FQ426808
EST:     ACTCCCACATCAGTGTTGGGCCTCCCAATTGGACAACATATAAGTTGCAA                         GGGTAAGGATGGTGAGGGTCAAGAAATTATCAAGCCATATACCCCAACTAC
genomic: ACTCCCACATCAGTGTTGGGCCTCCCAATTGGACAACATATAAGTTGCAAgtacggttgg ... tctcaaacagGGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgaactgatgtcactgctttatcctttttaattttggctattttctcaaacagGGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTACATTGGATTCTGATGTTGGATATTTTGAACTTGTTATAAAG
                           ttttaat  putative branch site (score: 3)
                                       ctattttctc  putative PPT
                   tttatcctttttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaaatgattgtaaatgctctaggatggtaatattttgtgcatcacatgaactgatgtcactgctttatcctttttaattttggctattttctcaaacagGGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTACATTGGATTCTGATGTTGGATATTTTGAACTTGTTATAAAG

ccaaatg
- - - - - - -aatgctc
- - - - - - - - - - - - - - - - - tttgtgc
- - - - - - - - - - - - - - - - - - - - - tcacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggctat