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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGGATGTTGGAGGCTTGCATGGATATGCAGCTGGAGTTGCAGCGCTCAGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttacaatctcaaaataattattcttgtactttgctgttgcgtggaaaaaagtgacaacacttaaatgagtgggaactaaaagtgcacctccttc...

Basic information

species Vitis vinifera
transcript Vv13s0019g05390.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os03g01720.1 (Oryza sativa), 5'ss of exon 5
CAAAGGATGTTGGAGGCTTGCATGGATATGCAGCTGGAGTTGCAGCGCTCAGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCA---GCTGGTGAACCAGgtttgtttacaatctcaaaataattattcttgtactttgctgttgcgtggaaaaaagtgacaacacttaaatgagtgggaactaaaagtgcacctccttc
     |||| | || ||||||||||| |||||| ||||||||||||||||  ||| ||| ||||| ||||||||||||||||| |||   || | |    |||||  |      |||||   |   |  ||||  ||  |  ||||       | | |  ||||||  || | ||||     ||||  |  | |    |    
---CAGATGCTAGAAGCTTGCATGGAGATGCAGATGGAGTTGCAGCGCTCCATCAAACAAGAAGTCTCTGCTGCTCTGAACCGCTCACTAGCCGTTCCTGCAGgtcagaagttgatctcttcaacctgtttctgctatctcactgt-------acatatctgacaaagctgagatgat----aacttgatattcttaacag--

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G006965_T01 (Zea mays), 5'ss of exon 5
CAAAGGATGTTGGAGGCTTGCATGGATATGCAGCTGGAGTTGCAGCGCTCAGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttacaatc----tcaaaataattat-tcttgtactttgctgttgcgtggaaaaaagtgacaacacttaaatgagtgggaactaaaagtgcacctccttc
|||||||||||||| |||||||||||||||||||| ||||||||||| || || || || |||||||| || ||  |||| || |    ||| || | ||||| ||  |  | |    |||   |   ||  | |  |||  || |||| | ||    ||      || | | ||   ||     |     | |           
CAAAGGATGTTGGAAGCTTGCATGGATATGCAGCTAGAGTTGCAGCGTTCTGTAAGGCAAGAAGTATCAGCAGCCTTGAATCGTTTCATTGGGGAGCAAGgttagtaaatcagcatggtcatttttgctacatttcctacagtggtgttacttgtttgaactaagaaatattcaaggaagcatttatatgtaatattagc-----

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G081965_T01 (Zea mays), 5'ss of exon 5
CAAAGGATGTTGGAGGCTTGCATGGATATGCAGCTGGAGTTGCAGCGCTCAGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttacaatctcaaaataattattcttgtactttgctgttgcgtggaaaaaagtgacaacacttaaatgagtgggaactaaaagtgcacctccttc----
|| |||||| |||| || |||||||| ||||||||||| |||||||| || || ||||| ||||| || |||||  |||| || |  || ||      ||||  |   |   |   || || |||||  | |||||  | |  |   |  || ||  |||  ||| | |  ||      ||| | ||  | |  | | |     
CAGAGGATGCTGGAAGCGTGCATGGACATGCAGCTGGAATTGCAGCGTTCTGTGAGACAAGAAGTGTCAGCTGCCTTGAATCGGTTTGCAGGACCTGAAGgtcagacaattcttctaacatcattatcgtagtact--gtttctatatctaataatatga--acaatgatttgcacccaaaccagaaacgtattttcattattt

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA20G33300.1 (Glycine max), 5'ss of exon 7
------------CAAAGGATGTTGGAGGCTTGCATGGATATGCAGCTGGAGTTGCAGCGCTCAGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttacaatctcaaaataattattcttgtactttgctgttgcgtggaaaaaagtgacaacacttaaatgagtgggaactaaaagtgcacctccttc
            || |||||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||||||||| |||| | |||||   ||| || || |  | ||      || ||| | |   | || | ||     ||      |  |  |       |||          | |||||| ||     
ATGAATCACATGCAGAGGATGTTGGAGGCCTGCATGGATATGCAACTGGAGTTGCAGCGCTCTGTCAGACAGGAAGTATCTGCTGCTCTGAACCGCTCAGgtagtgaaaatggtgtgatttct-tttctcttctatcattatagccatgtgtttttttactgagttttttttcttcttcctcttga--------cgatagtgcatctgt---

upper sequence: Vv13s0019g05390.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G34240.1 (Glycine max), 5'ss of exon 8
CAAAGGATGTTGGAGGCTTGCATGGATATGCAGCTGGAGTTGCAGCGCTCAGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtt-tacaatctcaaaataattattcttgtactttgctgttgcgtggaaaaaagtgacaacacttaaatgagtgggaactaaaagtgcacctccttc
|| |||||||||||||| |||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| ||||| |||| ||||||    |||  ||  |    | ||      || | | | ||| | || | ||   | ||      |  |     ||| |  ||||  | ||| |   |   |   |  
CAGAGGATGTTGGAGGCCTGCATGGATATGCAACTGGAGTTGCAGCGCTCTGTCAGACAGGAAGTATCTGCTGCTCTAAACCGCTCAGGTGGTGAGAATGgtgcgtgatttcttttctcttctatcaatgtagtaatgtgtttttttattgagtttttttcccctctttacaacagtgc-atctatattggttgcatttat

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|33404834|gb|CF210461.1|CF210461
EST:     AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCGGCTGGTGAACCGG                         GGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
genomic: AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttac ... attgtcacagGGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
EST: gi|110362870|gb|EC926428.1|EC926428
EST:     AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCGGCTGGTGAACCAG                         GGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
genomic: AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttac ... attgtcacagGGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
EST: gi|110402602|gb|EC960544.1|EC960544
EST:     AGTCAGACAGGAAGTATCTGCTGCTGTGAACCGATCGGCTGGTGAACCAG                         GGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
genomic: AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttac ... attgtcacagGGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
EST: gi|30302439|gb|CB979233.1|CB979233
EST:     AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCGGCTGGTGAACCAG                         GGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
genomic: AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttac ... attgtcacagGGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
EST: gi|110697361|gb|EE074284.1|EE074284
EST:     AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCGGCTGGTGAACCAG                         GGATGAGTGTAGAGACATCGGAAGATGGATCTAAATGGGGTCATGTGAGGA
genomic: AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttac ... attgtcacagGGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
EST: gi|110722021|gb|EE097887.1|EE097887
EST:     AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCGGCTGGTGAACCAN                         GGATGAGTGTANAGACATCGGGAG-ATGGATCTAAATGGGGTCATGTGAGG
genomic: AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttac ... attgtcacagGGATGAGTGTAGAGACATCGG-AGGATGGATCTAAATGGGGTCATGTGAGG
EST: gi|33404749|gb|CF210376.1|CF210376
EST:     AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCGGCTGGTGAACCGG                         GGATGAGTGTAGAGACATCGGAGGATGGATCTGATTGGGGTCATGTGAGGA
genomic: AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttac ... attgtcacagGGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
EST: gi|30297155|gb|CB973949.1|CB973949
EST:     AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCGGCTGGTGAACCAG                         GGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
genomic: AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttac ... attgtcacagGGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
EST: gi|110396940|gb|EC962647.1|EC962647
EST:     AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCGGCTGGTGAACCAG                         GGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
genomic: AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttac ... attgtcacagGGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
EST: gi|34362695|gb|CF404280.1|CF404280
EST:     AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCGGCTGGTGAACCAG                         GGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
genomic: AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttac ... attgtcacagGGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
EST: gi|110405556|gb|EC971098.1|EC971098
EST:     AGTCAGACAGGAAGTATTTGCTGTTTTGAACCGATCAGCTGGTGAACCAG                         GGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA
genomic: AGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttac ... attgtcacagGGATGAGTGTAGAGACATCGGAGGATGGATCTAAATGGGGTCATGTGAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAGGATGTTGGAGGCTTGCATGGATATGCAGCTGGAGTTGCAGCGCTCAGTCAGACAGGAAGTATCTGCTGCTCTGAACCGATCAGCTGGTGAACCAGgtttgtttacaatctcaaaataattattcttgtactttgctgttgcgtggaaaaaagtgacaacacttaaatgagtgggaactaaaagtgcacctccttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgggaa