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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcacaatcagatgcaagattttctcttctcagaaattggaatttacaagtgaacaaaatggttgaagaaattaaactatgggtactctgttcttgacagGGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATTGGGCCACGTTATGCT

Basic information

species Vitis vinifera
transcript Vv15s0046g02390.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os09g39680.1 (Oryza sativa), 3'ss of exon 8
--ttcacaatcagatgcaagattttctcttc---tcagaaattggaatttacaagtgaacaaaatggttgaagaa--attaaactatgggtactctgttcttgacagGGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATTGGGCCACGTTATGCT
  || | | ||   || |||  | |   |     |      |  |||    | | |||  |   |  || ||      || | ||     | |  | |  ||| ||||||   || || || ||||||||||| || ||||| |||||||| ||||| || ||||||||||| 
gtttgatattcttctgaaaggctattcatatggatttagcttctgaaccatctattgactattgtcttttaatgcttgttgatcttgatatccaatttctttggcagGGGAGTGATGCCTTTTCACAGTCTGGGCTATATTCGAATCACCAGGACATAGGCCCACGTTATGCA

upper sequence: Vv15s0046g02390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G088196_T01 (Zea mays), 3'ss of exon 8
-------------ttcacaatcagatgcaagattttctcttctcagaaattggaat--ttacaagtgaacaaaatggttgaagaaat-taaactatgggtactctgttcttgacagGGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATTGGGCCACGTTATGCT
                | ||| | |  ||      | | |    ||    ||  ||   ||||| ||   |  || ||   | |||| |   |||      || |    ||  |||||    || || || ||||||||||| || ||||| ||||||||||||||||| ||||||||||| 
gtttgatgcactccaaaaaataacactcatatggatttataagtagcttctgacatgactacaattggttactattgtgttataaatgtttgctagtttcgctgtccatttctcagGGTAGCGATGCTTTTTCACAGTCTGGCCTGTATTCAAATCACCAAGACATTGGACCACGTTATGCG

upper sequence: Vv15s0046g02390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G046681_T01 (Zea mays), 3'ss of exon 8
-----------ttcacaatcagatgcaagattttct---cttctcagaaattggaatttacaagtgaacaaaatggttgaagaaattaaactatgggtactctgttcttga---cagGGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATTGGGCCACGTTATGCT
           |||| || ||     | |  ||| |      ||    |   || |   |||| |||  ||  ||  ||    || |      ||| |   |||| | |     |||||    || || || ||||||||||| || ||||| |||||||||||||| || ||||||||||| 
gtttgatgcacttcagaaccaatcatatggatttataagtagcttccgacacggca---acaattga-taacttgtctgttataaatgtctgctggttttactgtccattgtctcagGGTAGCGATGCTTTTTCACAGTCTGGCCTGTATTCAAATCACCAAGACATAGGACCACGTTATGCG

upper sequence: Vv15s0046g02390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA20G00410.1 (Glycine max), 3'ss of exon 7
-----------------------------------------------ttcacaatcagatgcaagattttctcttctcagaaattggaatttacaagtgaacaaaatggttgaagaaattaaactatgggtactctg------ttcttgacagGGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATTGGGCCACGTTATGCT
                                               ||   | |    || |  |||   || |||   | ||       ||    | ||    |||    |  |  ||||  ||    || ||||      |||||||||||| || || |||||||| || ||||| || ||||||||||||||||||||||| ||||| ||||||
gttagagctaaatcgacttatattcctcagtttgaatttcctctatttttgaacttttttgaagcattagttcctctacaacataattccatatgttttaaatttatgcagaatcaccttaatttaaccataatctgctatttttcttgacagGGATCTGATGCATTCTCGCAATCTGGTCTGTATTCCAATCACCAAGACATTGGACCACGCTATGCT

upper sequence: Vv15s0046g02390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA07G07570.1 (Glycine max), 3'ss of exon 8
ttcacaatcagatgcaagattttctcttc--tcagaaattgg-aatttacaagtgaacaaaatggttgaagaaattaaactatggg-tactctgttcttgacagGGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATTGGGCCACGTTATGCT
 | | |   ||||  |    | |||       ||  | |||| || ||  || || | | ||  |||    ||  ||||| ||    |  | | | ||| |||||| || || ||||||||||| ||||| || ||||||||||||||||||||||| ||||| ||||||
gttagagctagattaatatatatcttcgaaaacatgatttggcaagttttaaatgtatataa-agttacctaatataaaccataatctgttatttcctttacagGGATCTGATGCATTCTCACAATCTGGTCTATATTCCAATCACCAAGACATTGGACCACGCTATGCT

upper sequence: Vv15s0046g02390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA18G46790.1 (Glycine max), 3'ss of exon 7
-----------------------ttcacaatcaga---tgcaagattttct---cttctcagaaattggaatttacaagtgaacaaaatggttgaaga-------aattaaactatgggtact--ctgttcttgacagGGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATTGGGCCACGTTATGCT
                       |||  | |  ||   | |   ||||| |   | | |         | |||  ||  |  |||||||| ||  | |       |||| ||| ||      |   | |||||||||||| || || ||||||||||| ||||| || ||||||| |||||||| |||||| ||||| ||||||
gtttgagcttgaacaacatatatttctgagtttgaattttcgctattttttaaccctttttttgtaaagcattagcacctctacaaaatgtttccatatgttctaaatttaaccataatcggttatttttcttgacagGGATCTGATGCATTCTCACAATCTGGTCTGTATTCCA-TCACCAAGTCATTGGACCACGCTATGCT

upper sequence: Vv15s0046g02390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA03G01060.1 (Glycine max), 3'ss of exon 8
--ttca--caatcagatgcaagattttctcttctcagaaattggaatttacaagtgaacaaaatggttgaagaaattaaactatgggtactctgtt-----cttgacagGGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATTGGGCCACGTTATGCT
  || |   |  | |||  |    || ||    |      |   |||||     | || ||  |         |  |||  ||    || ||||||      || |||||| || || || ||||| || ||||| || ||||||||||||||||||||||| ||||| ||||||
gtttgagctagactgatatatatcttcctggattttagtttcttaatttttttttaaataatttttagatgttacctaatataaccataatctgttatttgttttacagGGATCTGATGCGTTCTCGCAATCTGGTCTATATTCCAATCACCAAGACATTGGACCACGCTATGCT

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|34542806|gb|CF511038.1|CF511038
EST:     GCAATATTAGAACACCCGCTTTAGCAGTGCTATGCATGGCTTGCAGTCAG                         GGGTCAGACGCATTCTCACAGTCCGGACTCTATTCCAATCACCAAGACATT
genomic: GCAATATTAGAACACCCGCTTTAGCAGTGCTATGCATGGCTTGCAGTCAGgtttgagcta ... ttcttgacagGGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATT
EST: gi|30134343|gb|CB919681.1|CB919681
EST:     CTTTAGCAGTGCTATGCATGGCTTGCAGTCAG                         GGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATT
genomic: CTTTAGCAGTGCTATGCATGGCTTGCAGTCAGgtttgagcta ... ttcttgacagGGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATT
EST: gi|110685152|gb|EE063243.1|EE063243
EST:     GCAATGTTAGAACACCCGCTTTAGCAGTGCTATGCATGGCTTGCAGTCAG                         GGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATT
genomic: GCAATATTAGAACACCCGCTTTAGCAGTGCTATGCATGGCTTGCAGTCAGgtttgagcta ... ttcttgacagGGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATT
EST: gi|30134239|gb|CB919577.1|CB919577
EST:     GCAATGTTAGAACACCCGCTTTAGCAGTGCTATGCATGGCTTGCAGTCAG                         GGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATT
genomic: GCAATATTAGAACACCCGCTTTAGCAGTGCTATGCATGGCTTGCAGTCAGgtttgagcta ... ttcttgacagGGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATT
EST: gi|34542890|gb|CF511122.1|CF511122
EST:     GCAATATTAGAACACCCGCTTTAGCAGTGCTATGCATGGCTTGCAGTCAG                         GGGTCAGACGCATTCTCACAGTCCGGACTCTATTCCAATCACCAAGACATT
genomic: GCAATATTAGAACACCCGCTTTAGCAGTGCTATGCATGGCTTGCAGTCAGgtttgagcta ... ttcttgacagGGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaagtgaacaaaatggttgaagaaattaaactatgggtactctgttcttgacagGGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATTGGGCCACGTTATGCT
                                        ctctgttctt  CT-rich tract
                    aagaaattaaactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcacaatcagatgcaagattttctcttctcagaaattggaatttacaagtgaacaaaatggttgaagaaattaaactatgggtactctgttcttgacagGGGTCAGACGCATTCTCACAGTCTGGACTCTATTCCAATCACCAAGACATTGGGCCACGTTATGCT

- cacaatc
- - - - - gatgcaa
- - - - - - - - - - - tctcttc
- - - - - - - - - - - - - - - -agaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattaa