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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgagaaatactatttcaaggtcttgcgttgattgagaattatgtctctagtctagtcttaagttcatttgaaattttaaaagttcatttttacttttatctagaatgtctaggatctaaacagtaatatggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAACCATGAAGTGGGAAATATGATTGCCGAAGCAATGAGTAAAGTGGGTCGAA

Basic information

species Vitis vinifera
transcript Vv06s0004g00240.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g02380.2 (Oryza sativa), 3'ss of exon 5
-----gtaattgagaaatacta----tttcaaggtctt---gcgttgattgaga----attatgtctctagtc-tagtcttaagttcatttga---aattttaaaagttcatttttac----ttttatctagaatgtctaggatctaaacagtaatatggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAACCATGAAGTGGGAAATATGATTGCCGAAGCAATGAGTAAAGTGGGTCGAA
      |||| |  |    |||    |||||   | ||   |   || ||| |      |  ||| | | |    | |  | || |    |||   || |   |   || || | |      | |  | |    |||      | |||| |  | | |  |     ||||||||||||||||||| || |||||||| || || ||||| || |||||  ||||| | || |||||||| || || || ||||| || || ||  | |
gtaaaataatcgtcaggctctaatgctttcagaatgttttagttgtggttgtggcaacctggtgtttgttgcaacaatgcttagctagactgagtcaaatcagatgatttatctatgtagtatatgcttttttttgttctacttataaaaaacattttcttgctttagGTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAATTATGAAATCGGTAATATGATAGCAGAGGCTATGAGCAAGGTTGGCAGGA

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 5
gtaattgagaaatactatttcaaggtcttgcgttgattgagaattatgtctctagtctagtcttaagttcatttgaaattttaaaagttcatttttacttttatctagaatgtctaggat-ctaaacagtaatatggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAACCATGAAGTGGGAAATATGATTGCCGAAGCAATGAGTAAAGTGGGTCGAA
                                      || ||||   |  |   |  | |||||  ||||||| || |||||| | | | | ||  || ||    | ||| |  |  ||  |  ||    || || ||| ||||||||| ||||||||||| || |||||||| || |||||||| ||||| ||| ||||| | || |||||||| || || || ||||  || || || ||  
--------------------------------------gataattg-attcccgtttgaatctta--ttcatttcaacttttaagaatac-tattccctctt---caaaattttgaatatgttggactaacatttgatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAACTATGAAATTGGGAATATGATAGCTGAGGCTATGAAAAAGGTTGGGCGGC

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 4
-----------------------gtaattgagaaatactatttcaaggtcttgcgttgat-tgagaattatgtc-tctagtctagtcttaagttcatttgaaattttaaaagttcattt-ttacttttatctagaatgtctaggatctaaacagt---aatatggt--atcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAACCATGAAGTGGGAAATATGATTGCCGAAGCAATGAGTAAAGTGGGTCGAA
                         || |   ||| | | ||    |    || ||     ||   ||| | |  | || || | | ||    |  ||| | || || |  ||| | || ||  | ||||||    |||  ||  |  | |  ||     |  |||  ||  ||||||||||| |||||| | |||||||| ||||| || |||||||| |||||  ||||||| |||||||||||||| |||||| |||| | ||| ||| |||
gtgaagcatttttctattattgttgaaataccaaacattgttgtgtgtctgtgtgtaagcgtgtttattgtatggtgtactcaaattttcccattttttaatatgtttagtgtttaattatttttcttatctttt-tgttgagacttgataaggttctggttgggtggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAATTATGAAGTAGGAAATATGATTGCTGAAGCATTGAGCAGAGTTGGTAGAA

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 4
------------------------gtaattgagaaatactatttcaaggtcttgcgt-tgattgagaattatgtctctag------tctagtcttaagttcatttgaaattttaaaagttcatttttacttttatctagaatgtc--taggatctaaacagtaatatggt--atcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAACCATGAAGTGGGAAATATGATTGCCGAAGCAATGAGTAAAGTGGGTCGAA
                          || |   ||| | | ||    |    |  |  |||||   |  |  |   |||        | | | || | |  |||| |    |       | |||  |   |||   ||   | |   |  ||  | |   ||  |  |||  ||  ||||||||||| |||||| | |||||||| ||||| || ||||| || |||||  ||||||||||||||||||| || |||||| |||| | ||| ||| |||
gtgaagcatttttctacttattgttgaaataccaaacattgttgtgtgtctataagcatgattattacatggggtactaaaaatttcccaatttttaatatattttagtgctccgttactaattcattaatttgcttatctttttgttgagacttgatatgtggttgggtggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCTGGGAACAATTATGAAGTGGGAAATATGATAGCTGAAGCATTGAGCAGAGTTGGTAGAA

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 5
gtaattgagaaatactatttcaaggtcttgcgttgattgagaattatgtctctagtctagtcttaagttcatttgaaattttaaaagttcatttttacttttatctagaatgtctaggatctaaacagtaatatggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAACCATGAAGTGGGAAATATGATTGCCGAAGCAATGAGTAAAGTGGGTCGAA
                                               || || | | ||   |  |  ||  ||    |||||| |     ||   | | || |  | || ||   | || |||        |||       |||||||||||||||| || ||||||||||||||||||||||| || |||||| | ||| | |||||||||||||| ||||||||||| ||||||||  | |
-----------------------------------------------gtttcaaattta---tagaactctctttc--ttttaata---tgttaagagtctttttcaaaaggttctgaatgtaagt-----catgtcgatgtagGTTGAAGACAGTGAACTTGCAGATGTTGCAGCTGTTAGTGCGGGTAACAACGACGAAATTGGAAATATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 5
gtaattgagaaatactatttcaaggtcttgcgttgattgagaattatgtctctagtctagtcttaagttcatttgaaattttaaaagttcatttttacttttatctagaatgtctaggatctaaacagtaatatggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAACCATGAAGTGGGAAATATGATTGCCGAAGCAATGAGTAAAGTGGGTCGAA
                                                    || | | | ||||| |  |||   ||| |    || || |||    |  | |  || ||   |        | |  |  | ||| ||  ||||||||||||||||| ||||||||||||||||| |||||||||||||||||  | ||||| || ||||||||||| |||||||||   ||||| ||||| |
---------------------------------------------------gtattgttgacttaattagattcttaatct----agctcttttcatgtgctttagaggattcttgatcatgtagctcttttctgg-attgcagGTTGAAGACAGTGAACTAGCAGATGTTGCAGCAGTTAGTGCAGGAAACAATTACGAAGTAGGCAATATGATTGCAGAAGCAATGGCAAAAGTTGGTCGTA

upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaattgagaaatactatttcaaggtcttgcgttgattgagaattatgtctctagtctagtcttaagttcatttgaaattttaaaagttcatttttacttttatctagaatgtctaggatctaaacagtaatatggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAACCATGAAGTGGGAAATATGATTGCCGAAGCAATGAGTAAAGTGGGTCGAA
                                         || ||  | |   |   |  |||   |    || |  |||  | |||  ||          | | |||  |||||     ||     |    ||| |  | |||||||||||||||| || || ||||| |||||||||||||| || || ||||| ||||| |||| ||||||||| ||||||||||| ||||||||  | |
---------------------------------------gtaagtaactattatgctaaaacttccttcttcttaatttttcgagagtctat----------agcaagatggtctaaaggttatgtcat----tggaaatatagGTTGAAGACAGTGAACTTGCTGATGTGGCAGCTGTTAGTGCGGGTAATAACCACGAAGTTGGAAGTATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA

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|351017572|gb|FQ435925.1|FQ435925
EST:     AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
genomic: AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
EST: gi|110685246|gb|EE063449.1|EE063449
EST:     AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
genomic: AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
EST: gi|110725842|gb|EE102769.1|EE102769
EST:     AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCANGAA-CAAC
genomic: AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
EST: gi|351022807|gb|FQ428716.1|FQ428716
EST:     AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
genomic: AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
EST: gi|110701933|gb|EE080073.1|EE080073
EST:     AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
genomic: AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
EST: gi|110686609|gb|EE064441.1|EE064441
EST:     AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
genomic: AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
EST: gi|110699104|gb|EE077129.1|EE077129
EST:     AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
genomic: AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
EST: gi|349833403|gb|FQ420149.1|FQ420149
EST:     AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAGGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
genomic: AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
EST: gi|29782617|gb|CB348122.2|CB348122
EST:     AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
genomic: AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
EST: gi|30256253|gb|CB972096.1|CB972096
EST:     AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCA
genomic: AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCA
EST: gi|110713396|gb|EE089279.1|EE089279
EST:     AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
genomic: AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
EST: gi|30256318|gb|CB972161.1|CB972161
EST:     AGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
genomic: AGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
EST: gi|110689447|gb|EE065678.1|EE065678
EST:     AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACA-C
genomic: AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
EST: gi|351040630|gb|FQ438174.1|FQ438174
EST:     AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAAGACAGTGAGCTAGCAGATGTTGCAG
genomic: AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAG
EST: gi|71864487|gb|DT013542.1|DT013542
EST:     AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
genomic: AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
EST: gi|349815356|gb|FQ400511.1|FQ400511
EST:     AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATGTCAAAAGAG                         GTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC
genomic: AGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAGgtaattgaga ... ggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttttacttttatctagaatgtctaggatctaaacagtaatatggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAACCATGAAGTGGGAAATATGATTGCCGAAGCAATGAGTAAAGTGGGTCGAA
                             atctaaa  putative branch site (score: 3)
     ttacttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgagaaatactatttcaaggtcttgcgttgattgagaattatgtctctagtctagtcttaagttcatttgaaattttaaaagttcatttttacttttatctagaatgtctaggatctaaacagtaatatggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAACCATGAAGTGGGAAATATGATTGCCGAAGCAATGAGTAAAGTGGGTCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA