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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctaacttgtcttcttttctggggaggagacaccaaattcttcctaggaattttttttttgtagcaaaacactgaactgaattatgaatcctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCCTTCCTTCAGACCTTTGCAAAGATCGTTGAGAACCCAGAAAGCTTGACAT

Basic information

species Vitis vinifera
transcript Vv01s0011g03380.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g03380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g24320.1 (Oryza sativa), 3'ss of exon 5
-----gtctaacttgtcttcttttctggggaggagacaccaaattcttcctaggaattttttttttgtagcaaaacactgaactgaatta-tgaatcctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCCTTCCTTCAGACCTTTGCAAAGATCGTTGAGAACCCAGAAAGCTTGACAT
      ||| || | ||  | ||||   ||  |  | |  || || |   |  ||  |  || | || |||      |||||||   ||  |     | ||||||||| |||||||| ||||| ||| | ||||| ||||||||||| |||||||| ||||| ||||| ||||| |||||| ||||| | || || ||| | ||||
agcacatcttacctttcaacatttcactggttgcaata--aatttttctttcagagatacttctctgaagc----ttctgaactatgtttctcccaaccttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCATTCCTGCAGACATTTGCGAAGATCATTGAGGATCCTGAGAGCCTAACAT

upper sequence: Vv01s0011g03380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os08g33440.1 (Oryza sativa), 3'ss of exon 5
--gtctaacttgtcttcttttctggggagga--gacaccaaattcttcctaggaattttttttttgtagcaaaacactgaactgaattatgaatcctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCCTTCCTTCAGACCTTTGCAAAGATCGTTGAGAACCCAGAAAGCTTGACAT
   | || |||   |  |   |||   | |     |  | | || ||   | ||  ||| | | | ||| || | ||| |  || ||     |   ||||| |||| ||||| || ||||||||| ||||| | || ||||||||  ||||||| ||||| || || |||||||||||  ||||| | || || ||||| || |
agatatatcttacgtcttgaactgttaatgcttatctgcgatttatttgaatgacatttctgtatatagaaaca-actaaggtggatct---acatttttttagGTTAATGTCACTGCTGATCACAGAATTGTATACGGTGCTGATCTGGCAGCATTCCTGCAAACTTTTGCAAAGATTATTGAGGATCCTGAGAGCTTAACTT

upper sequence: Vv01s0011g03380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G121200_T01 (Zea mays), 3'ss of exon 5
gtctaacttgtcttcttttctggggagg-----agacaccaaattcttcctaggaattttttttttgtagcaaaacactgaactgaattatgaatcctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCCTTCCTTCAGACCTTTGCAAAGATCGTTGAGAACCCAGAAAGCTTGACAT
  || ||    |             |       |    ||   | | |  ||| ||    ||||   |    | |   |  |       ||   |  |||||||||| |||||||| ||||||||| | ||||||||||||||||| |||||||| ||||| || || ||||||||||| |||||| | || ||| || | ||||
--ctcacagaacaggggcaaaaaaaaaccccccacgatcctggtccataatagcaaccaattttccctgcagagatggttgatcctgccat---ttgtttttcagGTGAATGTTACTGCTGATCACAGGATTATCTATGGTGCTGATTTGGCAGCATTCCTGCAAACATTTGCAAAGATTGTTGAGGATCCTGAATGCCTCACAT

upper sequence: Vv01s0011g03380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G117786_T01 (Zea mays), 3'ss of exon 5
----gtctaacttgtcttcttttctggggaggagacaccaaattcttcctaggaattttttttttgtagcaaaacactgaactgaattatgaatcctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCCTTCCTTCAGACCTTTGCAAAGATCGTTGAGAACCCAGAAAGCTTGACAT
     |  || ||| ||        | |||      |  ||||     |         ||| | | || | ||    |    |  |  ||    | |||||||||| ||||| || ||||||||| | ||| | || |||||||| |||||||| || || || || |||||||||||  ||||| | || || ||||| || |
ttttctggaatttggctatggcatagtggacagagtatgaaatgacaacatcagggcatttgtatttaactaagttgt----ttcaacattttccttttttcagGTCAATGTCACTGCTGATCACAGGATTGTATACGGTGCTGATTTGGCAGCATTTCTACAAACTTTTGCAAAGATTATTGAGGATCCTGAGAGCTTAACTT

