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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtagttgtcaacttgtggtcaatgccatcttaaatattgtctatgaatatcacatataaatcttatactttatcttaactcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCGAAGAGCTGCTGTGATGGAGATGATGAGACAGAGAGCTGCAGAGGTTGCT

Basic information

species Vitis vinifera
transcript Vv09s0054g01780.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 16
----gtttgtagttgtcaacttgtggtcaatgccatcttaaatattgtctatgaatatcacatataaatcttatactttatct-taactcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCGAAGAGCTGCTGTGATGGAGATGATGAGACAGAGAGCTGCAGAGGTTGCT
    ||| ||  || |||  ||     |    || |      |  |   | || | || |||     | |   |||   | || ||    || ||| ||||| ||||||||| |  | ||| |||| ||||| |||||||||||| | || |||||||| |  || ||||||||||||||||| ||||| ||||||
gtgtgttggtgcttctcacttttgttccgtcaccttgccttgtgcttgatctgga-ataacaccctgaccacttacggaaactatacactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT

upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 15
-----------------gtttgtagttgtcaacttgtggtcaatgccatcttaaatattgtctatgaatatcacatataa----atcttatac--tttatcttaactcattc--agAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCGAAGAGCTGCTGTGATGGAGATGATGAGACAGAGAGCTGCAGAGGTTGCT
                  |      |  ||  |||||| ||  |||  | |   |    || ||  | |  ||  |   |    | || || |    | |  |||   || |  || ||||||||||||||| | || ||| |||||||||||||||||||  || | || ||||||||||  ||||||||||| |||||||| || || || || 
gtttgtccacgccctccatcccatctcatcctcttgtg-tctctgcggtttactactcagtgtagcattgccatctgcgatgtaacctgatcccgcctgtggtaaactatgcacagGGATCTGAAGGAGCATCTCAGAAGGTTGCAGCAGCAGTCTGATTCCCGGAGGAGGGCTGCTGTGAATGAGATGATGAGGCAGAGAGCGGCGGAAGTGGCC

upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 15
--------------------gtttgtagttgtcaacttgtggtcaatgccatcttaaatattgtctatgaatatcacatataaatcttatactttatcttaactcattca--gAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCGAAGAGCTGCTGTGATGGAGATGATGAGACAGAGAGCTGCAGAGGTTGCT
                     |||||     |  |  ||   ||  ||    |||  |||   |    |  |   | | |      |||  || | |  |||   || ||  | ||||||||||||||| | || ||| |||| |||||||||||||| ||| | || ||||||||||  || |||||||| || ||||| || ||||| |||
gtttgttgtcgtccctcctcttttgtgcacatacatatggtttctgtgttcacttgtatagcattgccgtctgcgatagacctgatttac-ctgtgtggtaaactatgcacagGGATCTGAAGGAGCATCTTAGAAGGTTGCAACAGCAGTCTGATTCCAGGAGGAGGGCTGCTGTGAATGAAATGATGAGGCAAAGAGCGGCGGAGGTCGCT

upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 18
gtttgtagttgtcaacttgtggtcaatgccatcttaaatattgtctatgaatatcacatataaatcttatactttatcttaactcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCGAAGAGCTGCTGTGATGGAGATGATGAGACAGAGAGCTGCAGAGGTTGCT
|||||||| |      |||     | |  |   |||| | || | |||  || |   || ||  |   |   ||||| |    | | |||||||| | ||||| ||| | |||||||||||||| |||||||||||  |||| ||||||||||||||||| |||||||| |||||||| ||||| ||||||
gtttgtagatcaggcattgccaatattctcgagttaactcttttttatagattttgtatgtat-taacactgtttatttgggttaaatcagAGATTTAAAGGAACATCTAAGGAGGCTGCAGCAACAGTCTGATTCACGGCGTAGAGCTGCTGTGATGGAAATGATGAGGCAGAGAGCCGCAGAAGTTGCT

upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 16
gtttgtagttgtcaacttgtggtcaatgccat--cttaaat-attgtctatgaatatcacatataaatcttatactttatcttaactcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCGAAGAGCTGCTGTGATGGAGATGATGAGACAGAGAGCTGCAGAGGTTGCT
|||||| |  ||||     | | || ||| ||  ||||| | | ||| |||  || |  | | || | | | | ||||   |    | | |||||||| | || || || || |||||| ||||||| ||||||||||| || |||||||||||||| |||||||||||||| |||||||||||||| ||||| 
gtttgtgg--gtcaggc-ataggcattgcaattacttaagtcactgtttatatattttgcgtgtataacattttcttt--ttgggttaaatcagAGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACGAAGAGCTGCTGTAATGGAGATGATGAGGCAGAGAGCTGCAGAAGTTGCC

upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 16
gtttgtagttgtcaacttgtggtcaatgccatcttaaatattgtctatgaatatcacatataaatcttatactttatcttaactcat-tcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCGAAGAGCTGCTGTGATGGAGATGATGAGACAGAGAGCTGCAGAGGTTGCT
|||||||| |      |||   | | |  | | ||||   |  | |||  || |  ||| ||  |  ||   ||||| |    | |  |||||||| | || || ||| | ||||| || ||||| |||||||||||  |||| ||||||||||| ||||| |||||||| |||||||| ||||| ||||||
gtttgtagatcaggcattgccattattctcgtgttaacactattttatagattttgcatgtat-taatactgtttatttgggtttaaatcagAGATTTAAAAGAACATCTAAGGAGACTTCAGCAACAGTCTGATTCACGGCGTAGAGCTGCTGTAATGGAAATGATGAGGCAGAGAGCCGCAGAAGTTGCT

upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 16
gtttgtagttgtca-acttgtggtcaatgccatcttaaatattgtct---atgaatatcacatataaatcttatactttatcttaactc------attcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCGAAGAGCTGCTGTGATGGAGATGATGAGACAGAGAGCTGCAGAGGTTGCT
 |||| |  | | | |   | ||   |    ||   |||  || | |   |  |||    |  || | |  |||   | ||  ||| ||      |||||| || || ||||| ||| |||| ||| | || ||||| || ||||||||||| |||||||| || ||||||||||||||||||||||||||||| || |||
-tttggatatattagaaccggggcataacatatggcaaagcttttttgaaaaaaatggtccgcatgatttgtattgatcattgtaaatcttctcaattcagGGACCTAAAGGAACATCTGAGAAGGTTACAACAGCAATCAGATTCTAGGCGGAGAGCTGCCGTCATGGAGATGATGAGACAGAGAGCTGCAGAAGTCGCT

upper sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 17
-----------gtttgtagttg--tcaacttgtggtcaatgccatcttaaatatt--gtctatg-aatatcacat--ataaatcttata---ctttatcttaactcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCGAAGAGCTGCTGTGATGGAGATGATGAGACAGAGAGCTGCAGAGGTTGCT
              || | ||   ||||| |    |  | | | |   | |||||  ||| ||   || |    |  || |   || |     | | | |       ||||| || || ||||||||| |||| ||  | |||||||| || |||||  |||| ||||| ||||| ||||| ||||||||||| ||||||||||| || |||
gtaaacaaacctcatgaaattacatcaaccttacatttaagacgtgaaacatatttggtccatttgattttgtgttgatgatcattgtgaacatctctgtctctctgttcagGGACCTAAAGGAGCATCTGAGAAGATTACAGCAGCAATCAGATTCACGGCGCAGAGCAGCTGTAATGGAAATGATGAGACAAAGAGCTGCAGAAGTCGCT

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|34542549|gb|CF510781.1|CF510781
EST:     CTTCATGCTCGAGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAG                         AGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCG
genomic: CTTCATGCTCGAGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAGgtttgtagtt ... actcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCG
EST: gi|34549013|gb|CF517245.1|CF517245
EST:     CTTCATGCTTGAGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAG                         AGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCG
genomic: CTTCATGCTCGAGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAGgtttgtagtt ... actcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCG
EST: gi|110731919|gb|EE106752.1|EE106752
EST:     CTTCATGCTCGAGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAG                         AGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCG
genomic: CTTCATGCTCGAGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAGgtttgtagtt ... actcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCG
EST: gi|34542459|gb|CF510691.1|CF510691
EST:     CTTCATGCTCGAGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAG                         AGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCG
genomic: CTTCATGCTCGAGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAGgtttgtagtt ... actcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCG
EST: gi|349827654|gb|FQ422522.1|FQ422522
EST:     CTTCATGCTCGAGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAG                         AGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCG
genomic: CTTCATGCTCGAGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAGgtttgtagtt ... actcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCG
EST: gi|110420804|gb|EC987084.1|EC987084
EST:     CTTCATGCTCGAGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAG                         AGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCG
genomic: CTTCATGCTCGAGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAGgtttgtagtt ... actcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCG
EST: gi|351012463|gb|FQ427064.1|FQ427064
EST:     CTTCATGCTCGAGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAG                         AGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCG
genomic: CTTCATGCTCGAGCTTGCAAGGAATCTGAATGCCATGTACCACGTTGCAGgtttgtagtt ... actcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatattgtctatgaatatcacatataaatcttatactttatcttaactcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCGAAGAGCTGCTGTGATGGAGATGATGAGACAGAGAGCTGCAGAGGTTGCT
                                        tcttaac  putative branch site (score: 2)
                                              ctcattc  CT-rich tract
             aatatcacatataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtagttgtcaacttgtggtcaatgccatcttaaatattgtctatgaatatcacatataaatcttatactttatcttaactcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCGAAGAGCTGCTGTGATGGAGATGATGAGACAGAGAGCTGCAGAGGTTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG