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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgaagttattcgcttatctgatatttccattgatgtaccctgtttggcctttgttgatgtccgtccttgttttaattatatgtttactcatgtgaacagGTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCAGCCACCACAGAGAGTGCCCTTGGATCCCTGGACAAGATCCCGTCTCTGC

Basic information

species Vitis vinifera
transcript Vv04s0044g00980.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g00980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G39250.1 (Glycine max), 3'ss of exon 5
ctgaagttattcgcttatctgatatttccattgatgtaccctgtttggcctttgttga-tgtccgtccttgttttaattatatgtttactcatgtgaacagGTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCAGCCACCACAGAGAGTGCCCTTGGATCCCTGGACAAGATCCCGTCTCTGC
 ||  |||||  | |||     |    || | || ||  | | |   |     ||||| | |    | | || || |  | |  | ||  | |   ||||||||||| || ||||| ||||||||||| ||| ||||  |  |||| |||||||||||||||||||  ||| | ||||||||| || | || |||||| ||
gtgttgttata-gtttaatacttcaaaccttcgaagttgcttataatgaggaggttgaatttgaaacttcgtatttaaaaaaattatatgctttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCAACTCCTCAGCCACCACAGAGAGCACCCCTTGATCCCTGGGCACGTTCTCGTCTCAGC

upper sequence: Vv04s0044g00980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G15680.1 (Glycine max), 3'ss of exon 5
-ctgaagttattcgcttatctgatatttccattgatgtaccctgtttggcctttgttgatgtccgtccttgttttaattatatgtttactcatgtgaacagGTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCAGCCACCACAGAGAGTGCCCTTGGATCCCTGGACAAGATCCCGTCTCTGC
  ||   |  ||   |  |   | |  | |   | ||       |   |   |||    ||    | | | ||  ||  | |  | ||  | |   ||||||||||| || ||||| ||||||||||| ||| ||||  |  | || |||||||||||||||||||  ||| | |||||||||||| | || |||||| ||
cttgttatagtttaatccttcaa-accttcgaagttgcttagaatgaagaggttgaaactgaaacttcgtattaaaaaaaaaattatatgctttgaaacagGTTTATTGACAGAGAAAATGAGCTTAGGCAGGCAAAGGCACCGACTCCTCAGCCACCACAGAGAGCACCCCTTGATCCCTGGACACGTTCTCGTCTCAGC

upper sequence: Vv04s0044g00980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G09770.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------ctgaagttattcgcttatctgatatttccattgatgtaccc-tgtttggcc--------tttgttgatg-tccg-----tccttgttttaattat-------atgtttactcatgtgaacagGTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCAGCCACCACAGAGAGTGCCCTTGGATCCCTGGACAAGATCCCGTCTCTGC
               |    ||||  |  | |||| | ||| |||| || |  || |||| |  |          |||| ||| |  |     |   || |  | | ||       ||  ||  |  | || | |||||||| || |||||||| |||||||| || |||||||| ||||||||||| ||||| ||  ||||||| ||||| || |||  |||||| || |||  |
gtaaaactagtttcttttctttatcagtctttctggt-tttacattcatatctccatgttagatcaaataagaagtgttaatgatttggaagctttctggtgaactaatttggtcgatacttgatactttggatagGTTTATTGACAGAGAGAACGAGCTTAGGCAATCAAAACCAGCAACACCTCAACCACCGCAACGAGTGCCATTGGACCCATGGGAAAGATCTCGGCTCACC

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|110709263|gb|EE084569.1|EE084569
EST:     CTTCGAACTCGCATACGAGTTGGTGATGCTGCACCAATGGCCTATATTGA                         GTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCA
genomic: CTTCGAACTCGCATACGAGTTGGTGATGCTGCACCAATGGCCTATATTGAgtaagattgt ... atgtgaacagGTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCA
EST: gi|110716795|gb|EE092087.1|EE092087
EST:     CTTCGAACTCGCATACGAGTTGGTGATGCTGCACCAATGGCCTATATTGA                         GTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCA
genomic: CTTCGAACTCGCATACGAGTTGGTGATGCTGCACCAATGGCCTATATTGAgtaagattgt ... atgtgaacagGTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCA
EST: gi|110702795|gb|EE079078.1|EE079078
EST:     CTTCGAACTCGCATACGAGTTGGTGATGCTGCACCAATGGCCTATATTGA                         GTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCA
genomic: CTTCGAACTCGCATACGAGTTGGTGATGCTGCACCAATGGCCTATATTGAgtaagattgt ... atgtgaacagGTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCA
EST: gi|351016180|gb|FQ435500.1|FQ435500
EST:     CTTCGAACTCGCATACGAGTTGGTGATGCTGCACCAATGGCCTATATTGA                         GTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCA
genomic: CTTCGAACTCGCATACGAGTTGGTGATGCTGCACCAATGGCCTATATTGAgtaagattgt ... atgtgaacagGTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCA
EST: gi|110710349|gb|EE086607.1|EE086607
EST:     CTTCGAACTCGCATACGAGTTGGTGATGCTGCACCAATGGCCTATATTGA                         GTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCA
genomic: CTTCGAACTCGCATACGAGTTGGTGATGCTGCACCAATGGCCTATATTGAgtaagattgt ... atgtgaacagGTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcctttgttgatgtccgtccttgttttaattatatgtttactcatgtgaacagGTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCAGCCACCACAGAGAGTGCCCTTGGATCCCTGGACAAGATCCCGTCTCTGC
                         ttttaat  putative branch site (score: 3)
                      ttgttttaattatatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgaagttattcgcttatctgatatttccattgatgtaccctgtttggcctttgttgatgtccgtccttgttttaattatatgtttactcatgtgaacagGTTTATAGATAGAGAGAATGAGCTTAGACAGTCAAAACCTGCAACACCTCAGCCACCACAGAGAGTGCCCTTGGATCCCTGGACAAGATCCCGTCTCTGC

- - - - - - - - - - - - - -ccattga
- - - - - - - - - - - - - - - - - - -accctgt
- - - - - - - - - - - - - - - - - - - - - - - -gcctttg