upper sequence: Vv01s0011g03380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G24830.2 (Glycine max), 3'ss of exon 5
--gtctaacttgtcttcttttctggggaggagacaccaaattcttcctaggaattttttttttgtagcaaaacactgaactgaattatgaa--tcctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCCTTCCTTCAGACCTTTGCAAAGATCGTTGAGAACCCAGAAAGCTTGACAT
   | ||  | |   |     |     | |  |  |  |||| ||  ||  |  | | |  | | |  ||      |  || ||   | ||  ||||||||||||| ||||| ||||||||||| |||||||| ||||| ||||||||||| || ||||| ||||| ||  | || ||| |||| |||||||||||| ||||||
tgttatagttaggagttaggaccatatatggaat-cagaattgtttttaaaagatctctaatcgaattaat---tgggtctaaaccctaaacttcctttttcagGTGAATGTAACAGCTGATCATCGAATTATTTATGGGGCTGACTTGGCCGCTTTCCTCCAGACATTCTCGAAAATCATTGAAAACCCAGAAAGCCTGACAT

upper sequence: Vv01s0011g03380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G25860.1 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------gtctaacttgtcttcttttctggggaggagacaccaaattcttcctaggaattttttttttg-tagcaa-aacactgaactgaattatgaatcctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCCTTCCTTCAGACCTTTGCAAAGATCGTTGAGAACCCAGAAAGCTTGACAT
                                    || |      ||   |   ||  | | |    |   |    |  |||    ||||   | || || ||  |||| ||    |  || |   |   ||  ||||| ||||| || || ||||| || ||| | ||||| ||||||||||| || || || || ||||||||||||||| ||||||| ||||| || ||||| |
gtaagttttattttgacttaataaacttcctgatgggtttggtgaatcacttcgacttagaaagtttaaaatacgattagctatagcttttggctatgctaacagtaacattg--tcgctttgttgttatgttggcagGTGAATGTGACTGCAGATCATCGCATTGTGTATGGAGCTGACTTGGCTGCTTTTCTCCAAACCTTTGCAAAGATCATTGAGAATCCAGATAGTTTGACCT

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|27582046|gb|CB004741.1|CB004741
EST:     ATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTG                         GTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
genomic: ATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttat ... cctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
EST: gi|29785993|gb|CB343386.2|CB343386
EST:     CTGTTGTCACTGATAAAGATGGATTTTTCAGTGTTAAAAGTAAAATGCTG                         GTAAATGTTACAGCTGATCACCGAATTATTTATGGTGCTGACTTGGCAGCC
genomic: CTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttat ... cctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
EST: gi|77587425|gb|DV222856.1|DV222856
EST:     CACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTG                         GTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
genomic: CACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttat ... cctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
EST: gi|110399056|gb|EC965543.1|EC965543
EST:     CTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTG                         GTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
genomic: CTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttat ... cctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
EST: gi|26259444|gb|CA810507.1|CA810507
EST:     CTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTG                         GTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
genomic: CTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttat ... cctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
EST: gi|77583069|gb|DV220571.1|DV220571
EST:     CTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTG                         GTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
genomic: CTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttat ... cctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggaattttttttttgtagcaaaacactgaactgaattatgaatcctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCCTTCCTTCAGACCTTTGCAAAGATCGTTGAGAACCCAGAAAGCTTGACAT
                                            tcctttttc  CT-rich tract
     attttttttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctaacttgtcttcttttctggggaggagacaccaaattcttcctaggaattttttttttgtagcaaaacactgaactgaattatgaatcctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCCTTCCTTCAGACCTTTGCAAAGATCGTTGAGAACCCAGAAAGCTTGACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - tgtcttc
- - - - - - - - - - -ggggagg
- - - - - - - - - - - - - - - acaccaa
- - - - - - - - - - - - - - - - - - - ttcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaaaac