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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattacctttttgggaaagtaggttactggaaaatctaagttcaacctgctatatggcttatcatctatttttatttttattcctcattggcagTGGAATTTTCGTATTGGTTTCACCCCCAGAGAGGGTTTGGTTATTTATTCTGTTGCATATATTGATGGTAGTCGAGGTCGAAGATCTGTGGCCCATAGGT

Basic information

species Vitis vinifera
transcript Vv00s0225g00090.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 6
gtgattacctttttgggaaagtaggttactg-gaaaatctaagttcaacctgctatatggcttatcatctatttttatttttattcctcattggcagTGGAATTTTCGTATTGGTTTCACCCCCAGAGAGGGTTTGGTTATTTATTCTGTTGCATATATTGATGGTAGTCGAGGTCGAAGATCTGTGGCCCATAGGT
|||  |   | | |       |    || |  ||  |  |||   |||     ||| |  |     |  || |   | ||||| |  |  |  ||||||||| || |||||||| |||||||| | |||||||||||| || ||||||||||||||| ||||||| || || || ||  |  |  | || |||||| 
gtgcattgttgtgtaaagcttttctctattatgatgagataaa--caaaaaaatatttccccctggaattaataacacttttaatgatgttgagcagTGGAACTTCCGTATTGGCTTCACCCCTAAAGAGGGTTTGGTCATCTATTCTGTTGCATATGTTGATGGCAGCCGTGGACGTCGGCCGATAGCTCATAGGC

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g04950.1 (Oryza sativa), 3'ss of exon 5
gtgattacctttttgggaaagtaggttactggaa-aatctaagt-tcaacctgcta-tatggcttatcatctatttttatttttattcctcattggcagTGGAATTTTCGTATTGGTTTCACCCCCAGAGAGGGTTTGGTTATTTATTCTGTTGCATATATTGATGGTAGTCGAGGTCGAAGATCTGTGGCCCATAGGT
    ||| ||   |    |    | ||||||    ||| ||| | |   | |  || |||    ||  |   |||   |      || ||  |   |||||||| ||||||||||| |||||||| | ||| ||||| ||| || |||||||||||||| ||||||| |  || || ||  || || | || || ||| 
---gttaactggctatctatagtgtttactgttttaatttaattattggcgtagtagtatctaataaaaatgattaaaaaaacattttctgttgaacagTGGAACTTTCGTATTGGCTTCACCCCTAAAGAAGGTTTAGTTCTTCATTCTGTTGCATATGTTGATGGAAACCGTGGCCGTCGACCTATCGCTCACAGGC

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 5
-----gtgattacctttt--tgggaaagtaggttactggaaaatctaagttcaacctgctata--tggcttatcatctatttttatttttattcctcattggcagTGGAATTTTCGTATTGGTTTCACCCCCAGAGAGGGTTTGGTTATTTATTCTGTTGCATATATTGATGGTAGTCGAGGTCGAAGATCTGTGGCCCATAGGT
      || ||| ||| |  |       |   ||  ||   | |  |  | | |   | || |  || || |  |   || |    | ||||| ||  |   |||||||| || |||||||| || || |||| ||| ||||| |||||| |||||||||||||| ||||||| |  || || ||  || || | || || ||| 
gttaactggttatcttctgtttcttgtttcaattgttgagcacttgagctactattagataaaactgactcaaaaa--atctcacctgttatttctattgaacagTGGAACTTCCGTATTGGCTTTACTCCCAAAGAAGGTTTAGTTATTCATTCTGTTGCATATGTTGATGGAAACCGTGGGCGTCGACCTATCGCTCACAGGC

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 5
gtgattacctttttgggaaagtaggttactggaaaatctaagttcaacctgctatatggcttatcatctattt--ttatttttattcctcattggcagTGGAATTTTCGTATTGGTTTCACCCCCAGAGAGGGTTTGGTTATTTATTCTGTTGCATATATTGATGGTAGTCGAGGTCGAAGATCTGTGGCCCATAGGT
                    |||  |   ||   ||    ||| | |      | ||    | |  |  | |   | |   ||| |  | || |||||||||| || |||||||| |||||||||| ||||||||||||||| ||||||||||| ||| |||||||||| || || || ||| || | || |||||| 
--------------------gtaattgtttgttgaactgcagtgctagtattaacataatgtcttctgaaataaataacacttaatggttat-ggcagTGGAACTTCCGTATTGGCTTCACCCCCAAAGAGGGTTTGGTTATCTATTCTGTTGCTTATGTTGATGGTAGCCGTGGACGTAGACCTATAGCACATAGGC

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 5
-----------gtgattacctttttgggaaagtaggttactggaaaatctaagttcaa-cctgctatatgg-------cttatcatctattttta---tttttattcctcattg---------gcagTGGAATTTTCGTATTGGTTTCACCCCCAGAGAGGGTTTGGTTATTTATTCTGTTGCATATATTGATGGTAGTCGAGGTCGAAGATCTGTGGCCCATAGGT-
            | | ||  ||||    ||| ||  | | |  |  ||| |  || |  ||| | | |            ||||||| || || |   ||  ||   || ||||         ||||||||||||||||||||| ||||| || || ||||||||||| ||| |||| || || ||||||||||| ||||| || |||||| ||||||||||||| | 
tggttgtttttctaagtatattttcca-aaactacatcattatatcatccatattgaggccttccaaaaaaaaaaaaatatatcatccatattgagaattgctaaaactgattgaccatttttgcagtGGAATTTTCGTATTGGATTCACTCCTAGGGAGGGTTTGGTAATTCATTCAGTAGCCTATATTGATGGAAGTCGGGGACGAAGACCTGTGGCCCATAGATT

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 5
gtgattacctttttgggaaagtaggttactggaaaatctaagttcaacctgctatatggcttatcatctatttttattt-ttattcctcattggcagTGGAATTTTCGTATTGGTTTCACCCCCAGAGAGGGTTTGGTTATTTATTCTGTTGCATATATTGATGGTAGTCGAGGTCGAAGATCTGTGGCCCATAGGT
||| ||   | | |    |||||  ||     |||    ||  ||||  |   ||     | || |  |  | | | |  ||     |  || ||||||||||||||||||||| ||||| || || ||||||||||||||| |||| || || ||||||||||| ||||| || || ||| | ||||||||||| |
gtggttgtttgtct----aagtatattttccaaaa---caacatcaatgtatcatccttatcatgaattgctataactgattgacaattttttgcagTGGAATTTTCGTATTGGATTCACTCCTAGGGAGGGTTTGGTTATTCATTCAGTAGCCTATATTGATGGAAGTCGGGGACGGAGACCAGTGGCCCATAGAT

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 5
----------gtgattacctttttgggaaagtaggttactggaaaatctaagttcaacctgctatatggcttatcatctatttttatttttattcct-cattggcagTGGAATTTTCGTATTGGTTTCACCCCCAGAGAGGGTTTGGTTATTTATTCTGTTGCATATATTGATGGTAGTCGAGGTCGAAGATCTGTGGCCCATAGGT
          ||   |  ||||||    ||| | |||  |   | |  |    | ||| ||  |       | | || | ||||| | | | | | |   |  ||||||||| ||||| || ||||| || || || || |||||||||||||||||||| || ||||||||||| |||||||| |||||  |||||||||| || |
gtgattgtttgtaccttactttttctagaagcaagttcattcgagacatg---taaacttgtaagtaaaagtgt-atttttttttttgtgtgtgcgtgtgtgtgcagTGGAACTTTCGCATCGGTTTTACTCCTAGGGAAGGTTTGGTTATTTATTCTGTAGCCTATATTGATGGAAGTCGAGGGCGAAGGCCTGTGGCCCACAGAT

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|71872208|gb|DT021263.1|DT021263
EST:     CTGAAGGACCTAGCTTTCGTGTTAATGGGTACTTTGTTGAATGGCAGAAG                         TGGAATTTTCGTATTGGTTTCACCCCTAGAGAGGGTTTGGTTATTTATTCT
genomic: CTGAAGGACCTAGCTTTCGTGTTAATGGGTACTTTGTTGAATGGCAGAAGgtgattacct ... tcattggcagTGGAATTTTCGTATTGGTTTCACCCCCAGAGAGGGTTTGGTTATTTATTCT
EST: gi|161721603|gb|FC070813.1|FC070813
EST:     CTGAAGGACCTAGCTTTCGTGTTAATGGGTACTTTGTTGAATGGCAGAAG                         TGGAATTTTCGTATTGGTTTCACCCCCAGAGAGGGTTTGGTTATTTATTCT
genomic: CTGAAGGACCTAGCTTTCGTGTTAATGGGTACTTTGTTGAATGGCAGAAGgtgattacct ... tcattggcagTGGAATTTTCGTATTGGTTTCACCCCCAGAGAGGGTTTGGTTATTTATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcaacctgctatatggcttatcatctatttttatttttattcctcattggcagTGGAATTTTCGTATTGGTTTCACCCCCAGAGAGGGTTTGGTTATTTATTCTGTTGCATATATTGATGGTAGTCGAGGTCGAAGATCTGTGGCCCATAGGT
                         tctatttttattttta  CT-rich tract
                   ttatcatctattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattacctttttgggaaagtaggttactggaaaatctaagttcaacctgctatatggcttatcatctatttttatttttattcctcattggcagTGGAATTTTCGTATTGGTTTCACCCCCAGAGAGGGTTTGGTTATTTATTCTGTTGCATATATTGATGGTAGTCGAGGTCGAAGATCTGTGGCCCATAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA