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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtgctgaagtaatgaaacctgctccatgtgttttaatttattgtctctcacatgattctgttcacgattcagGGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGGTTCAAGATG

Basic information

species Vitis vinifera
transcript Vv05s0051g00940.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0051g00940.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G58170.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtgtgctgaagta---atgaaacctgctccatgtgttttaatt--------tattgtctctca-catgattct-gttcacgattcagGGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGGTTCAAGATG
   | | | |   | ||    ||| || |      | |  |||  |         ||||||  || | |||  | |  | |  | ||  |||| ||||| |||||| ||||||||||| | ||||||||||||||||| || || || | |
--gtatttaccagaatatttgtgatacttatattttatcatttgctcacagacgctattgttactgaacattttgcaaggtttctatgtagGGCAATGATATGGATTCATCAAGGGGATTTCTCTCAGGAACCATGGACCGCTTTAAAACG
















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|22008454|gb|BQ793488.1|BQ793488
EST:     GTGATATACATGAAGAGGTAGAGAGCCACAATCGCATGCTTGATCGTGTG                         GGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGG
genomic: GTGATATACATGAAGAGGTAGAGAGCCACAATCGCATGCTTGATCGTGTGgtatgtgtgc ... cacgattcagGGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGG
EST: gi|110402034|gb|EC968667.1|EC968667
EST:     GTGATATACATGAAGAGGTAGAGAGCCACAATCGCATGCTTGATCGTGTG                         GGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGG
genomic: GTGATATACATGAAGAGGTAGAGAGCCACAATCGCATGCTTGATCGTGTGgtatgtgtgc ... cacgattcagGGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGG
EST: gi|37183816|gb|CF603170.1|CF603170
EST:     GTGATATACATGAAGAGGTAGAGAGCCACAATCGCATGCTTGATCGTGTG                         GGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACTATGGAACGG
genomic: GTGATATACATGAAGAGGTAGAGAGCCACAATCGCATGCTTGATCGTGTGgtatgtgtgc ... cacgattcagGGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGG
EST: gi|22009494|gb|BQ794528.1|BQ794528
EST:     GTGATATACATGAAGAGGTAGAGAGCCACAATCGCATGCTTGATCGTGTG                         GGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGG
genomic: GTGATATACATGAAGAGGTAGAGAGCCACAATCGCATGCTTGATCGTGTGgtatgtgtgc ... cacgattcagGGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGG
EST: gi|46918094|gb|CN547423.1|CN547423
EST:     GTGATATACATGAAGAGGTAGAGAGCCACAATCGCATGCTTGATCGTGTG                         GGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGG
genomic: GTGATATACATGAAGAGGTAGAGAGCCACAATCGCATGCTTGATCGTGTGgtatgtgtgc ... cacgattcagGGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGG
EST: gi|30127159|gb|CB912498.1|CB912498
EST:     GTGATATACATGAAGAGGTAGAGAGCCACAATCGCATGCTTGATCGTGTG                         GGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACTATGGAACGG
genomic: GTGATATACATGAAGAGGTAGAGAGCCACAATCGCATGCTTGATCGTGTGgtatgtgtgc ... cacgattcagGGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGG
EST: gi|110386397|gb|EC950990.1|EC950990
EST:     GTGATATACATGAAGAGGTAGAGAGCCACAATCGCATGCTTGATCGTGTG                         GGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGG
genomic: GTGATATACATGAAGAGGTAGAGAGCCACAATCGCATGCTTGATCGTGTGgtatgtgtgc ... cacgattcagGGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgctccatgtgttttaatttattgtctctcacatgattctgttcacgattcagGGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGGTTCAAGATG
                           ctctcac  putative branch site (score: 3)
                                      ttctgttc  putative PPT
        atgtgttttaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtgctgaagtaatgaaacctgctccatgtgttttaatttattgtctctcacatgattctgttcacgattcagGGGAATGAGATGGATGCATCAAGGGGAATCCTCTCAGGAACCATGGAACGGTTCAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG