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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcccttacacacaagcataatttcatagcatgcattcatcttccacatcccaatccttttcatttcagttgctgaaaggtgaagtttgtgaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGGCACACAATCTGCACATCACTGGCAGTGGTGGGAGGAAGCATGCTAGCAT

Basic information

species Vitis vinifera
transcript Vv04s0023g00380.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00380.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os11g28300.1 (Oryza sativa), 3'ss of exon 8
----------------------------------------------------------------------------------------------------atcccttacacacaagcataatttcatagcatgcattcatcttccacatcccaatccttttcatttcagttgctgaaaggtgaagtttgtgaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGGCACACAATCTGCACATCACTGGCAGTGGTGGGAGGAAGCATGCTAGCAT
                                                                                                     ||  |||       |  | || | ||| ||| | |  |   |  |  | |||  ||     || | | ||  |     |     | ||| |   ||||||| ||||| ||||||||||| |||||||||||||| || ||| || | || |||||  ||||||||||||| |||||  | || || |||||| | ||||
gtagtgctaccactcaactagcagcacatttttttttctatttcttaaccgagttaactctagctataagcacccaaaactgctgatataattgatctatttcatttattttactgagtgatgtgataacatac-tagaagatgaatcttccaggcccaaatatatgatttaatattttgctct-tatgttaccttgcagCTTGCAACCCACAAGAATGCAATCGGAGTAGCAGTTGGAGCATCATTGGGCCACACTGTCTGCACATCACTTGCAGTCATAGGTGGGAGCATGTTGGCAT

upper sequence: Vv04s0023g00380.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G151863_T02 (Zea mays), 3'ss of exon 8
----------------------------------------atcccttacacacaagcataatttcatagcatgcattcatcttc-cacatcccaatccttttcatttcagttgctgaaaggtgaagtttgtgaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGGCACACAATCTGCACATCACTGGCAGTGGTGGGAGGAAGCATGCTAGCAT
                                         |   | |   |      | ||   |||| |  | | ||  ||| ||      || ||| | | || ||     |      |   | |        |||||||||||||||||||||| || |||||||| |||||||| ||  || | ||||||||  | |||||||| || || ||||| ||||| |||||||| || |
gtaggatacttctccacttactgaaatcctttgatgtatcgtttttcattgaggtctgtgatactatagga-acctgcacattcgcaagcaaaaaacctgtaccttacaaagtttctttacttctgctatcaccaatgcagCTGGCAACACACAAGAACGCAATCGGAGTCGCAGTGGGAGCGTCACTGGGGCACACGGTGTGCACATCTCTCGCCGTGGTAGGAGGGAGCATGCTGGCGT

upper sequence: Vv04s0023g00380.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA18G47670.1 (Glycine max), 3'ss of exon 8
------------atcccttacacacaagcataatttcatagcatgcattcatcttccaca----tcccaatccttttcatttcagttgctgaaaggt--gaagtttgtgaatg-------tgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGGCACACAATCTGCACATCACTGGCAGTGGTGGGAGGAAGCATGCTAGCAT
            ||||| |  | |  | |||  | |  |  |  | ||| || ||    |    |    |||  |  |||| |     |  | |  |   | ||   | |||        |||||||||| || ||||| ||||| || ||||||||||| ||||| || ||||| ||||| ||||| || || ||||| |||||||||||||||||||| ||||
gtaagaaaactgatcccctgtagatcaacattttctgctttcgcg-attgattttgtctaattttgtttatcggtggcattcccccccccaacatttttcatgtcctttaattttccttctgcagCTGGCGACCCACAAAAATGCAATTGGAGTAGCAGTTGGGGCCACTATAGGACACACCATCTGTACCTCTCTGGCTGTGGTGGGAGGAAGCATGCTGGCAT

upper sequence: Vv04s0023g00380.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA09G38640.1 (Glycine max), 3'ss of exon 8
---------------------------------atcccttacacacaag-cataatttcatagcatgcattcatcttccacatcc-caatccttttcatttca-gttgctgaaaggtgaagtttgtgaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGGCACACAATCTGCACATCACTGGCAGTGGTGGGAGGAAGCATGCTAGCAT
                                 ||    | |   || |   |  |||  |   |     |  ||  |  |||    |  | ||||| |   |  ||  | |          || |   | ||||||||||||| ||||| ||||| || ||||||||||| ||||| || ||||| ||||| ||||| || || ||||| || ||||||||||||||||| ||||
gtaagaaaactgatcccctgtagatcaatcaacattttctgctttcacgatttggttttgtcttagtttattgtcggctgcattagtagcctttttcctcctacattttttatgtcctttaattttccttctgcagCTGGCAACCCACAAAAATGCAATTGGAGTAGCAGTTGGGGCCACTATAGGACACACCATCTGTACCTCTCTGGCTGTAGTGGGAGGAAGCATGCTGGCAT

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|110415417|gb|EC981325.1|EC981325
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|110375514|gb|EC940507.1|EC940507
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|33405511|gb|CF211138.1|CF211138
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|30303671|gb|CB980465.1|CB980465
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|110386306|gb|EC950891.1|EC950891
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|34320010|gb|CF372764.1|CF372764
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|110403098|gb|EC964255.1|EC964255
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|110398724|gb|EC965198.1|EC965198
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|110393823|gb|EC959339.1|EC959339
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|110689638|gb|EE066037.1|EE066037
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|30303609|gb|CB980403.1|CB980403
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|30133680|gb|CB919019.1|CB919019
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|30133597|gb|CB918936.1|CB918936
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|110369298|gb|EC933452.1|EC933452
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|161719466|gb|FC066414.1|FC066414
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|22007735|gb|BQ792769.1|BQ792769
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAACTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|110418308|gb|EC984450.1|EC984450
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|71866927|gb|DT015982.1|DT015982
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
EST: gi|110418385|gb|EC984534.1|EC984534
EST:     TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCG                         CTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG
genomic: TGACTTTTCTAGCCGAGTGGGGGGATCGCAGCCAGATCGCAACAATTGCGgttagaaatt ... gaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatcccaatccttttcatttcagttgctgaaaggtgaagtttgtgaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGGCACACAATCTGCACATCACTGGCAGTGGTGGGAGGAAGCATGCTAGCAT
            ttttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcccttacacacaagcataatttcatagcatgcattcatcttccacatcccaatccttttcatttcagttgctgaaaggtgaagtttgtgaatgtgcagCTGGCAACACACAAGAATGCGATCGGAGTAGCAGTGGGGGCAACAATAGGGCACACAATCTGCACATCACTGGCAGTGGTGGGAGGAAGCATGCTAGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - -acacaca
- - - - - - - - - - - - - - gcatgca
- - - - - - - - - - - - - - - - - - -catcttc
- - - - - - - - - - - - - - - - - - - - - - - catccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgaa