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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctgcattctgaactctaaatactagtgttgttcgaagttgacttagtttccattttttatctatctgtcatgttcttcttttctttcttctatattagctagctaatgcagattcttttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT

Basic information

species Vitis vinifera
transcript Vv16s0050g02670.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 4
gttctgcattctgaactctaaat--actagtgttgttcgaagttgacttagtttccattttttatctatctgtcatgttcttcttttctttcttctatattagctagctaatgcagattcttttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT
        |||| ||||    ||   ||| ||     | || |  |   |   || | | ||||| |||   |  | ||    | || | |   || |                   || |||| | ||||||| ||| | ||||| ||||| ||||| |||||||| ||||| |||||||  || || ||||||||||| || ||||| |||||| |||||||||| ||||
-------gttctcaacttctcatcacctattgacagccaaaataaaaaaaaaatctagtatttat-tatactttgtattacagtgttgtgtgacctgt-------------------tttttttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTTCCGCTTT

upper sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g33710.1 (Oryza sativa), 3'ss of exon 4
gttctgcattctgaactctaaatactagtgttgttcgaagttgacttagtttccattttttatctatctgtcatgttcttcttttctttcttctatattagctagctaatgcagattcttttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT
      ||||||  ||     |  ||||   ||| |  | |  | |        | ||| ||  ||     |   || |  |   || | || | ||| | ||  |||          || | | ||||||| ||| | ||||| || || || ||||||||||| ||||| ||| ||| ||| || ||||||||||| || ||||| ||| || |||||||||| || |
----gtcattcttcacctgctaggctagctgtgtgcatactacatt--------actttatacataaacaactaattttgttgaactattttttgtataacctgtcta---------tttctgtatgcagTCCTCAACCTATGGGAATGTTCTGGTGCTTGATGGTATTGTGCAGCTGACCGAAAAGGATGAATGTGCATACCAGGAAATGGTTACTCACCTTCCACTGT

upper sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 3
gttctgcattctgaactctaaatactagtgttgttcgaagttgacttagtttccattttttatctatctgtcatgttcttcttttctttcttctatattagctagctaatgcagattcttttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT
                                                |||    |  ||||   || |   |  |     ||| ||||      | ||   ||  |||    |  | |||| | ||||||||||| | ||||| ||||| |||||||||||||| |||||||| ||||  || || ||||||||||| || ||||| |||||| ||||||| || || |
------------------------------------------------gttcttttcatttactgatatcagaaatataaatttcctttggctcctgttgtgta--taaccttgtattttttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCT

upper sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G060896_T04 (Zea mays), 3'ss of exon 4
gttctgcattctgaactctaaatactagtgttgttcgaagttgacttagtttccattttttatctatctgtcatgttcttcttttctttcttctatattagctagctaatgcagattcttttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT
                                       ||| || |  | |     |   |   ||  |  |      |   ||     |  | | || |     ||| |  |     ||| | ||||||||||  | ||||| ||||| |||||||||||||| |||||||||||||  || || ||||||||||| || ||||| |||||| ||||||| || ||||
---------------------------------------gttcacatcatctgttcataccagaaataagaaaaaaaactgcatttggcttattctgtttg-----taacgtggtaatctttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTT

upper sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G047867_T01 (Zea mays), 3'ss of exon 4
gttctgcattctgaactctaaatactagtgttgttcgaagttgacttagtttccattttttatctatctgtcatgttcttcttttctttcttctatattagctagctaatgcagattcttttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT
                                       |||   ||  | ||       | |  |  ||  |       ||  ||  || | | || ||  ||||   | ||     || | || |||||| ||| | ||||| || || |||||||||||||| || ||||||||||  || || |||||||| || || ||||| ||| || |||||||||| || |
---------------------------------------gttatttttttatctgcgaaatctgcacgtgaaaacccgaactcgtcaatcat-tgtactaagtagcactttca----tttctgttcgcagTCTTCAACCTATGGAAATGTTCTTGTGCTTGATGGTATAGTTCAGTTGACTGACAAGGATGAATGCGCATACCAGGAAATGGTTACTCACCTTCCACTGT

upper sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 4
gttctgcattctgaactctaaatactagtgttgttcgaagttgacttagtttccattttttatctatctgtcatgttcttcttttctttcttctatattagctagctaatgcagattcttttattt-gcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT
                                                ||||    | || ||||   | | |||| ||   |  ||||    |  |   | |||   ||||  || |||| |||| |||||| ||| | ||||| ||||||||||| |||||||| || ||||| ||||  ||||| ||||||||||| || ||||||||||| ||||| |||||||| |
------------------------------------------------gtttggcctcttcatct---tataatgtacta--taactttaacgtgaaagggatag---atgctaatcctttcattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAAGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT

upper sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G13210.3 (Glycine max), 3'ss of exon 4
gttctgcattctgaactctaaatactagtgttgttcgaagttgacttagtttccattttttatctatctgtcatgttcttcttttctttcttctatattagctagctaatgcagattcttttattt-gcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT
                                                       |||  | |||   | | ||| | | || |   || | | ||   || |    |||||  || ||||| ||| |||||| |||   ||||| || |||||||| |||||||| || ||||| ||||  ||||  ||||||||||| || ||||||||||| ||||| |||||||| |
------------------------------------------------------gtttggtctcttcatcttatgatttactataaattttac-atgaaag-tgataaatgctaatccttttgttttgcagTCATCAATGTATGGGAATGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAGGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT

upper sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 5
gttctgcattctgaactctaaatactagtgttgttcgaagttgacttagtttccat-tttttatctatctgtcatgttcttcttt-tctttcttctatattagctagctaatgcag--attcttttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT
                                        ||||  |||  || ||  |||| ||    |||  |  || |||   ||||||||||||      ||  | | || |   ||||| | |||||||||  |  | || || || |||||||| || ||||| || || ||| ||| ||| |||||||||||||| |||||||||||||| || || || ||  | |
--------------------------------------gtttgagatagcatctatgcttttgtccgattgttcttatcatctgagtctttcttctat------taattgaggctgttgttcttctttttgcagTCAGCCACGTACGGAAAGGTGCTTGTTCTAGATGGTATCGTACAGCTGACCGAAAAAGATGAATGTGCATATCAGGAGATGATAGCCCATCTGCCTTTAT

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|110686791|gb|EE064831.1|EE064831
EST:     ATATTTTATTCCAGGGAAAGTCTGAGTTTCAAGAGATACTGGTTTTTGAG                         TCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGC
genomic: ATATTTTATTCCAGGGAAAGTCTGAGTTTCAAGAGATACTGGTTTTTGAGgttctgcatt ... ttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGC
EST: gi|71872710|gb|DT021765.1|DT021765
EST:     ATATTTTATTCCAGGGAAAGTCTGAGTTTCAAGAGATACTGGTTTTTGAG                         TCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGC
genomic: ATATTTTATTCCAGGGAAAGTCTGAGTTTCAAGAGATACTGGTTTTTGAGgttctgcatt ... ttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGC
EST: gi|161719336|gb|FC064840.1|FC064840
EST:     ATATTTTATTCCAGGGAAAGTCTGAGTTTCAAGAGATACTGGTTTTTGAG                         TCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGC
genomic: ATATTTTATTCCAGGGAAAGTCTGAGTTTCAAGAGATACTGGTTTTTGAGgttctgcatt ... ttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttcttttctttcttctatattagctagctaatgcagattcttttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT
                            agctaat  putative branch site (score: 3)
                                        ttcttttattt  putative PPT
           tttcttctatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctgcattctgaactctaaatactagtgttgttcgaagttgacttagtttccattttttatctatctgtcatgttcttcttttctttcttctatattagctagctaatgcagattcttttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG