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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag

Basic information

species Vitis vinifera
transcript Vv16s0098g01040.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 5'ss of exon 6
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag
|| || ||||| ||||| ||||| || |||||||||||||| ||||| ||||| ||||||||||     ||| | ||||| |||     | | |||   | |  | ||    |  | | | |   ||||     |  ||||||| |||
TCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAGgtatgctacaatttgcttgt-actctgtttttcgtt---atcctttatgctcatgtttctttggcatttg---atgcatttgatacag

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G173428_T02 (Zea mays), 5'ss of exon 5
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttact-tgtttatttgatgcag
||||| |||||||| |||||||| || |||||||||||||| ||||| ||||| ||||||||   ||   | ||||     |||  |  | |        |   | |||     || ||| |||| |||| | | |  | ||| |||||
TCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGgt---tccctacctac-----actcatgctataccactaggtgttcattctgtcat-tgt-tctgttttaatatatgcacttgctgcag

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G036634_T01 (Zea mays), 5'ss of exon 15
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag
||||| |||||||| |||||||| || |||||||||||||| ||||| ||||| ||||||||   ||   | ||||     |||  |  | |        |   | |||     || ||| |    || |  | |  | ||| |||||
TCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGgt---tccctacctac-----actcatgctataccactaggtgttcattctgtcat-tgttttgttttaatatatgcacttgttgcag

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G161649_T01 (Zea mays), 5'ss of exon 4
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttact-tgtttatttgatgcag
||||| |||||||| |||||||| || |||||||||||||| ||||| ||||| ||||||||   ||   | ||||     |||  |  | |            | |||     || ||| |||| |||| | | |  | ||| |||||
TCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGgt---tccctacctac-----actcatgctataccactagctgttcattctgtcat-tgt-tctgttttaatatatgcacttgctgcag

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G457231_T01 (Zea mays), 5'ss of exon 8
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgt---atttctgaatctac----ttgtcact----------tctagtgtggttgag----agcactaattggaaaatc---tgtatctga-tttacttgtttatttgatgcag---------------------------------------------------------------
||||| ||||||||||||||||| || |||||||| ||||| ||||| ||||| ||||||||    |  ||| |   |      |  ||||          |||    || ||       |  ||   | ||  | ||     ||||| |  ||| |  || | |  ||                                                                   
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGGTTTGGTACCTGCACTCATGCTACTACCACTAGgtattcattctgtcatgattctattttaatacacgtaggtcactcaagcatatctaaacttattctttgagtcaatatgtggtgaggttggtcgttctttactccaaacacaatctcccttctgtacaactaaaagtttgcag

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G069102_T01 (Zea mays), 5'ss of exon 6
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag
||||| ||||||||||||||||| || |||||||| ||||| ||||| ||||| ||||||||              |||  || |  | |   | |   | |||||  |    | |||||   || ||  ||  |||| |  | ||||
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGgt--------------ttggtacctacactcatgctactaccactatgtattcattctgt-catggtt--ctgttttaatacacgcag

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G454261_T01 (Zea mays), 5'ss of exon 2
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag
||||| ||||||||||||||||| || |||||||| ||||| ||||| ||||| ||||||||              |||  || |  | |   | |   | ||||| ||    | | |||   || ||  ||  |||| |  | | ||
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGgt--------------ttggtacctgcattcatgctactaccactagttatttattgtgt-catggtt--ctgttttaatacacgtag

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G123866_T01 (Zea mays), 5'ss of exon 11
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag
||||| ||||||||||||||||| || |||||||| ||||| ||||| ||||| ||||||||              |||  || |  | |   | |   | |||||  |    | |||||   || ||  ||  |||| |  | ||||
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGgt--------------ttggtacctgcactcatgctactaccactaggtattcattctgt-catggtt--ctgttttaatacacgcag

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G132286_T01 (Zea mays), 5'ss of exon 5
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttact-tgtttatttgatgcag
||||| |||||||| |||||||| || |||||||||||||| ||||| ||||| ||||||||   ||   | ||||     |||  |  | |        |   | |||     || ||| |||| |||| | | |  | ||| | |||
TCTGATGATGAACGGGAAATGTGTGCGAGGACTATTTACTGCACAAACATTGACAAGAAGgt---tccctacctac-----actcatgctataccactaggtgttcattctgtcat-tgt-tctgttttaatatatgcacttgctacag

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G044246_T01 (Zea mays), 5'ss of exon 2
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag------------------------------------------------------------------------------
||||| ||||||||||||||||| || |||||||| ||||| ||||| || || |||||||| ||  |   |  |||  |  || |||        |    || |   |      ||||| | | ||  ||     |   | | ||||                                                                              
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAGGT-TTGGTACCTGCACTCAT-GCTACTACCACTAG-

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G376619_T01 (Zea mays), 5'ss of exon 7
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag
||||| ||||||||||||||||| || |||||||| ||||  ||||| ||||| ||||||||              |||  || |  | |   | |   | || ||  |    | |||||   || ||  ||  |||| |  | ||||
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTACACAAACATTGACAAGAAGgt--------------ttggtacctgcactcatgctactaccattaggtattcattctgt-catggtt--ctgttttaatacacgcag

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G166091_T01 (Zea mays), 5'ss of exon 8
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag
||||| ||||||||||||||||| || || ||||| ||||| ||||| ||||| ||||||||              |||  || |  | |   | |   | |||||  |    | |||||   |||||  ||  |||| |  | ||||
TCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAGgt--------------ttggtacctgaactcatgctactaccactaggtattcattctgt-catgatt--ctgttttaatacacgcag

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G044246_T02 (Zea mays), 5'ss of exon 6
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag
||||| ||||||||||||||||| || |||||||| ||||| ||||| || || ||||||||              |||  || |  | |   | |   | |||||  |    | ||| |   || ||  ||  |||| |  |  |||
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAGgt--------------ttggtacctgcactcatgctactaccactaggtattcattctat-catggtt--ctgttttaatacacacag

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G349794_T01 (Zea mays), 5'ss of exon 7
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag
||||| ||||||||||||||||| || |||||||| ||||| ||||| ||||| |||| ||| ||  |   |  |||  |  || |||   |    |    || ||  |      ||||| | | ||  ||                 
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGATGgt-ttggtacctgcactcat-gctactaccattag-gtattcattatgtcatggttctgt-tttaatacacgcag-------------

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G014573_T01 (Zea mays), 5'ss of exon 4
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag
 |||| ||||||||||||||||| || ||||| || ||||| ||||| ||||| ||||||||              |||  || |  | |   | |   | || ||  |    | | |||    | | || ||   || |  | ||||
CCTGACGATGAACGTGAAATGTGTGCAAGGACAATCTACTGCACAAACATTGACAAGAAGgt--------------ttggtacctgcactcatgctactaccattaggtattcattatgtcatggttctattt---taatacacgcag

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G310936_T01 (Zea mays), 5'ss of exon 1
---------------------------------TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag
                                  |||| ||||||||||||||||| || |||||||| ||| | ||||| ||||| ||||||||              |||  || |  | |   | |   | |  || ||    | |||||   || ||  ||  |||| |  | ||||
ATGACATATATACTTATTTTCTGTGCTCTGCAGACTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACCGCACAAACATTGACAAGAAGgt--------------ttggtacctgcattcatgctactacctgtagttattcattctgt-catggtt--ctgttttaatacacgcag

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: PP1S62_224V6.1 (Physcomitrella patens), 5'ss of exon 6
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag---------------------
||||||||||| ||||||||||| ||  |||| || ||||||||||||||||| ||||||||      || |  | | |  | ||    |||  |        || |     | |||   ||| | ||||||   |  |||  |||                       
TCTGAAGATGAGCGTGAAATGTGTGCACGGACCATCTACTGTACAAATATTGACAAGAAGgtgaagtggagtgaaatag--aatttcgttgttct-----atgctgacgatgagatcc--atccgttttactgcctgcttttttgcgataagttgctcttctctttgtg

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: PP1S196_50V6.1 (Physcomitrella patens), 5'ss of exon 7
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttg----tca--cttctagtgtggttgagagcacta-------attggaaaatctgta---------tctgatttacttgtttatttgatgcag-----------------------------------------------------------------------------------------
|||||||| || ||||||||||| ||  | || || ||||||||||||||||||||||||||      || |  | | |    |||  |||||||  ||      ||| ||        | ||   |||||||          | ||   |  |||| |||| | ||                                                                                            
TCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtggagtgaaatagactttcattcttctaggctgccaattagccctgttcatttactgtctaatctgttgtgaaaagttatggcatggttgtgtattcgttgtgccatggttcacgaggtggtgggaagttttcatgctagtaccacattgtaatgtatggccggggctctgagcgagcagtgacttgatgcag

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|110394549|gb|EC959681.1|EC959681
EST:     AACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG                         GTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAG
genomic: AACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctga ... tttgatgcagGTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAG
EST: gi|254917332|gb|GR906158.1|GR906158
EST:     AACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG                         GTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAG
genomic: AACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctga ... tttgatgcagGTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAG
EST: gi|110406292|gb|EC971861.1|EC971861
EST:     AACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG                         GTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAG
genomic: AACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctga ... tttgatgcagGTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAG
EST: gi|110371491|gb|EC935557.1|EC935557
EST:     AACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG                         GTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAG
genomic: AACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctga ... tttgatgcagGTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAG
EST: gi|110385680|gb|EC950225.1|EC950225
EST:     AACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG                         GTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAG
genomic: AACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctga ... tttgatgcagGTGACCCAGGCAGAAGTCAAACTTTTCTTTGAATCAATTTGTGGAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttgtcacttctagtgtggttgagagcactaattggaaaatctgtatctgatttacttgtttatttgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG