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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGCACTTGCTGGCCTGAGACGAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAGgttggatagaagtttaatatgataaaatggttattatagtttttagaaacccaataatataatgctggtctctactcccttttgggataagaaatgccag...

Basic information

species Vitis vinifera
transcript Vv14s0171g00250.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00250.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os05g15360.6 (Oryza sativa), 5'ss of exon 1
----------------------------AAAGCACTTGCTGGCCTGAGACGAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAGgttggatagaagtttaatatgataaaatggttattatagtttttagaaacccaataatataatgctggtctctactcccttttgggataagaaatgccag
||||||||||| | | ||||| |||||||||| || |||||| ||||| | |||||||| || || ||||||||| | | || | | | | | |||| | | || | ||| | | | | | | | || || ||||
TGATAGTGCTGTTGTTTGAACTGAGCAAAAAGCACTTGCAGACTTGAGAAGAATCAATTTAGATGGTTTGAGATGGTGTGTATTTGACGCAAAGGGCCAGgttac-catttttctagtg-gttccagttgttaagcaaatattcatgggt--aatggttttttaccaagcctttgt---ttgtgtgatag----------

upper sequence: Vv14s0171g00250.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os05g15370.1 (Oryza sativa), 5'ss of exon 2
AAAGCACTTGCTGGCCTGAGACGAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAGgttggatagaagtttaatatgataaaatggttattatagtttttagaaacccaataatataatgctggtctctactcccttttgggataagaaatgccag
||||||||||| || ||||| |||||||||| || || ||| ||||||| |||||||| || || ||||||||| | || | | |||||||| || | || | ||| | | | | | || | || || ||||
AAAGCACTTGCAGGTTTGAGAAGAATCAATTTAGATGGATTGAGATGGCGTGTATTTGACGCAAAGGGCCAGgtt--accattcttctgctggttccaatggttaagctaatgttcatggga--aatgttttgac-caagctact--ttgtttgtgcgatag----------

upper sequence: Vv14s0171g00250.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G044584_T02 (Zea mays), 5'ss of exon 2
AAAGCACTTGCTGGCCTGAGACGAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAGgtt-ggatagaagtt-taatatga--taaaatggttattatagtttttagaaacccaataatataatgctggtctctactcccttttgggataagaaatgccag
||||||||||| || |||||| |||||| ||| || || ||||||||||| ||||||||||| || || |||||| |||| | || || | ||| | || | | | || | | | | | | | | | | |||| | | |
AAAGCACTTGCAGGTCTGAGAAGAATCAGTTTAGATGGGTTGCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattgtttttctagtttgagttgcaaggatgaacttattgtaaaaaggatagaggctgtgaggtaattttctatgtgatatag----------------

upper sequence: Vv14s0171g00250.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G163473_T01 (Zea mays), 5'ss of exon 2
AAAGCACTTGCTGGCCTGAGACGAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAGgtt-ggatagaagtt-taatatga-taaaatggttattatagtttttagaaaccca-ataatataatgctggtctctactcccttttgggataagaaatgccag
||||||||||| || |||||| |||||||||| || || | |||||||| ||||||||||| || || |||||| |||| | || || ||| || |||| | | | | |||| | | || | | | | | | | |
AAAGCACTTGCAGGTCTGAGAAGAATCAATTTAGATGGGCTTCGATGGCGCGTATTTGATGCTAAGGGTCAGgttaggattgtttttctagcttgagtagcatggatgaacttatctcaagaaggatagaggctacgaggtaaattttctatgtgatatag---------------

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|110381796|gb|EC935401.1|EC935401
EST:     GAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAG                         GTTCTTGGGAGGTTAGCATCTCAAATTTCTACTGTGATTCAAGGCAAGGAT
genomic: GAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAGgttggataga ... tttcctatagGTTCTTGGGAGGTTAGCATCTCAAATTTCTACTGTGATTCAAGGCAAGGAT
EST: gi|77585738|gb|DV221960.1|DV221960
EST:     GAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAG                         GTTCTTGGGAGGTTAGCATCTCAAATTTCTACTGTGATTCAAGGCAAGGAT
genomic: GAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAGgttggataga ... tttcctatagGTTCTTGGGAGGTTAGCATCTCAAATTTCTACTGTGATTCAAGGCAAGGAT
EST: gi|71870914|gb|DT019969.1|DT019969
EST:     GAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAG                         GTTCTTGGGAGGTTAGCATCTCAAATTTCTACTGTGATTCAAGGCAAGGAT
genomic: GAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAGgttggataga ... tttcctatagGTTCTTGGGAGGTTAGCATCTCAAATTTCTACTGTGATTCAAGGCAAGGAT
EST: gi|110382064|gb|EC938387.1|EC938387
EST:     GAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAG                         GTTCTTGGGAGGTTAGCATCTCAAATTTCTACTGTGATTCAAGGCAAGGAT
genomic: GAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAGgttggataga ... tttcctatagGTTCTTGGGAGGTTAGCATCTCAAATTTCTACTGTGATTCAAGGCAAGGAT
EST: gi|26257383|gb|CA808446.1|CA808446
EST:     GAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAG                         GTTCTTGGGAGGTTAGCATCTCAAATTTCTACTGTGATTCAAGGCAAGGAT
genomic: GAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAGgttggataga ... tttcctatagGTTCTTGGGAGGTTAGCATCTCAAATTTCTACTGTGATTCAAGGCAAGGAT
EST: gi|349826908|gb|FQ418999.1|FQ418999
EST:     GAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAG                         GTTCTTGGGAGGTTAGCATCTCAAATTTCTACTGTGATTCAAGGCAAGGAT
genomic: GAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAGgttggataga ... tttcctatagGTTCTTGGGAGGTTAGCATCTCAAATTTCTACTGTGATTCAAGGCAAGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGCACTTGCTGGCCTGAGACGAATCAATTTGGAAGGTTTGCGATGGCGAGTATTTGATGCCAAAGGCCAGgttggatagaagtttaatatgataaaatggttattatagtttttagaaacccaataatataatgctggtctctactcccttttgggataagaaatgccag

- - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taagaaa