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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCATTCAATGAGGAAGATTTATTGCACTATTGCTTCTCTTCAGCATATATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttctttcaacaatatttccaccatggataccaaaatcaagctatttagaatcatttttatcaatgaataagttcatatatatatatatacaca...

Basic information

species Vitis vinifera
transcript Vv01s0026g02490.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g02490.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA01G05750.1 (Glycine max), 5'ss of exon 7
ATTCATTCAATGAGGAAGATTTATTGCACTATTGCTTCTCTTCAGCATATATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttctttcaacaatatttccaccatggataccaaaatcaagctatttagaatcatttttatc-aatgaataagttcatatatatat-atatacaca-
  ||     |||||||||||||| | |  |||||||||||||||||||| ||||| ||| | ||||| || |||||||||||||||||||||||||| ||||||| || |||       |  ||  |   |   |    | ||  || |   ||  || |     ||  ||    || |  | |   ||  | | | | ||| 
TCTCCCATGATGAGGAAGATTTACTTCGGTATTGCTTCTCTTCAGCATACATTGTTGCTCTGCTTCACGACAGTCTTGGAATTGCTTTGGATGATGAGAGgtattcctgctt---gtttttcttttaaggtatttgaatatattgaggttgataacattacaggcattgaacatttaggccctttcgtacctgaaacaaacat

upper sequence: Vv01s0026g02490.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA02G11980.1 (Glycine max), 5'ss of exon 7
ATTCATTCAATGAGGAAGATTTATTGCACTATTGCTTCTCTTCAGCATATATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttctttcaacaatatttccaccatggataccaaaatcaagctatttagaatcatttttatcaatgaataagttcatata-tatatatatacaca---
  ||     ||||||| |||||| | |  ||||| |||||||||||||| ||||| ||||| ||||| || ||||| |||||||||||||||||||| ||||||| || |||       |  ||  |  ||   |    | ||| || |   ||  || |||   ||  |  | | ||| |  ||  || ||  | ||| |   
TCTCCCATGATGAGGACGATTTACTTCGTTATTGTTTCTCTTCAGCATACATTGTTGCTTTGCTTCACGACAGTCTGGGAATTGCTTTGGATGATGAGAGgtattcctgctt---gtttttcttttaaaatatttgaatatatcgaggttgataatattattggcattgaacatttagtcccaatggtacatgaa-acaaattt

upper sequence: Vv01s0026g02490.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT1G14250.1 (Arabidopsis thaliana), 5'ss of exon 8
ATTCATTCAATGAGGAAGATTTATTGCACTATTGCTTCTCTTCAGCATATATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttctttcaacaatatttccaccatggataccaaaatcaagctatttagaatcatttttatcaatgaataagttcatatata-tatatatacaca
   ||   || ||  || ||||    |  ||||||||||| |||||||||||| |  |  | |||||||||||||||||  ||||| | ||||||||||||||    || || ||  | |     ||  ||  || |    ||   | | ||  |   ||    ||| ||  || || |  || | |  | | | | ||  
CAACAACTAAAGACAAATATTTGCATCGTTATTGCTTCTCATCAGCATATATTATCTCAATGCTTCATGATAGTCTTGGTGTTGCTCTTGATGATGAAAGgtaaatgttattgcacaagt----tcaagatcaatgc----atgttggttttctgtgacaaagatataaacaaa-aactatatgtttgctttgtttgcag-

upper sequence: Vv01s0026g02490.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT1G14230.1 (Arabidopsis thaliana), 5'ss of exon 7
ATTCATTCAATGAGGAAGATTTATTGCACTATTGCTTCTCTTCAGCATATATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttctttcaacaatatttccaccatggataccaaaatcaagctatttagaatcatttttatcaatgaataagttcatatatatatatatacaca-
   |||| || || ||  ||||  | |  ||||||||||| |||||||||||| |  |  | |||||||||||||||||  ||||| | ||||||||||||||    || || ||  | |       | ||  ||       |   |  |   |||    | |  |  ||      |    ||   | | | | |  ||| 
CAACATTTAAGGACGAGAATTTGCTTCGGTATTGCTTCTCATCAGCATATATTATCTCAATGCTTCATGATAGTCTTGGTGTTGCTCTTGATGATGAAAGgtaaatgttattgcacaagttcaagatcaatcaatgttggttttctgtgacaaaga----tataaacaaaaagtcgaacctatgcttgttt-tgtctacag

upper sequence: Vv01s0026g02490.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT1G14240.4 (Arabidopsis thaliana), 5'ss of exon 7
ATTCATTCAATGAGGAAGATTTATTGCACTATTGCTTCTCTTCAGCATATATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttctttcaacaatatttccaccatg---gat--accaaaatcaagctatttagaatcatttttatcaatgaataagttcatatatatatatatacaca-
   ||    |||| ||| ||||      |||||| |||||  ||||||||| | |  |  | ||||||||||||||||| |||||| | ||||||||||||||  | ||  | ||  |||      ||  ||   |||  | ||||     | | ||| | | ||    ||| ||  || || |  |  | | | | | |   || 
CAACAACTGATGAAGAATATTTGCGTGGCTATTGTTTCTCAGCAGCATATACTATATCAATGCTTCATGATAGTCTTGGTATTGCTCTTGATGATGAAAGgtaaaatttactgcacaaattcaagaacattgtaagattaatcaaatgtgggtttttttgga-caaagatataaacaaa-aactatacgtttgtttttgtttgcag

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|71883132|gb|DT032187.1|DT032187
EST:     ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAG                         GATTGGATGCGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
genomic: ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttc ... ttatgaacagGATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
EST: gi|110426528|gb|EC992941.1|EC992941
EST:     GTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAG                         GATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
genomic: GTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttc ... ttatgaacagGATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
EST: gi|77588859|gb|DV223671.1|DV223671
EST:     ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAG                         GATTGGATGCGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
genomic: ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttc ... ttatgaacagGATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
EST: gi|30320456|gb|CD003718.1|CD003718
EST:     ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAG                         GATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
genomic: ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttc ... ttatgaacagGATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
EST: gi|32460777|gb|CD801951.1|CD801951
EST:     ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAG                         GATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
genomic: ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttc ... ttatgaacagGATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
EST: gi|71889044|gb|DT038099.1|DT038099
EST:     ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAG                         GATTGGATGCGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
genomic: ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttc ... ttatgaacagGATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
EST: gi|110703130|gb|EE079707.1|EE079707
EST:     ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAG                         GATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
genomic: ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttc ... ttatgaacagGATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
EST: gi|71875853|gb|DT024908.1|DT024908
EST:     ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAG                         GATTGGATGCGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
genomic: ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttc ... ttatgaacagGATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
EST: gi|110383305|gb|EC947670.1|EC947670
EST:     ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAG                         GATTGGATGCGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
genomic: ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttc ... ttatgaacagGATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
EST: gi|77583539|gb|DV220805.1|DV220805
EST:     ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAG                         GATTGGATGCGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
genomic: ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttc ... ttatgaacagGATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
EST: gi|110383715|gb|EC948106.1|EC948106
EST:     ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAG                         GATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
genomic: ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttc ... ttatgaacagGATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
EST: gi|110429886|gb|EC996398.1|EC996398
EST:     ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAG                         GATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
genomic: ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttc ... ttatgaacagGATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
EST: gi|77589606|gb|DV224084.1|DV224084
EST:     ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAG                         GATTGGATGCGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG
genomic: ATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttc ... ttatgaacagGATTGGATACGCAAATCAGGTGGGAGATATCCCACTGGATTGGGCCTTAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCATTCAATGAGGAAGATTTATTGCACTATTGCTTCTCTTCAGCATATATTGTGGCTTTTCTTCATGATAGTCTTGGAATTGCTTTGGATGATGAAAGgtattacttctttcaacaatatttccaccatggataccaaaatcaagctatttagaatcatttttatcaatgaataagttcatatatatatatatacaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaataag