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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaatttttatggctttactgtctttgtttttttcaaaagaaatttcagataattgatctggcatactttatttcttttgttttaagtcaacca...

Basic information

species Vitis vinifera
transcript Vv11s0206g00130.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os01g64650.1 (Oryza sativa), 5'ss of exon 2
AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgta-aacccaatttttatggctttactgtctttgtttttttcaaaagaaatttcagat--aattgatctggcatactttatttcttttgttttaagtcaacca
|||| || || || ||  ||||||| ||||||||||| ||| | |  ||||||||||| ||||||||||| ||||| ||||||||  | || ||  |||||  | ||  | ||  || | || |||| ||   | |  |   |    |  |  |||   ||| |   |  |||    |||   |   |  ||     |   
AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcctttgttcttgacattcctgtattgcatatccttgtatttgacctaggatcagattcacaagcaataagggattgtctccttgctattctca---

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G178244_T01 (Zea mays), 5'ss of exon 2
AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaa-acccaatttttatggctttactgtctttgtttttttcaaaagaaatttcagataattgatctggcatactttatttcttttgttttaagtcaacca-
||||||| || || ||  ||||||||||||| ||||||||  |||  ||||||||||| ||||||||||| ||||| ||||||||  | || || ||||||    |||   ||  ||   || |    | | |||  ||       || || || | |   ||   | |   | ||     |   || | |  ||     
AATATAAGGTTCACTCCCACAACAGAAATGGGCTTTGTGCGGTGGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATCAGgtaccgaccatgattcctgagattcccacatgtctttgcttttggttgaagttgagtttaccaatt--gtaagttgtagccagtcatttctcacccagttct

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA13G19950.1 (Glycine max), 5'ss of exon 2
AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaa-accca-atttttatggctttactgtctttgtttttttcaaaagaaatttcagataattgatctggcatactttatttcttttgttttaagtcaacca-
| || || |||||  | |||||||||||||||||||| ||  |||| ||||||||||| || || ||  |||| || || |||||  | ||||||||||| | || || ||   | | |  ||  ||    |    | ||||| | |  ||     |  ||| | ||| | | |       | |||||| |||        
AGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAACCAGgtgagactcagatcactgttggatttttgctgcttccgtattcaagacatgttat---tcgttgctttggaaaattaggaagatattgtttgaaggtgcatga

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|351017097|gb|FQ424524.1|FQ424524
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|33408128|gb|CF213755.1|CF213755
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|349824324|gb|FQ417683.1|FQ417683
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|71881424|gb|DT030479.1|DT030479
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|33408558|gb|CF214185.1|CF214185
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|110390655|gb|EC955577.1|EC955577
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|71876275|gb|DT025330.1|DT025330
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|71866199|gb|DT015254.1|DT015254
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|110709953|gb|EE085862.1|EE085862
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|351028488|gb|FQ444769.1|FQ444769
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|110691734|gb|EE070172.1|EE070172
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|71876274|gb|DT025329.1|DT025329
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|110725014|gb|EE101356.1|EE101356
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|294966596|gb|GW837731.1|GW837731
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|110709110|gb|EE084283.1|EE084283
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|71869605|gb|DT018660.1|DT018660
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|351018531|gb|FQ424638.1|FQ424638
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|351028310|gb|FQ427206.1|FQ427206
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
EST: gi|110371348|gb|EC935304.1|EC935304
EST:     TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG                         GTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA
genomic: TTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaa ... tgcctgacagGTGATAGATGAGTATCAGAAGAATTTTGGTGATTCGTGGAGGACTGTACAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgtaaacccaatttttatggctttactgtctttgtttttttcaaaagaaatttcagataattgatctggcatactttatttcttttgttttaagtcaacca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaaa