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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaaaacattgctctataagaagacccaatagcttctcatctcgtcatctatctgtgaatctgacttgtattgatttcattcttgttgttcccatcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTACTCTGGCTACCTTGTACCACCAGATAGTCATCAGAGCTATCCCATTCAAGACCAGAGCCTGAGAAA

Basic information

species Vitis vinifera
transcript Vv15s0046g02410.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g47220.1 (Oryza sativa), 3'ss of exon 2
gtaagtgaaaacattgctctataagaagacccaatagcttctcatctcgtcatctatctgtgaatctgactt----gtattgatttcattc-----ttgttgttcccatcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTACTCTGGCTACCTTGTACCACCAGATAGTCATCAGAGCTATCCCATTCAAGACCAGAGCCTGAGAAA
            ||| || ||| | ||| |   ||   |  | |   | | ||  | |  ||   || | ||    | | | | | |         ||| || | |   |||||||| ||||||||||| ||||||||||| ||| | || ||| || | ||||||||| | |||||||| || || |||||||||| |||  | | |    
-----------tattactgtatgataagtctacatcattagtgaggacatgattgagcaatggcacttaattacaagcactaactcccgctgcaatttgctggttctg-cagTGGATCTTCTGGGTTGGCCCCTTCATTGGCGCTGCCCTTGCTGCCATCTACCACCAGGTGGTCATCAGGGCAATTCCATTCAAGAGCAGGTCGTAACCTG

upper sequence: Vv15s0046g02410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g44630.3 (Oryza sativa), 3'ss of exon 2
gtaagtgaaaacattgctctataagaagacccaat-agcttctcatctcgtcatctatctgtgaatctgacttgtattgatttcattcttgttgttcccatcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTACTCTGGCTACCTTGTACCACCAGATAGTCATCAGAGCTATCCCATTCAAGACCAGAGCCTGAGAAA
 ||  |   | | |  |    ||  |        | |       |       |     |   || | |  | | ||   ||||   | |     ||     |||||||| ||||||||||| |||||| |||| ||| | |||||| || | ||||||||| |  ||||||| || ||||||||||||| |||  | | ||   
-tacttagtagcttaccagcttactagcctttgctcaagaaaagagtagaagacacgacaaagagtttttcct-tacaaattttggtatctaaattttg--cagTGGATCTTCTGGGTTGGTCCCTTCGTTGGCGCTGCCCTGGCTGCCATCTACCACCAGGTGATCATCAGGGCGATCCCATTCAAGAGCAGGTCTTAAGCCC

upper sequence: Vv15s0046g02410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AC209208.3_FGT002 (Zea mays), 3'ss of exon 3
gtaagtgaaa-acattgctctataagaagac-ccaatagcttctcatctcgtcatctatctgtgaatctgacttgtattgatttcattcttgttgttcccatcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTACTCTGGCTACCTTGTACCACCAGATAGTCATCAGAGCTATCCCATTCAAGACCAGAGCCTGAGAAA
 ||  ||  |   |||     || |         |||   | |   | |  || |||||  ||      || | || ||     |  | |  |||||     |||||||| |||||||| || ||||||||||| ||| |||||||| || | ||||||||| |  |||||||||| ||||| ||||||| |||  | | |    
-tagatggcatgtattaactaatgatcctttgttaatgcatgcatgtttaatcctctattggtaccgaggagtcgtgttataacc--tatgattgttttg--cagTGGATCTTCTGGGTCGGCCCCTTCATTGGCGCTGCTCTGGCTGCCATCTACCACCAGGTGATCATCAGAGCCATCCCGTTCAAGAGCAGGTCTTAA----

upper sequence: Vv15s0046g02410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G37730.1 (Glycine max), 3'ss of exon 3
gtaagtgaaaacattgctcta-taagaagacccaatagcttc-tcatctcgtcatctatctgtgaatctgacttgtat-tgatttcattcttgttgttcccatcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTACTCTGGCTACCTTGTACCACCAGATAGTCATCAGAGCTATCCCATTCAAGACCAGAGCCTGAGAAA
       ||||||||   ||| ||| |    | |||   |      | |    |  ||| | ||  |   |     || | ||||  ||  | ||||       |||||||||||||||||||||| |||||||||||| | || ||| |  |||| ||||||||||||||| |||| ||||| |||||||| || || |  |   
------taaaacattttactaataacacattctaatcattaaactctataaaaaaatatatatgccttaaataataatgtaattttttttattttgtggtttatagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTATCACCAGATAGTCATCCGAGCCATCCCTTTCAAGACAAGGGCTTAGGCTC

upper sequence: Vv15s0046g02410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G01860.1 (Glycine max), 3'ss of exon 3
gtaagtgaaaacattgctctataagaagacccaatagcttct-catctcgtcatctatctgtgaatctgacttgtattgatttcattcttgttgttcccatcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTACTCTGGCTACCTTGTACCACCAGATAGTCATCAGAGCTATCCCATTCAAGACCAGAGCCTGAGAAA
  ||        | |  | | |  | |  | |  ||  ||   |  | |   |  ||| | |     | | |  || ||   |  ||  | || |      ||||||||||||||||||||||| |||||||||||| | || ||| |  |||| ||||||||||||||| |||| || || |||||||| || || |  |   
--aaacatttttactaatttgt--gcattctcgttattttaaaccccacagaagatatatatatgctttaataataatgtaattttttattttatggtttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTGTATCACCAGATAGTCATCCGAGCCATTCCTTTCAAGACAAGGGCTTAGGCTC

upper sequence: Vv15s0046g02410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G02530.1 (Glycine max), 3'ss of exon 3
gtaagtgaaaacattgctctataagaagacccaatagcttct-catctcgtcatctatctgtgaatctgacttgtattga---tttcattcttgttgttcccatcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTACTCTGGCTACCTTGTACCACCAGATAGTCATCAGAGCTATCCCATTCAAGACCAGAGCCTGAGAAA
                   ||||   |   ||  |  ||| |    ||| |  | | |   ||||  ||||||   || |   ||| ||| |  ||||  |   ||||||||||||||||||||||| |||||||||||| | || ||  | || || ||||||||||| ||| |||| || ||||||||||| || |  | |  ||
------------------gtatatacatgtcctttcacttatgtgcctctttgttt-tgcatgaaagtgactttatttaactgtttaattttaattgtggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCAGCTTTATATCACCAGATAGTGATCCGAGCAATTCCATTCAAGACAAGGGGTTAATCAA

upper sequence: Vv15s0046g02410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G42950.1 (Glycine max), 3'ss of exon 3
gtaagtgaaaacattgctctataagaagacccaatagcttctcatctcgtcatctatctgtgaatctgacttg--tattgatttcattcttgttgttcccatcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTACTCTGGCTACCTTGTACCACCAGATAGTCATCAGAGCTATCCCATTCAAGACCAGAGCCTGAGAAA
                       | | | ||    |  |      ||| |  | | ||| |  |  ||||||   ||  | ||| ||| |  || |  |   ||||||||||||||||||||||| |||||||||||| | || ||| |  | || ||||||||||| ||| |||| || || |||||||| || |  | |  ||
---------------------gtatatgtcctttcacttatgtgcctctttgtttttct-tacaagtgacttatttaacggtttaattttgattttggcttacagTGGATTTTCTGGGTTGGACCTTTCATTGGAGCTGCCCTTGCTGCTGTATATCACCAGATAGTGATCCGAGCAATTCCTTTCAAGACAAGGGGTTAACCAA

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|351039371|gb|FQ461238.1|FQ461238
EST:     GTCTCGGGGCCGCCATCATCTACAACAGGGGGAATGCCTGGGATGACATG                         TGGATTTTCTGGGTTGGACCCTTCATTGAAGCTACTCTG
genomic: GTCTCGGGGCCGCCATCATCTACAACAGGGGGAATGCCTGGGATGACATGgtaagtgaaa ... ttcccatcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTACTCTG
EST: gi|110699569|gb|EE076680.1|EE076680
EST:     TCTCGGGGCCCGC-ATCATCTACAACAGGGGGAATGCCTGGGATGACATG                         TGGATTTTCTGGGGTGGNACCNT-CATTGGAGCTACTCTGGCTACCNNTGT
genomic: TCTCGGGGCC-GCCATCATCTACAACAGGGGGAATGCCTGGGATGACATGgtaagtgaaa ... ttcccatcagTGGATTTTCTGGGTTGG-ACCCTTCATTGGAGCTACTCTGGCTACCT-TGT
EST: gi|351012484|gb|FQ427085.1|FQ427085
EST:     GTCTCGGGGCCGCCATCATCTACNACAGGGGGAATGCCTGGGATGACATG                         TGGATTTTCTGGGGTGGACCCTTCATTGGAGCTACTCTGGCTACCTTGTAC
genomic: GTCTCGGGGCCGCCATCATCTACAACAGGGGGAATGCCTGGGATGACATGgtaagtgaaa ... ttcccatcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTACTCTGGCTACCTTGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcatctatctgtgaatctgacttgtattgatttcattcttgttgttcccatcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTACTCTGGCTACCTTGTACCACCAGATAGTCATCAGAGCTATCCCATTCAAGACCAGAGCCTGAGAAA
                         tattgat  putative branch site (score: 3)
                                    ttcttgttgttccc  putative PPT
                         tattgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgaaaacattgctctataagaagacccaatagcttctcatctcgtcatctatctgtgaatctgacttgtattgatttcattcttgttgttcccatcagTGGATTTTCTGGGTTGGACCCTTCATTGGAGCTACTCTGGCTACCTTGTACCACCAGATAGTCATCAGAGCTATCCCATTCAAGACCAGAGCCTGAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT