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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATTTAAGATAATTGTGACTGATCCTGATTCAGTTCTGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAGgtaatctttgtttatgaagaacctcaccatattcttcctgttgatgacaatggccacttttcatgtccctcattttatag

Basic information

species Vitis vinifera
transcript Vv13s0067g01710.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g01710.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA18G02820.1 (Glycine max), 5'ss of exon 3
GCATTTAAGATAATTGTGACTGATCCTGATTCAGTTCTGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAGgta-atctttgt-ttatgaagaacctcaccatatt------cttcctgttgatgacaatggccacttttcatgtccctcatt--ttatag
|| || || ||||||||||||||||||||| | ||| | | | | ||||||||||||||||| ||||||||||||||||| || |||||| || ||| | | |     || || |||| ||       ||  |   |  ||   ||| | |  | |  | |   |  ||    ||||
GCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACTCGTGAAGTTAAGGAAGTTGGCCCTGATGGGCAAGAGgtatatatttttatcagagtaaaactgaccacatctcacaactcacaagtcttgtttatgactaaatatattttttgttgttgcccatag

upper sequence: Vv13s0067g01710.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA11G35600.1 (Glycine max), 5'ss of exon 3
GCATTTAAGATAATTGTGACTGATCCTGATTCAGTTCTGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAGgtaatctttgtttatgaag--aacctcaccatattct-----tcctgttgatgacaatggccacttttcatgtccctcattttatag
|| || || ||||||||||||||||||||| | ||| | | | | ||||||||||||||||| |||||||||||||| || || |||||||   || ||     ||  || || |||| ||  |     || |||| ||||| |       ||||  |||| |||||       
GCTTTCAAAATAATTGTGACTGATCCTGATACTGTTTTAAGTACTCTCACTCGTGAAGTTAAGGAAGTTGGCCCTGACGGGCAAGAGgtaaatatttttatcagagtaaaactgaccacatcttgcaagtcttgtttatgactaaatgtttttttattgtcgctcatag-----
















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|349810224|gb|FQ401670.1|FQ401670
EST:     TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAG                         GTGACAAGGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
genomic: TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAGgtaatctttg ... cattttatagGTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
EST: gi|349810908|gb|FQ405896.1|FQ405896
EST:     CGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAG                         GTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
genomic: TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAGgtaatctttg ... cattttatagGTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
EST: gi|110698113|gb|EE075755.1|EE075755
EST:     TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAG                         GTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
genomic: TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAGgtaatctttg ... cattttatagGTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
EST: gi|110720646|gb|EE096749.1|EE096749
EST:     TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAG                         GTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
genomic: TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAGgtaatctttg ... cattttatagGTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
EST: gi|71870361|gb|DT019416.1|DT019416
EST:     TGAATTCCCTCACTCGTGAAGTTAAAGATGTTGGCCCTGATGGACAGGAG                         GTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
genomic: TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAGgtaatctttg ... cattttatagGTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
EST: gi|32268823|gb|CD717982.1|CD717982
EST:     TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAG                         GTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
genomic: TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAGgtaatctttg ... cattttatagGTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
EST: gi|30305055|gb|CB981849.1|CB981849
EST:     TGAATTCCCTCACTCGTGAAGTTAAAGATGTTGGCCCTGATGGACAGGAG                         GTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
genomic: TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAGgtaatctttg ... cattttatagGTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
EST: gi|110401163|gb|EC967762.1|EC967762
EST:     TGAATTCCCTCACTCGTGAAGTTAAAGATGTTGGCCCTGATGGACAGGAG                         GTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
genomic: TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAGgtaatctttg ... cattttatagGTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
EST: gi|110686590|gb|EE064398.1|EE064398
EST:     TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAG                         GTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
genomic: TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAGgtaatctttg ... cattttatagGTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
EST: gi|110708703|gb|EE086544.1|EE086544
EST:     TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAG                         GTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA
genomic: TGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAGgtaatctttg ... cattttatagGTGACAAAGGTGGTCCCTGCTATATCTGAGGAAGTGAAGGATGCTTTGGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATTTAAGATAATTGTGACTGATCCTGATTCAGTTCTGAATTCCCTCACTCGTGAAGTTAAAGAAGTTGGCCCTGATGGACAGGAGgtaatctttgtttatgaagaacctcaccatattcttcctgttgatgacaatggccacttttcatgtccctcattttatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA