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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttttgtggtttttgatgccctattacttttcttgatgcctaatagtggtgtcttggcaacattcgatttttagctgtaaagcttatccttattgataaatagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAGTACAGTGTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAA

Basic information

species Vitis vinifera
transcript Vv10s0116g00670.t01
intron # 8
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G31720.1 (Glycine max), 3'ss of exon 2
gtatcctttt-gtggtttttgatgccctattacttttcttgatgcctaatagtggtgtcttggcaacattcgatttttagctgtaaagcttatccttattgataaatagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAGTACAGTGTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAA
| ||||||||  |   |||   |      ||| || | ||   | |||  ||||       |     ||||  | |  |||| | |   || |||||||||||  | |||||||||||||||||||||||||||||||||||||||||||||||| ||||||||  |||| |||||||||||||||||||| ||||| ||||| || ||
gcatcctttttattaatttatttatttatttatttatttttgggtctatgagtgcaaga--gattgtattctttatccagctatga---ttttccttattgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAAGCAGTACAAAGTGGTAATGTTGAGGATGCAATTGAAAAAGTGAATGACTTAAA

upper sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA15G07570.3 (Glycine max), 3'ss of exon 3
gtatccttttgtggtttttgatgccctattacttttcttgatgcctaatagtggtgtcttggcaacattcgatttttagctgtaaagcttatccttattgataaatagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAGTACAGTGTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAA---
|||||||||| |   ||    |      ||  || | ||   | |||  ||||       |     ||||  | |  |||| | |   || |||||||||||  | ||||||||||||||||||||||||||||||||||||||||||||| |||||||||||  |||| || ||||| ||||||||||| ||||| ||||| || ||   
gtatcctttttt---ttaatctatttatttgtttatttttgggtctatgagtgcaaga--gattgtattctttatccagctatga---ttttccttattgatctacagcagACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAATCC

upper sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA15G07570.2 (Glycine max), 3'ss of exon 3
gtatccttttgtggtttttgatgccctattacttttcttgatgcctaatagtggtgtcttggcaacattcgatttttagctgtaaagcttatccttattgataaatagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAGTACAGTGTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAA
|||||||||| |   ||    |      ||  || | ||   | |||  ||||       |     ||||  | |  |||| | |   || |||||||||||  | ||||||||||||||||||||||||||||||||||||||||||||| |||||||||||  |||| || ||||| ||||||||||| ||||| ||||| || ||
gtatcctttttt---ttaatctatttatttgtttatttttgggtctatgagtgcaaga--gattgtattctttatccagctatga---ttttccttattgatctacagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAAAAGGCAGTACAAAGTGGTAACGTTGAAGATGCAATTGAAAAAGTGAATGACTTAAA

upper sequence: Vv10s0116g00670.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G61150.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatccttttgtggtttttgatgccctattacttttcttgatgcctaatagtggtgtcttggcaacattcgatttttagctgtaaagcttatccttattgataaatagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAGTACAGTGTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAA
||||||||||   | || || |      ||  | ||  ||      ||| |  |||| |       |    || |    || |  | |||  |||||| || ||| |||||| ||||||||||| || || || ||||| ||||||||||| ||||| || ||    || ||||| |||||||| ||||| ||||| |||||||||||
gtatcctttttctgattctggttttgagtttttgtttatgg-----aattggtgtgtttgatgtttagcttatctactccttttgaactt--ccttatcgagaaacagCAGAGATAGATCTTGCGACCATTACTGATCGAATGGCTGTTAAAAAGGCTGTTCAAAACGGAAATGTCGAGGATGCGATTGAAAAAGTTAATGATTTGAA

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|110415950|gb|EC981891.1|EC981891
EST:     GAAAAGTTCCGAATGGAATCTGGAACAGAAC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAG
genomic: GAAAAGTTCCGAATGGAATCTGGAACAGAACgtatcctttt ... tgataaatagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAG
EST: gi|110408401|gb|EC974037.1|EC974037
EST:     GAAAAGTTCCGAATGGAATCTGGAACAGAAC                         CAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAG
genomic: GAAAAGTTCCGAATGGAATCTGGAACAGAACgtatcctttt ... tgataaatagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtcttggcaacattcgatttttagctgtaaagcttatccttattgataaatagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAGTACAGTGTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAA
 attcttatt  putative branch site 
                                      tccttatt  putative PPT
                                         ttattgataaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttttgtggtttttgatgccctattacttttcttgatgcctaatagtggtgtcttggcaacattcgatttttagctgtaaagcttatccttattgataaatagCAGACATAGATCTTGCAACAATAACAGATCGCATGGCTGTTAAGAAGGCAGTACAGTGTGGGAATGTTGAGGATGCAATTGAGAAAGTAAATGATTTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG