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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCGACTCTGCATAACTGGGGGCTCTGCTGGTGGATATACAACATTAGCTGCTCTTGCTTTCAGAGAAACGTTCAAAGCTGGAGCTTCCTTGTATGGTgtgagttcttgatcgagcgattttttcagatacatttggttgtcctgtctttaacacagttgatttggatatctccacctaaaataactaagaaactgtc...

Basic information

species Vitis vinifera
transcript Vv18s0001g11140.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g11140.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GRMZM2G120302_T02 (Zea mays), 5'ss of exon 14
TGATCGACTCTGCATAACTGGGGGCTCTGCTGGTGGATATACAACATTAGCTGCTCTTGCTTTCAGAGAAACGTTCAAAGCTGGAGCTTCCTTGTATGGTgtgagttcttgatcgagcgattttttcagatacatttggttgtcctgtctttaacacagttgatttggatatctccacctaaaataactaagaaactgtc
  | || || || || |||||  | || || |||||||| || || |||||| | ||||| |||||||| |||||||| |||||||||||  | |||||||| ||||      |       | |  | ||||  | |  || ||   ||||   |  ||    ||   |||| ||    ||                   
GCAGCGCCTTTGTATTACTGGTAGATCAGCAGGTGGATACACTACTTTAGCTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagtt----gccataaatatgtgccggatatttgtatttttctattctt--gctgagcaatttaccatatgtctcattag------------------

upper sequence: Vv18s0001g11140.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA08G42730.1 (Glycine max), 5'ss of exon 14
TGATCGACTCTGCATAACTGGGGGCTCTGCTGGTGGATATACAACATTAGCTGCTCTTGCTTTCAGAGAAACGTTCAAAGCTGGAGCTTCCTTGTATGGTgtgagttcttgatcgagcgattttttcagatacatttggttgtcctgtctttaacacagttgatttggatatctccacctaaaataa--ctaagaaactgtc----
 || ||||| || || || || |||||||||||||| ||||| || ||||||||||||||||| | |||||| || || ||||| ||||| ||||||||||||||| |    ||     |  ||  ||| |||||||      | |    |||    | |  | ||    || |   | | |||||    | |  || |       
GGAGCGACTTTGTATTACAGGTGGCTCTGCTGGTGGGTATACCACCTTAGCTGCTCTTGCTTTTAAAGAAACTTTTAAGGCTGGGGCTTCTTTGTATGGTgtgagtgcaacttctgat-accttagcag-tacatttt----ccttaagattatagtaatctacttaatcattttaccatgaaatagggttcatgaatttctgact

upper sequence: Vv18s0001g11140.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA18G11480.1 (Glycine max), 5'ss of exon 14
TGATCGACTCTGCATAACTGGGGGCTCTGCTGGTGGATATACAACATTAGCTGCTCTTGCTTTCAGAGAAACGTTCAAAGCTGGAGCTTCCTTGTATGGTgtgagttcttgatcgagcgattttttcagatacatttggttgtcctgtcttta-acacagttgatttggatatctccacctaaaataactaagaaac-tgtc--
 || || || || || |  ||||||||||||||||| ||||| || || ||||  |||||||||||||| || ||  | ||||| ||||| |||||||||||||||     |||    |||  ||  |  | | | |    ||    | | ||   || ||  || |  || |  |      ||  || ||| || | |     
GGAGCGGCTGTGTATTATGGGGGGCTCTGCTGGTGGGTATACCACCTTGGCTGTCCTTGCTTTCAGAGATACTTTTCAGGCTGGGGCTTCTTTGTATGGTgtgagtg---aatcttttgatacttctatttccctctcac-gtttaatttctatgtactgtcaatgtaaattttacactgccaaccaagtaaaaatcataatag

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|110426220|gb|EC992621.1|EC992621
EST:     CTTGCTTTCAGAGAAACGTTCAAAGCTGGAGCTTCCTTGTATGGT                         GTAGCTGACTTGTCCCTGTTGCGAGCGGAAACTCACAAATTTGAGTCTCAT
genomic: CTTGCTTTCAGAGAAACGTTCAAAGCTGGAGCTTCCTTGTATGGTgtgagttctt ... ccatgaatagGTAGCTGACTTGTCCCTGTTGCGAGCGGAAACTCACAAATTTGAGTCTCAT
EST: gi|110386297|gb|EC950880.1|EC950880
EST:     CTGCTCTTGCTTTCAGAGAAACGTTCAAAGCTGGAGCTTCCTTGTATGGT                         GTAGCTGACTTGTCCCTGTTGCGAGCGGAAACTCACAAATTTGAGTCTCAT
genomic: CTGCTCTTGCTTTCAGAGAAACGTTCAAAGCTGGAGCTTCCTTGTATGGTgtgagttctt ... ccatgaatagGTAGCTGACTTGTCCCTGTTGCGAGCGGAAACTCACAAATTTGAGTCTCAT
EST: gi|352777768|gb|FQ466821.1|FQ466821
EST:     CTGCTCTTGCTTTCAGAGAAACGTTCAAAGCTGGAGCTTCCTTGTATGGT                         GTAGCTGACTTGTCCCTGTTGCGAGCGGAAACTCACAAATTTGAGTCTCAT
genomic: CTGCTCTTGCTTTCAGAGAAACGTTCAAAGCTGGAGCTTCCTTGTATGGTgtgagttctt ... ccatgaatagGTAGCTGACTTGTCCCTGTTGCGAGCGGAAACTCACAAATTTGAGTCTCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCGACTCTGCATAACTGGGGGCTCTGCTGGTGGATATACAACATTAGCTGCTCTTGCTTTCAGAGAAACGTTCAAAGCTGGAGCTTCCTTGTATGGTgtgagttcttgatcgagcgattttttcagatacatttggttgtcctgtctttaacacagttgatttggatatctccacctaaaataactaagaaactgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taagaaa