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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttgactatgtcatttttattttgaagttcatagattgcttcgctgttaatttttttttaattttcatgcttattcaccaactcgatcagcgatttctttaatcatgctttcttgaagCTCAAATTCCACCATCGTACCATTATTTGAAAAGATGCTAAGTGCCAGTGATGCTGGTCGTATTGGTCGTTTAGTGCTCCCAAAAGCATGTGCTGAA

Basic information

species Vitis vinifera
transcript Vv08s0058g01300.t01
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0058g01300.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G32810.1 (Glycine max), 3'ss of exon 9
gtatccttgactatgtcatttttattttgaa--gttcatagattgcttcgctgttaat---ttttttttaattttcatgcttattcaccaactcgatcagcgatt--tctttaatcatgctttcttgaagCTCAAATTCCACCATCGTACCATTATTTGAAAAGATGCTAAGTGCCAGTGATGCTGGTCGTATTGGTCGTTTAGTGCTCCCAAAAGCATGTGCTGAA
|||  ||   ||||       ||||| ||||    | | ||  | |||    ||| ||    || || | ||||| ||   || ||   | ||   |      ||   | | | ||||| | | || ||| |||||||| || ||||| ||| | |||||||||||||| ||||| |||||||||||||| |||||||| || ||  | ||||||||||||||||||
gtaatctgtcctataaa----ttattatgaatcactgacaggatacttactggttgatacacttattattattttgatagctaatctttaccttagtatttccttaaccatgattcatgatatgttcaagTTCAAATTCTACAATCGTGCCACTCTTTGAAAAGATGCTTAGTGCAAGTGATGCTGGTCGAATTGGTCGCTTGGTTTTACCAAAAGCATGTGCTGAA

upper sequence: Vv08s0058g01300.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G04330.1 (Glycine max), 3'ss of exon 6
gtatccttgactatgtcatttttattttgaagttcatagattgcttc-----gctgttaatttttttttaattttcatgcttattcaccaactcgatcagcgatttctttaatcatgctttcttgaagCTCAAATTCCACCATCGTACCATTATTTGAAAAGATGCTAAGTGCCAGTGATGCTGGTCGTATTGGTCGTTTAGTGCTCCCAAAAGCATGTGCTGAA
   |  ||   | | | | || |  ||      |   ||  | |||      | |  |||  || || | ||||| ||   || ||   | ||   | |     ||    | ||||| | | || ||| |||||||| || || || ||| | |||||||||||||| ||||| |||||||||||||| |||||||| || ||  | ||||||||||||||||||
--gtaattagttctataaattattattaatcactggcaggatacttacacaggttaataaacttattattattttgatagctactctttaccttagt-atttccttaaccattcatgatatgttcaagTTCAAATTCTACGATTGTGCCACTCTTTGAAAAGATGCTTAGTGCAAGTGATGCTGGTCGAATTGGTCGCTTGGTTTTACCAAAAGCATGTGCTGAA

upper sequence: Vv08s0058g01300.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S31_242V6.1 (Physcomitrella patens), 3'ss of exon 5
gtatccttgactatgtcatttttattttgaagttcatagattgcttcgctgttaatttttttttaattttcatgcttattcaccaactcgatcagcgatttct--ttaatcatgctttcttgaagCTCAAATTCCACCATCGTACCATTATTTGAAAAGATGCTAAGTGCCAGTGATGCTGGTCGTATTGGTCGTTTAGTGCTCCCAAAAGCATGTGCTGAA
||||||||  ||| ||  | ||||||   |  |   || || |    | |       ||   | | |||  |   | |||   |||    |||  |  |||    || |  |||| ||     ||| || |  | ||||||   ||  | || || || ||||| |||||||||||||| ||||| ||||||||||| ||||| ||||||||||| || || 
gtatccttt-ctaagtt-tgtttattcaaatttgtgtaaatagg---ggttacgggattcagtgagtttcgagtatcatt--acaatctaatcttcagttttcacttgacaatgcatt---acagCACACAAACTACCATCACTCCTCTGTTCGAGAAAATGCTGAGTGCCAGTGATGCCGGTCGGATTGGTCGTTTGGTGCTTCCAAAAGCATGCGCCGAG

upper sequence: Vv08s0058g01300.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S42_132V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatccttgactatgtcat---ttttattttgaagttcatagattgcttcgctgttaatttttttttaattttcatgcttattcaccaactcgatcagcgatttctttaatcatgctttcttgaagCTCAAATTCCACCATCGTACCATTATTTGAAAAGATGCTAAGTGCCAGTGATGCTGGTCGTATTGGTCGTTTAGTGCTCCCAAAAGCATGTGCTGAA
||||||||    || ||||   ||  ||||   | ||| | |  ||    | | ||    ||||| | |||||| |        ||    |  ||      | |  || |  |||  || ||      ||||  ||||||||   || || || || || ||||| |||||||| ||||||||||| ||||||||||| ||||| ||||||||||||||||| 
gtatcctttcagatttcatgcattcaatttctgatttcgtgggatgagg-gtttttgggatttttatgattttcttaaaagggtacagtttaaattg----tgtacttgacaatgtatt-ttagTATGCAAA--CCACCATCACTCCCTTGTTCGAGAAAATGCTGAGTGCCAGCGATGCTGGTCGGATTGGTCGTTTGGTGCTTCCAAAAGCATGTGCTGAG

upper sequence: Vv08s0058g01300.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ17236 (Selaginella moellendorffii), 3'ss of exon 4
gtatccttgactatgtcatttttattttgaagttcatagattgcttcgctgttaatttttttttaattttcatgcttattcaccaactcgatcagcgatttctttaatcatgctttcttgaagCTCAAATTCCACCATCGTACCATTATTTGAAAAGATGCTAAGTGCCAGTGATGCTGGTCGTATTGGTCGTTTAGTGCTCCCAAAAGCATGTGCTGAA
                                                               ||| ||    | |  ||| ||   |   |    | |||  |||    |  ||| ||     || |  || |  ||   |||  | || || ||  | || ||||||||||| ||||| |||||||| || || || || |||||||||||||| || 
--------------------------------------------------------------gtaagtt----gttcgttctccttttttcttcttgtttttcttatgactcatttgtt-----tccagCTCTAAAATTACACCCCTGTTCGAGAAAGTACTCAGTGCCAGTGACGCTGGACGTATTGGACGATTGGTTCTTCCAAAAGCATGTGCGGAG

upper sequence: Vv08s0058g01300.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ30938 (Selaginella moellendorffii), 3'ss of exon 4
gtatccttgactatgtcatttttattttgaagttcatagattgcttcgctgttaatttttttttaattttcatgcttattcaccaactcgatcagcgatttctttaatcatgctttcttgaagCTCAAATTCCACCATCGTACCATTATTTGAAAAGATGCTAAGTGCCAGTGATGCTGGTCGTATTGGTCGTTTAGTGCTCCCAAAAGCATGTGCTGAA
                                                                       | | || ||| |   |    |      ||  |||  | |||  |  ||     || |  || |  ||   |||  | || || ||  | || ||||||||||| ||||| |||||||| || || || || |||||||||||||| || 
---------------------------------------------------------------------gtaag-ttgttcgctctccttttttcttcttgtttttcttatgactcatttgt-ttccagCTCTAAAATTACACCCCTGTTCGAGAAAGTACTCAGTGCCAGTGACGCTGGACGTATTGGACGATTGGTTCTTCCAAAAGCATGTGCGGAG

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|46917866|gb|CN547195.1|CN547195
EST:     CGTTATTGGCCGAGGATCACAGACCAGGAATTGCAGCAAATATCTGGAGA                         CTCAAATTCCACCATCGTACCATTATTTGAAAAGATGCTAAGTGCCAGTGA
genomic: CGTTATTGGCCGAGGATCACAGACCAGGAATTGCAGCAAATATCTGGAGAgtatccttga ... tttcttgaagCTCAAATTCCACCATCGTACCATTATTTGAAAAGATGCTAAGTGCCAGTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgcttattcaccaactcgatcagcgatttctttaatcatgctttcttgaagCTCAAATTCCACCATCGTACCATTATTTGAAAAGATGCTAAGTGCCAGTGATGCTGGTCGTATTGGTCGTTTAGTGCTCCCAAAAGCATGTGCTGAA
 ttctttaat  putative branch site 
                                          tgctttctt  putative PPT
                             atttctttaatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttgactatgtcatttttattttgaagttcatagattgcttcgctgttaatttttttttaattttcatgcttattcaccaactcgatcagcgatttctttaatcatgctttcttgaagCTCAAATTCCACCATCGTACCATTATTTGAAAAGATGCTAAGTGCCAGTGATGCTGGTCGTATTGGTCGTTTAGTGCTCCCAAAAGCATGTGCTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG