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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttatagctcattaaaatttatgttctgtatcagattattagccaactaaatttctactgaatgttaatcttctttcttcattgtcttggttgggctcaggggttgacctcttgtacttgtttaattgacattaaattactctcaatatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTGAAGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAA

Basic information

species Vitis vinifera
transcript Vv08s0007g04210.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 3
gtaattttatagctcattaaaatttatgttctgtatcagattattagccaactaaatttctactgaatgttaatcttctttcttcattgtcttggttgggctcaggggttgacctcttgtacttgtttaattgacattaaattactctcaatatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTGAAGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAA
                                                                    || |  ||  ||  |  | ||  |   ||    |||||   |    |  | | |||      |||   | ||  || |   |   | |  |||| || || ||||| || |||||||||||| | |||||||||||||| ||||||||  |||||||||||||||||||||||||||||||||| || || |
--------------------------------------------------------------------gtcaggctg-ttcatcgaatgattgctttaatgtcaggatat----ttctctgcttagaaggttgttgtaaacgtattggtatattgtacagGTCTTCCTTTTTGCAAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g59990.2 (Oryza sativa), 3'ss of exon 3
gtaattttatagctcattaaaatttatgttctgtatcagattattagccaactaaatttctactgaatgttaatcttctttcttcattgt--cttggttgggc--tcaggggttgacctcttgtacttgtttaattgacattaaattactctcaatatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTGAAGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAA
                                                                      ||| | ||||| | |||||    |||   |  |  ||   | || |  |   |    | ||  ||  |  || || |  ||||    | |  |||| ||||| |||||||| || ||||||||| | |||||||||||||| ||||||||  | ||||||||||||||||| |||||||||||||| || || |
---------------------------------------------------------------------gtaaccctctttgtccattgaagtttgaaagtccaatctatgattaagttagggggtcttttgcatacaatttcaagtgttctct---tctgcagGTTTTTCTGTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCCAAGCTTACCTGGACAGCTATGTACAGGAAGCAGCACAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g12250.1 (Oryza sativa), 3'ss of exon 3
gtaattttatagctcattaaaatttatgttctgtatcagattattagccaactaaatttctactgaatgttaatcttctttcttcattgtcttggttgggctcaggggttgacctcttgtacttgtttaattgacattaaattactct-caatatat-ttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTGAAGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAA
                                                                              |   | | ||| |  | | ||   ||   ||  |   |     ||    || ||   || || ||  |    ||  ||| | ||||||| || ||| | || || || |||||| | |||||||||||||| ||||||||| | |||||||| ||||||||||||||||| ||||| || || |
-----------------------------------------------------------------------------gtgagtactttggcaagat-ggatacacatgtgtaggacaaaagctaacctatttctgatcaatttctttggtaaactatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTGAAGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G110328_T04 (Zea mays), 3'ss of exon 3
gtaattttatagctcattaaaatttatgttctgtatcagattattagccaactaaatttctactgaatgttaatcttctttcttcattgtcttggttgggctcaggggttgacctcttgtacttgtttaattgacattaaattactctcaatatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTGAAGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAA
                                                                           | ||  ||    | | || ||  |       |  | |  |  |  | |  | | || || |  ||| |||      | |||  |||| || || |||||||| |||||||||||| | |||||||||||||| ||||||||  ||||||||||||||||||| |||||||||||||| || || |
-------------------------------------------------------------------------gttactagctatcatatttttgtaaga---gatgtctaagattataaaatcttcttatggaaag-aaactacatatgttttat--agGTTTTCCTTTTTGCCAACTCAAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCAATGTACAGGAAGCAGCACAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G142640_T03 (Zea mays), 3'ss of exon 2
gtaattttatagctcattaaaatttatgttctgtatcagattattagccaactaaatttctactgaatgttaatcttctttcttcattgtcttggttgggctcaggggttgacctcttgtacttgtttaattgacattaaattactctcaatatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTGAAGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAA
                                                                    ||||  ||   |  | |||| |  |     |  | |   | | |       |  |||||    ||  |  || ||||  |   | |||  |||| || || |||||||| || ||||||||| | |||||||||||||| ||||||||  ||||||||||||||||||| |||||||||||||| || || |
--------------------------------------------------------------------gtta--ctcgctgttacatttttataag-agatttataagcttatagaaaatgtttgtta---tggaaagaacttacatttgttctat--agGTCTTCCTTTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCAATGTACAGGAAGCAGCACAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G074898_T01 (Zea mays), 3'ss of exon 3
gtaattttatagctcattaaaatttatgttctgtatcagattattagccaactaaatttctactgaatgttaatcttctttcttcattgtcttggttgggctcaggggttgacctcttgta-cttgtttaattgacattaaattactctcaatatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTGAAGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAA
                                                                    ||||  |||  |  | |||| | |    | || |     ||   | |  | || | || |    || ||   || |||  ||  | | | ||||| || || |||||||| || ||||||||| | |||||||||||||| ||||||||  ||||||||||||||||||| |||||||||||||| || || |
--------------------------------------------------------------------gtta--cttgctgttacattttttgtaataggttt----gtaagctttatatagcatgatcttatggcaaggaaataca-tctgtttttgtagGTTTTCCTTTTTGCCAACTCGAAATGCAAGCGCTACTTCCACAACCGCCTGAAGCCTGCAAAGCTTACCTGGACAGCAATGTACAGGAAGCAGCACAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G34700.1 (Glycine max), 3'ss of exon 2
gtaattt----tatagctcattaaaatttatgttc-tgtatcagattattagccaactaaatttctactgaatgttaatct--tctttcttcattgtcttggttgggctcaggggttgacctcttgtacttgtttaattgacattaaattactctcaatatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTGAAGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAA
|| |  |    |||  |||||| || |||  ||   ||||||  || |||  |   ||  || |  | |      | || |  || || || ||| |   | ||   ||  |    |    | |  ||||  | | |  |   ||   ||  |      || | ||||| || || |||||||| |||||||| ||| |||| ||||||||||| |||||||| |||||||| |||||||| || |||||||| |||||||| ||||
gtgacataaaatatgtctcattgaattttgggtggatgtatctcatcattt-cagtctggatgttcaatttgctatgatttgatcatttttaattatggggttttttctttgttactagt-tatgatactgatatgag-ggtttttgtttgtt----gaatctatagGTTTTCCTGTTTGCCAACTCAAAATGTAAGCGGTATTTCCACAACCGCCTGAAGCCCTCAAAGCTCACCTGGACTGCTATGTACAGAAAGCAACACAAAA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G07680.1 (Glycine max), 3'ss of exon 2
gtaattttatagctcattaaaatttatgttctgtatcagattattagccaactaaatttcta--ctgaatgttaatcttctttcttcattgtcttggttgggctcagg---ggttgacctcttgtacttgtttaattgacatta---aattactctcaatatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTGAAGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAA
                | | |   ||||||    ||   ||| |  |   |   | | | |    |  || |  || |||| | | | ||| |    |     |||     | | |   | |  || || ||  | ||| ||     | ||  |      ||||  |||| || || ||||| || || ||||| |||||||| ||||||||| || |||||||||||||||| |||||||| || |||||||| |||||||| || |
---------------gtgacataatatgtttctcattgaattttgggttgatgtattgtgttattttgatatggatgttctgtgtactttgacaaaatcatcatcaattttgatcgttttttactagttattatactgatataggggatttgtttgttgaatatacagGTTTTCCTGTTTGCTAACTCGAAATGTAAGAGGTATTTCCACAACAGGTTGAAGCCATCAAAGCTCACCTGGACTGCAATGTACAGAAAGCAACACAAGA

upper sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G53020.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaattttatagctcattaaaatttatgttctgtatcagattattagccaactaaatttctactgaatgttaatcttctttcttcattgtcttggttgggctcaggggttgacctcttgtacttgtttaattgacattaaattactctcaatatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTGAAGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAA
                                                    |   | | |  ||||| || | ||  |      ||||  ||| ||   ||  |    ||   | | ||  | || |        || |||   |   | | | || |||| ||  | |||   || |||||||| |||||||||||||| |||  | |||||||||| |||||| | ||||| ||||||||||| |||||||| || |
--------------------------------------------------gttggttcttttatgaatcttcagctaatcaa---attgatttgtttatactttgcaaatg--ttttggttttagtct--------tttaatggtttgtattgttttcagGTTTTCTTGTTTCTTAACTCAAAATGTAAGAGGTACTTCCATAACAAGTTGAAGCCATCCAAGCTTGCATGGACTGCCATGTACAGAAAGCAACACAAGA

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|33408532|gb|CF214159.1|CF214159
EST:     CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAG                         GTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTG
genomic: CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAGgtaattttat ... atatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTG
EST: gi|110404057|gb|EC970014.1|EC970014
EST:     CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAG                         GTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTG
genomic: CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAGgtaattttat ... atatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTG
EST: gi|26262650|gb|CA813713.1|CA813713
EST:     CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAG                         GTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTG
genomic: CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAGgtaattttat ... atatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTG
EST: gi|26261571|gb|CA812634.1|CA812634
EST:     CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAG                         GTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTG
genomic: CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAGgtaattttat ... atatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTG
EST: gi|110398469|gb|EC964851.1|EC964851
EST:     CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAG                         GTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTG
genomic: CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAGgtaattttat ... atatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTG
EST: gi|26261679|gb|CA812742.1|CA812742
EST:     CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAG                         GTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACNCGGCT
genomic: CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAGgtaattttat ... atatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAAC-CGGCT
EST: gi|294966178|gb|GW839401.1|GW839401
EST:     CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAG                         GTGTTTCTATTTGCCAATTCGAAATGCAAGAGGTACTTCCACAACCGGCTG
genomic: CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAGgtaattttat ... atatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTG
EST: gi|71867860|gb|DT016915.1|DT016915
EST:     CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAG                         GTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTG
genomic: CCAAGATATACCCTGGGAAAGGAATCAGATTTGTTCGTTCAGATTCTCAGgtaattttat ... atatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggttgacctcttgtacttgtttaattgacattaaattactctcaatatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTGAAGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAA
                       aattgac  putative branch site (score: 3)
                    tttaattgacattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttatagctcattaaaatttatgttctgtatcagattattagccaactaaatttctactgaatgttaatcttctttcttcattgtcttggttgggctcaggggttgacctcttgtacttgtttaattgacattaaattactctcaatatatttagGTGTTTCTATTTGCCAATTCAAAATGCAAGAGGTACTTCCACAACCGGCTGAAGCCATCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAACATAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA