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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGATTTACATGCTCCCTCTAGGTCGTGGAGATTCCAAGGCCCGAAGCTATCATGGATGGGGGACGAAGTTTGACTCTTTCTGGTGCTGCTATGGGACAGgtctggacttatatatatattatgttctcaaatatgaggatttgctttctcaatttccttttgattctaaatgaattcagacagcctgatattctctgcatgttatctctgttggcttatggtctctgatattatttcttttcagggtttcatacatcttatagtttcttcttgctacccctgtag

Basic information

species Vitis vinifera
transcript Vv06s0004g01770.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01770.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os02g10190.1 (Oryza sativa), 5'ss of exon 8
ATGATTTACATGCTCCCTCTAGGTCGTGGAGATTCCAAGGCCCGAAGCTATCATGGATGGGGGACGAAGTTTGACTCTTTCTGGTGCTGCTATGGGACAGgt---ctggacttatatatatattatgttctcaaatatgaggatttgctttctcaatttccttttga-----ttctaaatgaattcagacagcctgatatt-ctctgcatgttatctctgttggc-ttatggtctctgatattat----ttcttttcagggtttcatacatcttatagtttcttcttgctacccctgtag
|||||||||||||| ||||  |  | ||||   || || ||      ||||||||| ||||| || |||| |||||| |||||||| || ||||||||||||       |    | |   |  |   |  | ||   ||  | |||    |   ||| |     | |     |   |||| ||| | |  |   |  |||| || ||| |||  | ||  | |   || ||     |   |||         |||    |||  | |   ||||   |  ||||||   | |   |  ||
ATGATTTACATGCTACCTCAGGCCCCTGGACGGTCTAAAGCGGTTTCCTATCATGGTTGGGGAACAAAGTATGACTCCTTCTGGTGTTGTTATGGGACAGgtaaataaaatgcttctgagttctgcttatttaacactgctgcttttacatgaaaatattgcggtaacagtttgtcaaattaataccgtgattttagtattactttgcttgtgttttcattcgaagttgtgaaaatttgaattgaaaggcaatttatcaggtggcctgtttctttatggatcttct-atttcatttacag

upper sequence: Vv06s0004g01770.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA12G05980.1 (Glycine max), 5'ss of exon 8
ATGATTTACATGCTCCCTCTAGGTCGTGGAGATTCCAAGGCCCGAAGCTATCATGGATGGGGGACGAAGTTTGACTCTTTCTGGTGCTGCTATGGGACAGgtctggacttatatatatattatgttctcaaatatgaggatttgctttctcaatttccttttgattctaaatgaattcagacagcctgatattctctgcatgttatctctgttggcttatggtctctgatattatttcttttcagggtttcatacatcttatagtttcttcttgctacccctgtag
|||||||| ||||| || ||||||  ||  | ||| |||||  |||     ||| | ||||| ||  |||||||||||||||||||||||||||| |||||| |  | || | |   |  |||  |  | ||  ||      | |||| |||| | |    |  || ||  | ||| ||   |  || |  |||| |   ||||     | || |                                                                       
ATGATTTATATGCTTCCACTAGGTTTTGCGGTTTCAAAGGCTAGAACTGGACATAGTTGGGGAACACAGTTTGACTCTTTCTGGTGCTGCTATGGAACAGgtatacaattgttttgtttatatacttccgaaactgca----ttctttttcaactccaccatactttta--tcaat-catttaatctcaatttctttttctgtt-----tattag-----------------------------------------------------------------------

upper sequence: Vv06s0004g01770.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA11G14000.1 (Glycine max), 5'ss of exon 9
ATGATTTACATGCTCCCTCTAGGTCGTGGAGATTCCAAGGCCCGAAGCTATCATGGATGGGGGACGAAGTTTGACTCTTTCTGGTGCTGCTATGGGACAGgtctggacttatatatatattatgttctcaaatatgaggatttgctttctcaatttccttttgattctaaatgaattcaga-cagcctgatattctctgcatgttatctctgttggcttatggtctctgatattatttcttttcagggtttcatacatcttatagtttcttcttgctacccctgtag
|||||||| ||||| || ||||||| ||| | |||||||||   ||  || ||| | ||||| ||    |||||||||||||||||||||||||| || ||| || | |||| |   |   ||  | || ||  ||   |    ||     | |||| |  | |    || |  | ||  | | | |   ||||||    |   |||     |||| |||| |                                                                
ATGATTTATATGCTTCCACTAGGTCTTGGGGTTTCCAAGGCTAAAACTTACCATAGTTGGGGAACACCATTTGACTCTTTCTGGTGCTGCTATGGAACGGgtgtgcatttattttgtttagatactttccaaactgca-acaaactgcacaattttcttggtcaactcaactatactcttatcggtcatttattctaaaaaaaatat-----ttggtttatag----------------------------------------------------------------

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|110699440|gb|EE076439.1|EE076439
EST:     TCATGGATGGGGGACGAAGTTTGACTCTTTCTGGTGCTGCTATGGGACAG                         GAATTGAATCATTCTCGAAGTTAGGAGATTCCATATACTTTGAAGAAGAGG
genomic: TCATGGATGGGGGACGAAGTTTGACTCTTTCTGGTGCTGCTATGGGACAGgtctggactt ... acccctgtagGAATTGAATCATTCTCGAAGTTAGGAGATTCCATATACTTTGAAGAAGAGG
EST: gi|71855680|gb|DT004735.1|DT004735
EST:     TCATGGACGGGGGACGAAGTTTGACTCTTTCTGGTGCTGCTATGGGACAG                         GAATTGAATCATTCTCGAAGTTAGGAGATTCCATATACTTTGAAGAAGAGG
genomic: TCATGGATGGGGGACGAAGTTTGACTCTTTCTGGTGCTGCTATGGGACAGgtctggactt ... acccctgtagGAATTGAATCATTCTCGAAGTTAGGAGATTCCATATACTTTGAAGAAGAGG
EST: gi|71861518|gb|DT010573.1|DT010573
EST:     TCATGGATGGGGGACGAAGTTTGACTCTTTCTGGTGCTGCTATGGGACAG                         GAATTGAATCATTCTCGAAGTTAGGAGATTCCATATATTTTGAAGAAGAGG
genomic: TCATGGATGGGGGACGAAGTTTGACTCTTTCTGGTGCTGCTATGGGACAGgtctggactt ... acccctgtagGAATTGAATCATTCTCGAAGTTAGGAGATTCCATATACTTTGAAGAAGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGATTTACATGCTCCCTCTAGGTCGTGGAGATTCCAAGGCCCGAAGCTATCATGGATGGGGGACGAAGTTTGACTCTTTCTGGTGCTGCTATGGGACAGgtctggacttatatatatattatgttctcaaatatgaggatttgctttctcaatttccttttgattctaaatgaattcagacagcctgatattctctgcatgttatctctgttggcttatggtctctgatattatttcttttcagggtttcatacatcttatagtttcttcttgctacccctgtag

- - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT