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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTGGGGCTTGGAATAGATGTTTGAATCACCTTCTGACTCTTGCAGAGTCCCATATTGAATCTGTCATCCTTGCAAAGTTTATTGAAGCTGTACAGAGgtacttccttttcttagcctctaaacttctttccatgttctcctaagcttaatgaggtgtggtgttgttcttgcaccag

Basic information

species Vitis vinifera
transcript Vv00s0662g00010.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0662g00010.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os11g39220.2 (Oryza sativa), 5'ss of exon 4
GCTTTGGGGCTTGGAATAGATGTTTGAATCACCTTCTGACTCTTGCAGAGTCCCATATTGAATCTGTCATCCTTGCAAAGTTTATTGAAGCTGTACAGAGgtacttccttttctta-------gcctctaaacttc-----tttccatgttctcctaagcttaatgag-gtgtggtgttgttcttgcaccag--------------------------------------
| ||||| || |||||||||||||| || || || || || ||||| || || || ||||| |||||||| ||||| |||||||| ||||| ||  | |||||  | |||   ||           |||| | |||     || |  |||||| | |   |   ||    |||     |||   || ||||                                       
GATTTGGTGCATGGAATAGATGTTTAAACCATCTGCTCACACTTGCGGAATCACACATTGAGTCTGTCATTCTTGCGAAGTTTATAGAAGCGGTCAAAAGgtaaattcttcggttgcatccgcatttctatatttccccacttgcactgttctaccatcttgcttgcttatgttacactgtctatgaaccacatcaaatgaggtgatgtaatcatggtgcatatatgcag

upper sequence: Vv00s0662g00010.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G419782_T02 (Zea mays), 5'ss of exon 6
GCTTTGGGGCTTGGAATAGATGTTTGAATCACCTTCTGACTCTTGCAGAGTCCCATATTGAATCTGTCATCCTTGCAAAGTTTATTGAAGCTGTACAGAGgtacttccttttcttagcctctaa----acttctttccatg-----ttctcctaagcttaatgaggtgtggt-gttgttcttgcaccag-----------
| || || || |||||||||||| |||| || || || || || ||||| || || || || |||||||||||||||||||| |||||| | ||  | |||||  | |||    |    |||      | | ||||  |||     || ||  || | | | |    |       ||   | | |  |            
GTTTCGGTGCGTGGAATAGATGTCTGAACCATCTGCTTACGCTCGCAGAATCACACATCGAGTCTGTCATCCTTGCAAAGTTCATTGAATCGGTGAAAAGgtaaattcttcaaatgagttcttgcaccagtgctttgaatgaattattttctgaaacatcaagccacgaaaccactgagatagtaaaaaccagggagtgc

upper sequence: Vv00s0662g00010.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA05G31390.1 (Glycine max), 5'ss of exon 5
GCTTTGGGGCTTGGAATAGATGTTTGAATCACCTTCTGACTCTTGCAGAGTCCCATATTGAATCTGTCATCCTTGCAAAGTTTATTGAAGCTGTACAGAGgtacttcctt--ttcttagcctcta------aacttctttccatgttc--tcctaagcttaatgaggtgtggtgttgttct-----tgcaccag
  ||||| || |||||||||||||||||||||||| |||| ||||||||||| |||||||| || ||||||||||| || ||||||||||| || ||||||| |||||||  ||| |||||  |       | || ||||   || ||  |  |    || ||    | |    |||   |     ||| ||||
ATTTTGGTGCATGGAATAGATGTTTGAATCACCTTTTGACACTTGCAGAGTCACATATTGAGTCAGTCATCCTTGCTAAATTTATTGAAGCCGTGCAGAGgtgcttccttagttcctagcccttgtgtattatctcctttatttgctcaattttgtattttatccaattttaacttgacttatatatgcgccag

upper sequence: Vv00s0662g00010.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ07036 (Selaginella moellendorffii), 5'ss of exon 5
GCTTTGGGGCTTGGAATAGATGTTTGAATCACCTTCTGACTCTTGCAGAGTCCCATATTGAATCTGTCATCCTTGCAAAGTTTATTGAAGCTGTACAGAGgtacttccttttcttagcctctaaacttctttccatgttctcctaagcttaatgaggtgtggtgttgttcttgcaccag
||||||| || |||||| | || ||||| ||||| || ||||| || ||||| ||||||||||| ||||| ||||||||||| |||||||||||  |  ||||  |  || ||        |   |   | |  | ||| || |  | |  |                           
GCTTTGGTGCATGGAATCGCTGCTTGAACCACCTCCTCACTCTGGCCGAGTCACATATTGAATCCGTCATTCTTGCAAAGTTCATTGAAGCTGTCAACCGgtaagttgttctcccgtttcgtctccaggtatgaaagttttcgtgtgttgcag--------------------------

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|33403925|gb|CF209552.1|CF209552
EST:     TCCCATATTGAATCTGTCATCCTTGCAAAGTTTATTGAAGCTGTACAGAG                         TTGTCCTGAGGAGACTCGAGTAACTTTGAAACTTGTCTGTGATCTTTATGC
genomic: TCCCATATTGAATCTGTCATCCTTGCAAAGTTTATTGAAGCTGTACAGAGgtacttcctt ... cttgcaccagTTGTCCTGAGGAGACTCGAGTAACTTTGAAACTTGTCTGTGATCTTTATGC
EST: gi|33404010|gb|CF209637.1|CF209637
EST:     TCCCATATTGAATCTGTCATCCTTGCAAAGTTTATTGAAGCTGTACAGAG                         TTGTCCTGAGGAGACTCGAGTAACTTTGAAACTTGTCTGTGATCTTTATGC
genomic: TCCCATATTGAATCTGTCATCCTTGCAAAGTTTATTGAAGCTGTACAGAGgtacttcctt ... cttgcaccagTTGTCCTGAGGAGACTCGAGTAACTTTGAAACTTGTCTGTGATCTTTATGC
EST: gi|18459311|gb|BM437589.1|BM437589
EST:     TCCCATATTGAATCTGTCATCCTTGCAAAGTTTATTGAAGCTGTACAGAG                         TTGTCCTGAGGAGACTCGAGTAACTTTGAAACTTGTCTGTGATCTTTATGC
genomic: TCCCATATTGAATCTGTCATCCTTGCAAAGTTTATTGAAGCTGTACAGAGgtacttcctt ... cttgcaccagTTGTCCTGAGGAGACTCGAGTAACTTTGAAACTTGTCTGTGATCTTTATGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTTGGGGCTTGGAATAGATGTTTGAATCACCTTCTGACTCTTGCAGAGTCCCATATTGAATCTGTCATCCTTGCAAAGTTTATTGAAGCTGTACAGAGgtacttccttttcttagcctctaaacttctttccatgttctcctaagcttaatgaggtgtggtgttgttcttgcaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG