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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaaatcccaatcaatgctggtagtctctatctagtaaccttcatggtatttatcggacatcacacactgacatctctcctttactttcaagGATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAGGAAAAGATGGCTTTGATTGAGAAGCTTGAGCAACAAAAATTAAAGAACC

Basic information

species Vitis vinifera
transcript Vv01s0150g00130.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0150g00130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g63360.1 (Oryza sativa), 3'ss of exon 3
---------------gtataaaatcccaatcaatgctggtagtctctatctagta---accttcatggtatttatcggacatcaca-cactgac-----atctctcctttactttcaagGATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAGGAAAAGATGGCTTTGATTGAGAAGCTTGAGCAACAAAAATTAAAGAACC
                  |||||| |    ||       |  |  ||| | ||||   |  ||| |        |   |||| |||  | |||      || ||  | | |      ||||||||||||| |||||||| || || |||||||| |||||  | ||||| ||||||| ||| |||||  ||||||| |||   ||||     |   |  
gtacagattcctccaaattaaaatgctccgcatctagcttcattactaccgagtacatatgttcgttcctcacttacaacattacaatattgatgatcaatgtcatcctcatgaatcagGATGACATTGGTGACAAATCAGTTTTTATGTTCAACGCCCTCCCTGAAGAAGAAAAGAAGGCCTTGATACAGAAGCTCGAGATGCAAACTGAGACCGATG

upper sequence: Vv01s0150g00130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G024389_T02 (Zea mays), 3'ss of exon 3
gtataaaatcccaatcaatgctggtagtctctatctagtaac--cttcatggtatttatcggacatcacacactgacatctctcctttactttcaagGATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAGGAAAAGATGGCTTTGATTGAGAAGCTTGAGCAACAAAAATTAAAGAACC
                   |     | |||||  | ||| ||  |||| || |     ||| || | ||   ||||||        | ||     |||||||| | || ||||||||||| ||||||||||| || ||  | ||||||||||||| ||||| |||  |||| || |||   |||||     |  |  
-------------------gtaaacaatctctgcc-agtgacagcttcctgat-----tcgaacctgac---ctgacaatg-----tcaccaatcagGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAGGAAAAGAAGGCTTGGATCCAGAAACTCGAGAGGCAAAAGGGGCAAGAGT

upper sequence: Vv01s0150g00130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G39400.2 (Glycine max), 3'ss of exon 2
--gtataaaatcccaatcaatgctggtagtctctatctagtaaccttcatggtatttatcggacatcacacactgacatctctcctttactttcaagGATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAGGAAAAGATGGCTTTGATTGAGAAGCTTGAGCAACAAAAATTAAAGAACC
   |||  | |   | |     ||  |  | |  ||  | | |  || ||  | || || |  | |   || |   |   |   | | |   ||||||||||||| || ||||| ||||| |||||||||||| | ||| | |  || || | ||  || ||| |||||||  | || || |||||| |  ||||  
gtatatttacttttacttttctctttttctgttcatacaattagttt-ata-tcttcattgatcttgggactcatgc---ttaacatcaaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGACGAGAGGAAAGCCTTGCTTGAGAAATTAGAACAGCAAAAAATTCAGAATT

upper sequence: Vv01s0150g00130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ31711 (Selaginella moellendorffii), 3'ss of exon 4
gtataaaatcccaatcaatgctggtagtctctatctagtaaccttcatggtatttatcggacatcacacactgacatctctcctttactttcaagGATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAGGAAAAGATGGCTTTGATTGAGAAGCTTGAGCAACAAAAATTAAAGAACC
                       |||| |  | |||  |  | ||||     | ||  ||| |  || ||||| ||                  |||||||||||| ||||||||| | |||||||| ||||||||  |  ||   ||  ||  |||  || |   |   |  |     ||| || |  || |  
-----------------------gtagaccttctctgcttcctttcaaatcttctaaaggaaaaaac-cactgcca------------------gGATGACATTGGGGACAAATCTATCTTCATGTTTAATGCCCTACCAAAAAGCGAGCAGGAGGCAGTGCTGCGGTCACGGGCAATGCAAGAAATGCAGGAAA

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|71874593|gb|DT023648.1|DT023648
EST:     TGGCACTCTTCGTGATATTTGCAAGCAGAAAGTTCACTCAGCCTATCAAG                         GATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAG
genomic: TGGCACTCTTCGTGATATTTGCAAGCAGAAAGTTCACTCAGCCTATCAAGgtataaaatc ... tactttcaagGATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAG
EST: gi|22015058|gb|BQ800092.1|BQ800092
EST:     TGGCACTCTTCGTGATATTTGCAAGCAGAAAGTTCACTCAGCCTATCAAG                         GATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAG
genomic: TGGCACTCTTCGTGATATTTGCAAGCAGAAAGTTCACTCAGCCTATCAAGgtataaaatc ... tactttcaagGATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAG
EST: gi|26262925|gb|CA813988.1|CA813988
EST:     TGGCACTCTTCGTGATATTTGCAAGCAGAAAGTTCACTCAGCCTATCAAG                         GATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAG
genomic: TGGCACTCTTCGTGATATTTGCAAGCAGAAAGTTCACTCAGCCTATCAAGgtataaaatc ... tactttcaagGATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAG
EST: gi|110395282|gb|EC960940.1|EC960940
EST:     TGGCACTCTTCGTGATATTTGCAAGCAGAAAGTTCACTCAGCCTATCAAG                         GATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAG
genomic: TGGCACTCTTCGTGATATTTGCAAGCAGAAAGTTCACTCAGCCTATCAAGgtataaaatc ... tactttcaagGATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttcatggtatttatcggacatcacacactgacatctctcctttactttcaagGATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAGGAAAAGATGGCTTTGATTGAGAAGCTTGAGCAACAAAAATTAAAGAACC
                                  catctctcctttactt  CT-rich tract
          tatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaaatcccaatcaatgctggtagtctctatctagtaaccttcatggtatttatcggacatcacacactgacatctctcctttactttcaagGATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAGGAAAAGATGGCTTTGATTGAGAAGCTTGAGCAACAAAAATTAAAGAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC