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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgatttttttctccctcaatttttacaatgatggattcatgacagtgtcagcttaaagtgagcaattatttcctaccttttttgctgttgtttaaaaatgcttgtccctctctctcttggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTGTTGGGAGTAAAACCAGAGGAGGTTGTTCATGTAGGAGATGACCGGAGGA

Basic information

species Vitis vinifera
transcript Vv08s0007g05350.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g05350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G170915_T01 (Zea mays), 3'ss of exon 2
gtaagtgatttttttctccctcaatttttacaatgatggattcatgacagtgtcagcttaaagtgagcaattatttcctaccttttttgctgttgtttaaaaatgcttgtccctctctctcttggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTGTTGGGAGTAAAACCAGAGGAGGTTGTTCATGTAGGAGATGACCGGAGGA
                    |  || || |   | |    || ||  |  | | | |  ||      | ||| ||||| | |   ||| |  |   || ||| | |||||  || | |    |    | ||||||| |||||||||||||||||| | ||||||| | || || ||||||||  | || ||  | || || || | ||| ||| | || || || || || |
--------------------tggatattca-gttcaaaattttattgccatataatcacaata----ccattgtttccaagcaacttt-ccatg--ttgaaatttcttgtttctgtgtactgt----atcagGTTGCAGCAGAGAAGCCAAATCCAATAATATTTTTGAAGGCCTGTGAGTTCATAGGTGTGTAGCCCGAAGAAGCTGTGCATTTTGGTGACGATCGTAGAA

upper sequence: Vv08s0007g05350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G41250.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaag-tgatttttttctccctcaatttttacaatgatggattcatgacagtgtcagcttaaagtgagcaattatttcctaccttttttgctgttgtttaaaaatgcttgtccctctctctcttggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTGTTGGGAGTAAAACCAGAGGAGGTTGTTCATGTAGGAGATGACCGGAGGA
||||| | |  | |||     |  || |||    ||||| || |   ||  | |  |  | | ||| | || || ||   |  ||||| | ||         |||| ||                   ||||||||||||| || || ||||| || || || ||  |||||||||||||||| || | ||| || || ||||| |  |||||||||||||||||||| ||||
gtaagataacctcttttcgtttatatatttttgttgatg-atccgaaacgttttgggagtga-gtgtgtaaatactta--aggtttttggttg---------aatgttt-------------------aacagGTTGAAGCGGAAAAACCAAACCCGACTATCTTCTTAAAAGCTTGTGAGTTATTAGAAGTGAATCCCGAGGATGCGGTTCATGTAGGAGATGACCGTAGGA
















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|30299817|gb|CB976611.1|CB976611
EST:     AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
EST: gi|22014371|gb|BQ799405.1|BQ799405
EST:     AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
EST: gi|110395612|gb|EC961279.1|EC961279
EST:     AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
EST: gi|110429697|gb|EC996199.1|EC996199
EST:     AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
EST: gi|22014482|gb|BQ799516.1|BQ799516
EST:     AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
EST: gi|26258618|gb|CA809681.1|CA809681
EST:     AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACCATATTTCTAAAAACCTTGTGAGTT
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGC-TTGTGAGTT
EST: gi|33403871|gb|CF209498.1|CF209498
EST:     AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTCCAATATTTCTAAAAGCTTGCGAGTTG
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
EST: gi|22011451|gb|BQ796485.1|BQ796485
EST:     AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
EST: gi|71871882|gb|DT020937.1|DT020937
EST:     AGGCATTGAATTGCAATTACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
EST: gi|110725316|gb|EE101677.1|EE101677
EST:     AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAACTGAA                         GTTGAAGCNAAA-AA-CCAAATCCTACA-TATTTCTA
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGC-AGAGAAGCCAAATCCTACAATATTTCTA
EST: gi|110366475|gb|EC930383.1|EC930383
EST:     AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
EST: gi|33409774|gb|CF215401.1|CF215401
EST:     AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
EST: gi|26264895|gb|CA815958.1|CA815958
EST:     AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
EST: gi|33409859|gb|CF215486.1|CF215486
EST:     AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
EST: gi|34320237|gb|CF372991.1|CF372991
EST:     AGGCATTGAATTGCAATTACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
EST: gi|22014205|gb|BQ799239.1|BQ799239
EST:     AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
EST: gi|71877965|gb|DT027020.1|DT027020
EST:     AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACAATATTTCT
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCT
EST: gi|32265433|gb|CD716286.1|CD716286
EST:     ACTGGTTTGATGCTGTGGCAGTGTCAGCTGAA                         GTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
genomic: ACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTG
EST: gi|110712773|gb|EE088110.1|EE088110
EST:     AGGCATTGAATTGCAATCACTGGGTTGATGCTGTGGCAGTGTCAACTGAA                         GTTTGA-GCAAANAAACCNAATCCTACAATATTTCTAAAAGCTTG
genomic: AGGCATTGAATTGCAATCACTGGTTTGATGCTGTGGCAGTGTCAGCTGAAgtaagtgatt ... tggaaaacagGTT-GAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaccttttttgctgttgtttaaaaatgcttgtccctctctctcttggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTGTTGGGAGTAAAACCAGAGGAGGTTGTTCATGTAGGAGATGACCGGAGGA
                          tgcttgtccctctctc  CT-rich tract
             tgttgtttaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgatttttttctccctcaatttttacaatgatggattcatgacagtgtcagcttaaagtgagcaattatttcctaccttttttgctgttgtttaaaaatgcttgtccctctctctcttggaaaacagGTTGAAGCAGAGAAGCCAAATCCTACAATATTTCTAAAAGCTTGTGAGTTGTTGGGAGTAAAACCAGAGGAGGTTGTTCATGTAGGAGATGACCGGAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA