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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttttgtcctctctcctctcctagttggctatggaccataacacttatttgatttttgcagctctatattttgtgcttcttggttgtatgatttcagcaacggccctgcttatgtgaaaatttcttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTTGATTTCCATAAGGATATGGACTTCTGGCAGCAAGATAAGTGGAGTGGAA

Basic information

species Vitis vinifera
transcript Vv05s0020g00460.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g20180.1 (Oryza sativa), 3'ss of exon 5
gtgagttttgtcctctctcctctcctagttggctatggaccataacacttatttgatttttgcagctctatattttgtgcttcttggttgtatgatt-tcagcaacggccctgcttatgtgaaaatttcttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTTGATTTCCATAAGGATATGGACTTCTGGCAGCAAGATAAGTGGAGTGGAA
                                                     ||| | |||  |     | |||| |  ||  |  |  ||  ||| | |     |    ||  | |   || | || | | |  |||| ||||| ||||| || |||||||||||||| || ||| |||| ||||||||||| || || || ||||| ||||||||||| |||||||||  ||| |
----------------------------------------------------gtgagtgttgatgagtcctcttttttcttttcttttcataaaattgttatttgtgaatttgact-tactaacacttatactt-tagGTTAATGCTAGCGGGCAGTTCTGTGGTGTTGCTGAAATGGTTGGTCCTGTTGATTTTCACAAAGACATGGATTTCTGGCAGCAGGATAAGTGGTCTGGGA

upper sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g22630.1 (Oryza sativa), 3'ss of exon 5
gtgagttttgtcctctctcctctcctagttggctatggaccataacacttatttgatttttgcagctctatattttgtgcttcttggttgtatgatttcagcaacggccctgcttatgtgaaaatttcttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTTGATTTCCATAAGGATATGGACTTCTGGCAGCAAGATAAGTGGAGTGGAA
                                          |||      | | || | | ||   ||| ||||  |   | |||  |||  ||||  |  |       |  || || ||    || || || ||||| ||||  || || |  ||||||||  | || |||||| |||| ||||||||||| |||||||| |||||||| |||   || ||||| |||| ||| |
-----------------------------------------gtaa-gtacctctaatgtattcaaa-ctacatttattcagtgttgtctgt--gattaaaata------ttaattctgggatttcttgtttat-cagGTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTTGATTTTCATAAGGACATGGACTTTTGGTGTCAGGATAAATGGACTGGCA

upper sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G056573_T01 (Zea mays), 3'ss of exon 6
gtgagttttgtcctctctcctctcctagttggctatggaccataacacttatttgatttttgcagctctatattttgtgcttcttggttgtatgatttcagcaacggccctgcttatgtgaaaatttcttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTTGATTTCCATAAGGATATGGACTTCTGGCAGCAAGATAAGTGGAGTGGAA
                                                 ||||   || ||| |  || |||   | |   || || ||     | |||| |||  | | |  ||   ||        || || ||||| ||||  || || || ||||||||  | || |||||| |||| ||||||||||| || ||||| ||||||||||||   || ||||| ||||  ||  
--------------------------------------------gtgagtattgatttattgaacatccataaaattta--tcatgctta---aagttcaacaattgactttttttaatg--------tttat-cagGTGAATGGGAGTGGGCACTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTTGATTTTCACAAGGACATGGACTTCTGGTGTCAGGATAAATGGACCGGCT

upper sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G04270.1 (Glycine max), 3'ss of exon 2
gtgagttt-tgtcctctctcctctcctagttggctatggacc---ataacacttatttgatttttgcagctctatattttgtgcttcttggttgtatgatttcagcaacggccctgcttatgtgaaaatttcttc--atacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTTGATTTCCATAAGGATATGGACTTCTGGCAGCAAGATAAGTGGAGTGGAA
||||||||   |  |       ||   | |  | | ||   |    |     || ||| || ||   | ||  |  || ||||| ||| ||   | |   |||    |     |||    |||     ||| ||   ||  |||| |||||||| || ||||| ||||| ||||||||||||||||| |||||||| ||| ||||||| |||||||| |||||||||||||| |||||||| |
gtgagtttacattatgatgatgctttcaatgagttttgattctgctttttttttttttaatcttcatacctaaac-ttatgtgcatct-ggaaatttcccttctatgatcatgctgacattgttttccttttttgcaatgtagGTTAATGCAAGTGGTCAATTTTGTGGGGTTGCAGAGATGATTGGACCTGTTGACTTCAATAAGGACATGGACTTTTGGCAGCAAGATAAATGGAGTGGGA

upper sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G36110.1 (Glycine max), 3'ss of exon 6
gtgagttt-tgtcctctctcctctcctagttggctatggaccataacacttatttgatttttgcagctctatattttgtgcttcttggttgtatgatttcagcaacggccctg---cttatgtgaaaatttcttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTTGATTTCCATAAGGATATGGACTTCTGGCAGCAAGATAAGTGGAGTGGAA
||||||||   |  |      ||    | |  | | ||   |     | ||   |||| |  |||   ||| ||| ||||| ||| ||   | |   |||    |     |||    || |       ||| |  ||  |||| |||||||| || ||||| ||||| ||||| ||||||||||| |||||||| ||| ||||||| |||||||| |||||||||||||| |||||||| |
gtgagtttacattatgatgattcattcaatgagttttgattct--gtattttactgatct--gcatacctaaattatgtgcatct-ggaaatttcccttctatgatcatgctgacattttttcccttttttttcaatgtagGTTAATGCAAGTGGTCAATTTTGTGGGGTTGCTGAGATGATTGGACCTGTTGACTTCAATAAGGACATGGACTTTTGGCAGCAAGATAAATGGAGTGGGA

upper sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G03590.1 (Glycine max), 3'ss of exon 5
gtgagt-tttgtcctctctcctctcctagttggctatggaccataacacttatttgatttttgcagctctatattttgtgcttcttggttgtatgatttcagcaacggccctgcttatgtgaaaa----tttcttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTTGATTTCCATAAGGATATGGACTTCTGGCAGCAAGATAAGTGGAGTGGAA
|||||| ||  |  ||  |  | |  |   ||  | | || | |    |||  |  | ||||  |  | | |||| | |    | |   || | | |     ||  | |  | ||||||| |       ||| |  || ||||| |||||||| || || |||||||| || ||||||||| ||||  | ||||||||  | ||| |||||||||| |||||||||||||| ||||||||||
gtgagtgttcattatcaatgatatgttcaatgagttttgatcctggttctttat--aattttatatttttctattctctatcacctatatgcaagctaatcacactgacttttcttatgtaatgttgcttttttcaatgcagGTTAATGCAAGTGGGCAGTTCTGTGGGGTAGCAGAGATGGTTGGTACAGTTGATTTTAACAAGAATATGGACTTTTGGCAGCAAGATAAATGGAGTGGAA

upper sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G14490.1 (Glycine max), 3'ss of exon 6
gtgagt-tttgtcctctctcctctcctagttggctatggaccataacacttatttgatttttgcagc-tctatattttgtgcttcttggttgta---tgatttcagcaacggccctgcttatgtgaaaatttcttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTTGATTTCCATAAGGATATGGACTTCTGGCAGCAAGATAAGTGGAGTGGAA
|||||| ||  |  |||     |    | |  | | ||  ||      |||||   |||| |  |   | | |||| | |  |   |   || |   | ||  |    ||    ||  |    ||    ||| |  || ||||| |||||||| || || |||||||| |||||||||||| ||||  | ||||| ||    ||| |||||||||| |||||||||||||| ||||||||||
gtgagtgttcattatcttgatacgatcaatgtgttttgatcctggttccttat--aatttgtatattatttctattctttattatctatatgcaagctaatcacgctgacttttcttttaccatgttgctttttaaatgcagGTTAATGCAAGTGGACAGTTCTGTGGGGTTGCAGAGATGGTTGGTACAGTTGACTTTAGCAAGAATATGGACTTTTGGCAGCAAGATAAATGGAGTGGAA

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|161717120|gb|FC069558.1|FC069558
EST:     GGATAGCTCTGGGGAAACGGAGGGGCTGTCCTATTTTTCTGTTCTTCTCT                         GTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTT
genomic: GGATAGCTCTGGGGAAACGGAGGGGCTGTCCTATTTTTCTGTTCTTCTCTgtgagttttg ... cttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTT
EST: gi|30321411|gb|CD004673.1|CD004673
EST:     GGATAGCTCTGGGGAAACGGAGGGGCTGTCCTATTTTTCTGTTCTTCTCT                         GTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTT
genomic: GGATAGCTCTGGGGAAACGGAGGGGCTGTCCTATTTTTCTGTTCTTCTCTgtgagttttg ... cttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTT
EST: gi|30135735|gb|CB921073.1|CB921073
EST:     GGATAGCTCTGGGGAAACGGAGGGGCTGTCCTATTTTTCTGTTCTTCTCT                         GTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTT
genomic: GGATAGCTCTGGGGAAACGGAGGGGCTGTCCTATTTTTCTGTTCTTCTCTgtgagttttg ... cttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTT
EST: gi|71862152|gb|DT011207.1|DT011207
EST:     GGATAGCTCTGGGGAAACGGAGGGGCTGTCCTATTTTTCTGTTCTTCTCT                         GTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTT
genomic: GGATAGCTCTGGGGAAACGGAGGGGCTGTCCTATTTTTCTGTTCTTCTCTgtgagttttg ... cttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTT
EST: gi|30321832|gb|CD005094.1|CD005094
EST:     GGATAGCTCTGGGGAAACGGAGGGGCTGTCCTATTTTTCTGTTCTTCTCT                         GTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTT
genomic: GGATAGCTCTGGGGAAACGGAGGGGCTGTCCTATTTTTCTGTTCTTCTCTgtgagttttg ... cttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTT
EST: gi|27581269|gb|CB003964.1|CB003964
EST:     GGATAGCTCTGGGGAAACGGAGGGGCTGTCCTATTTTTCTGTTCTTCTCT                         GTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTT
genomic: GGATAGCTCTGGGGAAACGGAGGGGCTGTCCTATTTTTCTGTTCTTCTCTgtgagttttg ... cttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggttgtatgatttcagcaacggccctgcttatgtgaaaatttcttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTTGATTTCCATAAGGATATGGACTTCTGGCAGCAAGATAAGTGGAGTGGAA
                                          tttcttcat  CT-rich tract
                               ttatgtgaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttttgtcctctctcctctcctagttggctatggaccataacacttatttgatttttgcagctctatattttgtgcttcttggttgtatgatttcagcaacggccctgcttatgtgaaaatttcttcatacagGTCAATGCAAGCGGCCAATTCTGTGGTGTTGCAGAGATGATTGGCCCTGTTGATTTCCATAAGGATATGGACTTCTGGCAGCAAGATAAGTGGAGTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA