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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCGTTGCAGCAATACCAGGGACCTTTTTCTGTGCATGGTATGCTTCCCAGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagctgtatttcatcagaaccattgttacattggatgtctccatttgctagcatgaacctattcatattagttttgggttacttatttttacca...

Basic information

species Vitis vinifera
transcript Vv06s0009g03520.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os02g02530.3 (Oryza sativa), 5'ss of exon 5
GATCGTTGCAGCAATACCAGGGACCTTTTTCTGTGCATGGTATGCTTCCCAGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagctgtatt-tcatcagaaccattgttacattggatgtctccatttgctagcat---gaacctattcatattagttttgggttactt---atttttacca-----------------------------------
  | |||||| |||| |||||    || || ||   |||||||||| |  |||||||||||||||| |||||| | |||||  |  |||||||||||||||| || |   ||| || |  | |||   |  ||||   || ||   |  | |  |||   |     | ||   || ||  ||| ||  || ||    |  |||||                                     
AGTTGTTGCATCAATCCCAGGATTTTTCTTTTGCATATGGTATGCTGCGAAGAAGCATTGGCTAGCAAACAATGTTTTGGGGATTTCTTTCTGCATTCAGgtatg-cttttgtgttattttgagatataaggttaatatgcattattgaaataactatggttcaagagcttcacaaatatgttctgttttcctcccaaactttacttggagagaaacctacttgattctctttatcttacag

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA04G08510.1 (Glycine max), 5'ss of exon 6
GATCGTTGCAGCAATACCAGGGACCTTTTTCTGTGCATGGTATGCTTCCCAGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagctgtatttcatcagaaccattgttacattggatgtctccatttgctagc--atgaacctattcatattagttttgggttacttatttttacca
| ||||||| | ||| || ||||| ||||| ||||| ||||||||||  ||||||||||||||||| || ||||||||||| || |||||||| |||||||||||     | |  |  ||   ||   |  ||   || |     |         |    || |   | || ||| ||  |||  | ||   ||||  |   
GGTCGTTGCTGGAATCCCTGGGACATTTTTTTGTGCCTGGTATGCTTTGCAGAAGCATTGGCTAGCAAATAATATATTGGGTCTTGCTTTCTGTATTCAGgtttgttgcttttcctatatataaatgttatttttttttgtcaattgagccaatcaattgattatgttttttatactaaatttttggtatccatttccat--

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA06G08620.2 (Glycine max), 5'ss of exon 6
GATCGTTGCAGCAATACCAGGGACCTTTTTCTGTGCATGGTATGCTTCCCAGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagctgtatttcatcagaaccattgttacattggatgtctccatttgctagc--atgaacctattcatattagttttgggttacttatttttacca
| ||||||| | ||| || ||||| ||||| ||||||||||||||||  | ||||||||||||||| || ||||||||||| || || ||||| |||||||||||     | |  |  ||   ||    || |   ||||     | |     | |    || |   | || ||| ||  ||| || ||   ||||| |   
GGTCGTTGCTGGAATCCCTGGGACTTTTTTTTGTGCATGGTATGCTTTGCGGAAGCATTGGCTAGCAAATAATATATTGGGTCTTGCCTTCTGTATTCAGgtttgttgcattttctatatataaatgtctgattttttggtcaattgcgccaaccaattgattatattttttatactaaattttgggtatccattttcat--

upper sequence: Vv06s0009g03520.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA14G21190.1 (Glycine max), 5'ss of exon 1
GATCGTTGCAGCAATACCAGGGACCTTTTTCTGTGCATGGTATGCTTCCCAGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagctgtatttcatcagaaccattgttacattggatgt-ctccatttgctagcatgaacctattcatattagttttg-ggttacttatttttacca
||||||||| ||||| || || |||||||| ||||| |||||||| |  | ||||||||||||||| || ||||||||||| || |||||||| || |||||||||    |   |||   |      ||  ||   |    | | ||    | |     | | |    || ||   | |  || ||||| |  | |||    
GATCGTTGCTGCAATCCCTGGAACCTTTTTTTGTGCGTGGTATGCCTTGCGGAAGCATTGGCTAGCAAATAATATATTGGGTCTTGCTTTCTGTATACAGgtttggtgcttaactttttacctgtgtatatttgtttgaattctactttcctggtctaaaaggatgcctttatggaactaatgtggttagtattctttgg--

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|71877015|gb|DT026070.1|DT026070
EST:     AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAG                         GGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
genomic: AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagc ... ccatttgcagGGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
EST: gi|27579299|gb|CB001994.1|CB001994
EST:     AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAG                         GGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
genomic: AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagc ... ccatttgcagGGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
EST: gi|110391760|gb|EC956760.1|EC956760
EST:     CTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAG                         GGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
genomic: CTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagc ... ccatttgcagGGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
EST: gi|110361505|gb|EC924984.1|EC924984
EST:     AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAG                         GGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
genomic: AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagc ... ccatttgcagGGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
EST: gi|77579348|gb|DV218502.1|DV218502
EST:     AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAG                         GGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
genomic: AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagc ... ccatttgcagGGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
EST: gi|161717568|gb|FC066896.1|FC066896
EST:     AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAG                         GGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
genomic: AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagc ... ccatttgcagGGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
EST: gi|349812621|gb|FQ409780.1|FQ409780
EST:     AGAAGCATTGGCTAGCCAACAATATGTTGGGCCTCGCTTTCTGCATTCAG                         GGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
genomic: AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagc ... ccatttgcagGGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
EST: gi|110730433|gb|EE107509.1|EE107509
EST:     AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAG                         GGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
genomic: AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagc ... ccatttgcagGGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
EST: gi|110708740|gb|EE086629.1|EE086629
EST:     AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAG                         GGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
genomic: AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagc ... ccatttgcagGGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
EST: gi|71874644|gb|DT023699.1|DT023699
EST:     AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAG                         GGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG
genomic: AGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagc ... ccatttgcagGGTATTGAAATGCTCTCACTTGGGTCTTTTAAAACTGGTGCCATCCTTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCGTTGCAGCAATACCAGGGACCTTTTTCTGTGCATGGTATGCTTCCCAGAAGCATTGGCTAGCCAACAATATATTGGGCCTCGCTTTCTGCATTCAGgtttggcagctgtatttcatcagaaccattgttacattggatgtctccatttgctagcatgaacctattcatattagttttgggttacttatttttacca

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