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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggctttcaaatcgtcttcattttctctcaaccactgttcattttttttcatag

Basic information

species Vitis vinifera
transcript Vv06s0004g06860.t01
intron # 28
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 28
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggctttcaaatcgtcttcattttctctcaaccactgttcat-tttttttcatag
 || |||||| | ||||| || || || ||  | || ||||  ||||||||||||||||||||||| ||| | |||||||| ||||| ||||| |||||||||   | |||    |   | |||  | |  | || |  | |    | || |||  |  ||| ||    | |  ||  |    ||
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgttt---ccgttcatgtgtt-tgggactattcatttacgtacagttttccataacaacaaagcttgcttcatgtgcag

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 28
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggctttcaaatcgtcttcattttctctcaaccactgttcat-tttttttcatag
 || |||||| | ||||| || || || ||  | || ||||  ||||||||||||||||||||||| ||| | |||||||| ||||| ||||| |||||||||   | |||    |   | |||  | |  | || |  | |      || |||  |  ||| ||    | |  ||  |    ||
TTGTCTCTTTATTTGTTATGACTTGATCCGTGCGGATGTTGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCATTCCCCTATCTGTTACAGgtatcttgttt---ccgttcatgtgtt-tgggactattcatttacgaacagttttccataacaacaaagcttgcttcgtgtgcag

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GRMZM2G062042_T02 (Zea mays), 5'ss of exon 13
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttgg------ctttcaaatcgtcttcat-----tttctctcaaccactgttcattttttttcatag
 ||||||||  | || |||||  | || ||||| || || |  ||||||||||||||||||||||| ||| | |||||||||||||| || || |||||||||     |   ||    || |||||     |       ||| || |  ||   |||       || ||      || |     | | | |  ||
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgcgccgacgtctacttacatacagttaccatagtaacatccctactgtgctatgtgactgtctgcgcag

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GRMZM2G115138_T01 (Zea mays), 5'ss of exon 12
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggc------tttcaaatcgtcttcattttctctcaaccactgttc-attttttttcatag----
 ||||||||  | || |||||  | || ||||| || || |  ||||||||||||||||||||||| ||| | |||||||||||||| || || |||||||||     |   ||    || |||||     | |      || || |  ||   |||  |  |    | ||||| | || |   |   |      
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgtgccgacgtctatttacatacagttaccatagtaacatccctactgtgctatgtgactgtgtgcgcag

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GRMZM2G395549_T01 (Zea mays), 5'ss of exon 13
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggctttcaaatcgtcttcattttctctcaaccactgttcattttttttcatag
 ||||||||  | || |||||  | || ||||| || || |  ||||||||||||||||||||||| ||| | |||||||||||||| || || |||||||||     |   |||   || |||||     | | |  |  |    | || |||  |  |   ||    |   | | | |  ||
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttttgtccatgttcgcgccgacgtctat-ttacatacagtttaccatagtaacatccctactatgtgcgcag

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GRMZM2G091121_T01 (Zea mays), 5'ss of exon 8
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggc------tttcaaatcgtcttcattttctctcaaccactgttc-attttttttcatag----
 ||||||||  | || |||||  | || ||||| || || |  ||||||||||||||||||||||| ||| | |||||||||||||| || || |||||||||     |   ||    || |||||   | | |      || || || ||   |||  |  |    | ||||| | || |   |   |      
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTACAGgtacgtagtaatttctgtccatgttcgtgtcgacgtctatttacatatagttaccatagtaacatccctactgtgctatgtgactgtgtgcgcag

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GRMZM5G804382_T01 (Zea mays), 5'ss of exon 5
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggctttcaaatcgtcttcattttctctcaaccactgttcat-tttttttcatag
 ||||||||  | || |||||  | || ||||| || || |  ||||||||||| ||||||||||| ||| | ||||||||||||||||| || || |||||||  || || | ||   | | |   |    | | |    |  | |  | |||         ||  | |||  |   |    ||
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCGTGGATGAACAACATGTTGGACTTTGCCTTCCCATACCTGTTGCAGgtaacttacttctgtc---catatctgacggtgatgtttgtttatgtataatttactatggtaac-atccatgctgcgtgtgcag

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 26
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggctttcaaatcgtcttcattttctctcaaccac-tgttcattttttttcatag------------
 ||||||||  | || |||||  | || |||||||| || |  ||||||||||||||||||||||| ||| | |||||||||||||| || || || ||||||     |   ||    || |||||     | | |  |  |    | || |||  |  |   || | |  | | |  |   |              
TTGCCTCTTCATTTGCTACGACCTGATCCGGCCAGATGTGGCTCTTGAGCTTGCATGGATGAACAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtacgtagtaatttctgtccatgttcgtgccgacgtctat-ttacatacagtttaccatagtaacatctctactgtgctatgtgactgtgtgcgcag

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GRMZM5G822591_T01 (Zea mays), 5'ss of exon 5
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggctttcaaatcgtcttcattttctctca--accactgttcatttttttt-catag
 ||||||||  | || |||||  | || ||||| || || |  |||||||||||||||||||| || ||| | |||||||||||||| || || || |||||||   | || ||||  ||     || |   | | |    |    |  | |||        |  |   | |||  |   |    ||
CTGCCTCTTCATTTGCTACGACCTGATCCGGCCGGATGTCGCTCTTGAGCTTGCATGGATGAATAACATGGTGGACTTTGCCTTCCCGTACCTGTTGCAGgtaactaacttatttctgcccgtacctgtggtgatgtttgtttacatatagtttactatggtaataacatccatcctgcgtgtgcag

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 26
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgtt--ctatttggctttcaaatcgtcttcattttctctcaaccactgttcattttttttcatag---------
 ||||||||||||||||| ||| |||| |||||||| ||||  |||||||| || ||||||||||||||||| || ||||| |||||||| |||||||||||| | | |    |      | |||  |||| |   || |     |  ||   || || | ||  | |  |||||||||   ||           
TTGCCTCTTTGTCTGTTATGATATAATACGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATTTTGCTTTCCCATACCTCTTACAGgtatattttccactggggtttcgttcactatatttattactggatgatttttcttccttttaatga-taatcattttttaatatttcccccctag

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 28
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaact----------atttgtttcacccttgttctatttggct-----ttcaaatcgtcttcattttctctcaaccac-tgttcattttttttcatag----------------------------------------------------------------
 |||||||| |||||||| ||| |||| |||||||| ||||  |||||||| || ||||||||||||||||| || ||||| |||||||| |||||||||||| | |           ||| |||      |||   ||  ||||       |||         | |       ||  ||  |     ||| ||||                                                                    
TTGCCTCTTCGTCTGTTATGATATAATACGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATTTTGCTTTCCCATACCTCTTACAGgtatattttcccctggggtttcttttttttatgtgaaatggggctaaaagcccaaggaaaagagactaaacaggaatgacacgaggggtttctttcgctatatgtattactggatgatttttcttccttttattgataaccattttttaatatttcccccctag

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 28
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggctttcaaatcgtcttcattttctctcaaccactgttca-ttttttttcatag----
|||||||||||||||||| ||| | || |||||||| ||||  ||||||||  | ||||||||||||||||| || ||||| || ||||||||||||||||||   |||||||||     || |  |  |   |     ||   | ||| |||| |   ||  | | |  | | ||||||  |      
ATGCCTCTTTGTCTGTTATGATATTATACGGCCAGATGTTGCTCTTGAGCTATCTTGGATGAACAATATGATTGATTTTGCTTTTCCATATCTCTTACAGgtatg-tatttgttt-gtggttatatttatcaacagatgaaatatattctttttttgctaaaaattttgaaatgtttttttgtttgaag

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 28
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 28
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggctttcaaatcgtcttcattttctctcaaccact-----gttcattttttttcatag
|||||||||||||||||| ||| | ||  ||||||| ||||  |||||||| || ||||||||||||||||| || ||||| || ||||||||||| ||||||    ||||||||     || |  |  |   |     ||   | ||| |||| |   || || |      || |||||| ||   ||
ATGCCTCTTTGTCTGTTATGATATTATATGGCCAGATGTTGCTCTTGAGCTAGCTTGGATGAACAATATGATTGATTTTGCTTTTCCATATCTCTTGCAGgtatgg-atttgttt-gtggttatatttatcaacagatgaaatatattctttttttgctaaacattttgaaatttatttttgtttgaag

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|30251298|gb|CB969031.1|CB969031
EST:     TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAG                         TTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGAGATCATT
genomic: TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatt ... tttttcatagTTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT
EST: gi|30133211|gb|CB918550.1|CB918550
EST:     ATATCTCTTACAG                         TTTATTCGTGAGTACACGGGCGAAGTAGATGACCTTGTCAAGGACAGAATT
genomic: ATATCTCTTACAGgtaaactatt ... tttttcatagTTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT
EST: gi|30252228|gb|CB969779.1|CB969779
EST:     TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAG                         TTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT
genomic: TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatt ... tttttcatagTTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT
EST: gi|349826023|gb|FQ415828.1|FQ415828
EST:     TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAG                         TTTATTCGTGAGTACACGGGC
genomic: TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatt ... tttttcatagTTTATTCGTGAGTACACGGGC
EST: gi|30251483|gb|CB969216.1|CB969216
EST:     TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAG                         TTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT
genomic: TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatt ... tttttcatagTTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT
EST: gi|30252223|gb|CB969774.1|CB969774
EST:     TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAG                         TTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT
genomic: TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatt ... tttttcatagTTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT
EST: gi|30252315|gb|CB969866.1|CB969866
EST:     TTGCATGGATGAACAATATGATCGANTTTGCCTTCCCATATCTCTTACAG                         TTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT
genomic: TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatt ... tttttcatagTTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT
EST: gi|110699699|gb|EE076936.1|EE076936
EST:     TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAG                         TTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT
genomic: TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatt ... tttttcatagTTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT
EST: gi|30251472|gb|CB969205.1|CB969205
EST:     TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAG                         TTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT
genomic: TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatt ... tttttcatagTTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT
EST: gi|45771749|gb|CN007601.1|CN007601
EST:     TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAG                         TTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT
genomic: TTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatt ... tttttcatagTTTATTCGTGAGTACACGGGCAAAGTAGATGACCTTGTCAAGGACAGAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCCTCTTTGTCTGTTACGATTTAATTCGGCCAGACGTTGTCCTTGAGCTTGCATGGATGAACAATATGATCGACTTTGCCTTCCCATATCTCTTACAGgtaaactatttgtttcacccttgttctatttggctttcaaatcgtcttcattttctctcaaccactgttcattttttttcatag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA