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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgacacttagttgtatgccaccacaattctcctttggcaacttctctttatttatggtgtttgtaatttacttttctacgttgacaataggctga...

Basic information

species Vitis vinifera
transcript Vv06s0004g04430.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os05g38550.2 (Oryza sativa), 5'ss of exon 5
GTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgacacttagttgtatgccaccacaattctcctttggcaacttctctttatttatggtgtttgtaatttacttttctacgttgacaataggctga------------
||||||||||||||| |||| ||||| |||||||| || || || |||||||| || || ||||| |||||||| || ||||||| ||||  ||||| |  |    |||||||| |       |   |  |||  |   |  ||   | | ||   ||  | |  ||    |   | |            
GTTGAAAGTATAGTTCTGAGCATCATTTCGATGCTCTCTAGTCCAAATGATGAGTCTCCAGCAAATATTGAAGCGGCTgtaagtg-cactc-gttgtctatc--tgcaattctctt------gccctttcttacgtgctgcatta--agtctagacttacaagaggaacggaaaattattctgctgctcc

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os01g62244.3 (Oryza sativa), 5'ss of exon 3
GTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgacacttagttgtatgccaccacaattctcctttggcaacttctctttatttatggtgtttgtaatttacttttctacgttgacaataggctga----
||||| || |||||| |||| ||||| |||||||||||  | || |||||||||||||| ||||| |||||||| || ||||||  ||||||    | ||| |    ||||      |  |   | ||| |      |||||| | |    |  | |    |   ||     ||  ||    
GTTGAGAGCATAGTTCTGAGCATCATTTCGATGCTTTCTGGTCCAAATGATGAATCACCAGCAAATATTGAAGCAGCTgtaagtt-cacttaac-atttgctatggaaattgagaact--ctgttcctcctgggccttggtgtatatggcattttatctgtcacggagggatgggggaagag

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G007276_T01 (Zea mays), 5'ss of exon 4
GTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgacacttagttgtatgccaccacaattctcct---ttggcaacttctctttatttatggtgtttgtaat--ttacttttctacgttgacaataggctga
||||||||||||||| |||| ||||| || ||||| || || || ||||| || || || ||||| ||||||||||| ||||||| |||       ||| ||  | |  |    ||   | || ||     ||  | |  |  | |||||  |  || |  | | ||||| | ||  ||    
GTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCCgtaagtg-caccctacaatattccctctctctctctctgggtaggaaaacaaactgcagtagttttttttgtcctgcttccagtgcaacgtttaaaagcgg----

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G012052_T01 (Zea mays), 5'ss of exon 5
GTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgacacttagttgtatgccaccacaattctcctttggcaacttctctttatttatggtgtttgta-atttacttttctac-gttgacaataggctga-
||||||||||||||| |||| ||||| |||||||| || || || ||||| || || || || || || |||||||| ||||||| |||   |   ||| |   | |  |    || |  |    |||| |     |   |  ||| | |  | ||||| | | | |  || |    ||  
GTTGAAAGTATAGTTCTGAGCATCATTTCGATGCTCTCTAGTCCAAATGACGAGTCTCCAGCGAATATCGAAGCTGCCgtaagtg-cacacggcattattctctctctctctctctctctc--tctctcataggaaaacataattgcagaagttcttttgtgcagcttccagtgcaatgcc

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA12G06960.1 (Glycine max), 5'ss of exon 5
GTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgacac--ttagttgtatgccaccacaattctcctttggcaacttctctttatttatggtgtttgtaatttacttttctacgttgacaataggctga--
|| || |||||||| ||||||||||||||||||||||||||||||||||||||||| ||||||||  |||||||||||||||||  ||   || ||| ||   || |  | || || |||  | |||| | | |||   | | |     |||  |    |    ||| || | | ||||   
GTAGAGAGTATAGTATTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCAgtaagtttcataatttgttatactgcaacttacttgtctttt--ctacttatttgtatcc-tagagaagacaatgcaagcatgactgtt-actagatgctgcag

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA11G14980.1 (Glycine max), 5'ss of exon 5
GTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagt--gacacttagttgtatgccaccacaattctcctttggcaacttctctttatttatggtgtttgtaattta--cttttctacgttgacaataggctga
|| || |||||||| |||||||||||||| |||||||||||||||||||||||||| ||||||||  |||||||||||||||||  ||   ||  || | | | |||  | || || ||   | |||| | | |||   | | |     |||  |  | |  || |  | | |    || ||
GTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCAgtaagtttgatcatttcttatttacaacc-tacttgtctttc--ctacttatttgtatcc-tagagaagacaatgcaagcatgactgctattagatgccgcaga

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA13G40990.1 (Glycine max), 5'ss of exon 5
GTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgacacttagttgtatgccaccacaattctcctttggcaacttctcttt---atttatggtgtttgtaatttacttttctacgttgacaataggctga--
|| || |||||||| || |||||||||||||||||||| || |||||||||||||| ||||||||  |||||||||| ||||||     ||     | |         ||| |  ||  ||||| | ||  |      |||  | |   || | |     ||   |   | || |||   |  
GTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCGgtaagt-----ttgaccattttgtgattttattttatttcagcaacctttccctcagtcctatcttatggctactatttgcatcctagaaaagaaaaggtaaacc

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA15G04470.1 (Glycine max), 5'ss of exon 5
GTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgacacttagttgt-atgccaccacaattctcctttggcaacttctctttatttatggtgtttgtaatttacttttctacgttgacaataggctga-
|| || |||||||| || |||||||||||||||||||| || |||||||||||||| || |||||  |||||||||| ||||||   ||    |||| || | |    | |||| |        | ||  |    |  |   | |  | |||| | |  |   |   | || |||   | 
GTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCGgtaagtttgaccattttgtgattctattttatttctgcaacctttccctcagtcctatcttatggctacttatttgcatcccagag--aagaaaaggtaaac

upper sequence: Vv06s0004g04430.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S75_236V6.1 (Physcomitrella patens), 5'ss of exon 7
GTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagt--gacacttagttgtatgccaccacaattctcctttggcaacttctctttatttatggtgt-ttgtaatttacttttctacgttgacaataggctga
|| || |  ||  |||| || |||||||| ||||| ||||| |||||||||||||||||||| || || || ||||| |||||   ||   ||  ||  |   ||     | |    | |  |   ||||  ||  | |     | || ||   |   |    | |  |||| |       
GTGGAGACAATTCTTTTAAGCATCATATCTATGCTCTCCAGTCCTAATGATGAATCACCTGCTAATATAGATGCTGCGgtaaggtggaagttttcttcaaaatcatgttcaattaattctctcgttttcttgttgctaacataatattctagactttgtgctaaggcagacacttaat---

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|110710545|gb|EE086990.1|EE086990
EST:     CAATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA                         AAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCCGATGT
genomic: CGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgaca ... ataattgcagAAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCAGATGT
EST: gi|110364996|gb|EC928664.1|EC928664
EST:     CGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA                         AAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCAGATGT
genomic: CGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgaca ... ataattgcagAAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCAGATGT
EST: gi|110407296|gb|EC972893.1|EC972893
EST:     CAATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA                         AAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCCGATGT
genomic: CGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgaca ... ataattgcagAAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCAGATGT
EST: gi|110696034|gb|EE074731.1|EE074731
EST:     CAATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA                         AAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCCGATGT
genomic: CGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgaca ... ataattgcagAAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCAGATGT
EST: gi|110695874|gb|EE074387.1|EE074387
EST:     CAATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA                         AAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCCGATGT
genomic: CGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgaca ... ataattgcagAAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCAGATGT
EST: gi|110706251|gb|EE081613.1|EE081613
EST:     CAATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA                         AAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCCGATGT
genomic: CGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgaca ... ataattgcagAAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCAGATGT
EST: gi|110693589|gb|EE069952.1|EE069952
EST:     CAATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA                         AAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCCGATGT
genomic: CGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgaca ... ataattgcagAAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCAGATGT
EST: gi|110376683|gb|EC941750.1|EC941750
EST:     CAATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA                         AAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCCGATGT
genomic: CGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgaca ... ataattgcagAAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCAGATGT
EST: gi|110696006|gb|EE074671.1|EE074671
EST:     CAATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA                         AAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCCGATGT
genomic: CGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgaca ... ataattgcagAAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCAGATGT
EST: gi|30124774|gb|CB910113.1|CB910113
EST:     CAATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCA                         AAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCCGATGT
genomic: CGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgaca ... ataattgcagAAGGAATGGAGAGATAGGAGGGATGAATTCAAGAAAAAGGTGAGCAGATGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGAAAGTATAGTTTTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCACCTGCAAACATTGAAGCTGCAgtaagtgacacttagttgtatgccaccacaattctcctttggcaacttctctttatttatggtgtttgtaatttacttttctacgttgacaataggctga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaccac