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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTCGATTTGAGTGGCATTCTCACTGTGTTTTTCTGTGGTATCGTAATGTCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCAAgtaagtagcttcataccttctgtatggacatttgcttttgatcatgcattctttggtaatgcttatgctaatgtactattggatggatcacag

Basic information

species Zea mays
transcript GRMZM2G311165_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G311165_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 5'ss of exon 8
TGCTCGATTTGAGTGGCATTCTCACTGTGTTTTTCTGTGGTATCGTAATGTCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCAAgtaagtagcttcataccttctgtatggacatttgcttttgatcatgcattctttgg---taatgcttatgctaatgtactattgga-----tggatcacag-----------------------------
|||| ||||||||||| ||||| || ||||| ||||||||||| |||||||| |||||||| ||||| ||||||||||| ||||| ||||||||||||||||||||| ||| ||   || | |  | | | ||  | ||     | |||| |||     | ||| ||      ||||| |    ||     || ||||||                              
TGCTTGATTTGAGTGGTATTCTTACGGTGTTCTTCTGTGGTATTGTAATGTCGCACTATACCTGGCATAATGTAACAGAGAGTTCCAGGGTCACAACCAAgtaagtatctttatggtttgtttcagcaaacttattattccattttcatttttttaacttgatgatttcaaatatgtatttcctgaaattgtgtatcacactgatgcttctctaattgtatactctatag

upper sequence: GRMZM2G311165_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA10G30020.1 (Glycine max), 5'ss of exon 10
TGCTCGATTTGAGTGGCATTCTCACTGTGTTTTTCTGTGGTATCGTAATGTCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCAAgtaagtagcttcataccttctgtatggacatttgcttttgat-catgcattctttggtaatgcttatgctaatgtactattggatggatc--acag
|     || ||||||||||||||||||| || || |||||||| || ||||| || ||||| ||||| || || || || ||||| ||  |||| |||||||| ||          |||||  |  ||  |   |   | ||  |  |  ||   |   |||| ||    ||  || | |        ||   |||
TATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCAAgtatgt----------cttctaaacagatttcctcaagttatgtacactgtccaagtctatgcatacctaaacatattttcacccaactcttgcag

upper sequence: GRMZM2G311165_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
TGCTCGATTTGAGTGGCATTCTCACTGTGTTTTTCTGTGGTATCGTAATGTCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCAAgtaagtagcttcat--accttctgtatggacatttgcttttgatcatgcattctttggtaatgct---tatgctaatgtacta--ttggatgg-atcacag
|     || ||||||||||||||||||| || |||||||| || || ||||| || ||||||||||| ||||| || || || |||||  | || ||||||||  |    | |   |  ||||  | |   |  |   | ||    |   |    | ||||  ||   ||   | || || ||   |   ||   | ||||
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctaaacaaatttcttcaagctaagctatatatggatctatttggggtagtaacactgtctaatttgatatattaaactacttgctgttacag

upper sequence: GRMZM2G311165_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA19G42900.1 (Glycine max), 5'ss of exon 9
TGCTCGATTTGAGTGGCATTCTCACTGTGTTTTTCTGTGGTATCGTAATGTCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCAAgtaagtagcttcataccttctgtatggacatttgcttttgatcatgcattctttggtaatgcttatgctaatgtactattggatggatcacag-------------
|     || ||||||||||||| ||||| || |||||||| || || ||||| || ||||||||||| ||||| || || || |||||  | || ||||||||  |  ||  | || ||||  | |   | ||   | ||    |   |   ||||   |  | |  |   |||   ||| |||  || | |              
TATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatc-ctctagacattcttcaagctaagttatatatggatctatttgggttgggggtagtaacac---tgtctaatttgatttattaaaacttgttgttacag

upper sequence: GRMZM2G311165_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA20G37370.1 (Glycine max), 5'ss of exon 10
TGCTCGATTTGAGTGGCATTCTCACTGTGTTTTTCTGTGGTATCGTAATGTCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCAAgtaagtagcttca-taccttctgtatggacatttgcttttgatcatgcattctttggtaatgcttatgctaatgtactattggatggatcacag
||  | || ||||||||||||||||||| || || ||||| || || ||||| || ||||| ||||| ||||| || || ||||| ||  |||| |||||||| ||    | | ||  ||   |   || ||  ||      ||    | ||| ||   || | ||  |  || |   ||   |    |  |||
TGTCCTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGGATTGTCATGTCTCATTATACCTGGCATAATGTGACTGAGAGTTCAAGAATCACTACCAAgtatgtcttctaaatagatttcctcaagatatacgcacactgtcca--agtctatgc--atacctaaacatatttttcatccaactc-ttgcag

upper sequence: GRMZM2G311165_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT5G27150.1 (Arabidopsis thaliana), 5'ss of exon 10
TGCTCGATTTGAGTGGCATTCTCACTGTGTTTTTCTGTGGTATCGTAATGTCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCAAgtaagtagcttcataccttctgtatggacatttgcttttgatcatgcattct--ttggtaatgcttatgctaatgtactattggatggatcacag
|  |||| ||||| || || ||||||||||||||||||||||| || ||||| || || || ||||| |||||||| || || || ||  | ||||| ||||| | |   |  ||  ||||     | | ||||||     | |  | ||||   |   |||| ||||  ||   |  | || |||| | ||   
TTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAAAgtatgcaaactt-tagtttctcc---gccttttgctgagattaacactttctacctcccaatgattatcttatgatttttttcgatgaaacag--

upper sequence: GRMZM2G311165_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 5'ss of exon 9
TGCTCGATTTGAGTGGCATTCTCACTGTGTTTTTCTGTGGTATCGTAATGTCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCAAgtaagt---agcttca----taccttct----gtatgga---catttgcttttgatcatgcattcttt-ggtaatgcttatgcta-atgtactattggatg--gatcacag---------
|| || |||| ||||||||||||||||| || || || || || || ||||||||||| || ||||| || || || |||||||| || ||||| || |||||||    | |||||    ||  ||||     | ||||   ||||| ||| | ||  |   || |      ||   ||||| |  ||||| | |  | |   | | |            
TGTTCTATTTAAGTGGCATTCTCACTGTATTCTTTTGCGGGATTGTCATGTCACACTACACCTGGCATAACGTGACTGAAAGTTCAAGAGTCACCACAAAgtaagctaaatcttcagaaatattttctcaaaatctggaacccattttcttattattttattttttcccaaaaaaaattatgttgcatgtattttctgtttctgtttatgatttttgcag

upper sequence: GRMZM2G311165_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 5'ss of exon 10
TGCTCGATTTGAGTGGCATTCTCACTGTGTTTTTCTGTGGTATCGTAATGTCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCAAgtaagtagcttcat----accttctgtatggacatttgcttttgatcatgc-attctttggtaatgcttatgctaatgtactattggatggatcacag--------------------
|| || |||| |||| ||||||||||||||| || || || || || ||||| ||||| || ||||| ||||| || |||||||| || || || |||||||| ||   ||       |  |   |||| || |||   |  |  |||| | ||| |     |||| | ||   | |||  | |||      | ||||                    
TGTTCTATTTAAGTGCCATTCTCACTGTGTTCTTTTGCGGGATTGTCATGTCTCACTACACATGGCATAATGTGACTGAAAGTTCAAGAGTGACTACCAAgtatgttaattatccaggaagtgaagtattgaaattcattcatcttcattccattttgccaaaatgttgattaaactgtgatgttgctgatgttacagttcttaccaaatgtttgcag

upper sequence: GRMZM2G311165_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 5'ss of exon 9
TGCTCGATTTGAGTGGCATTCTCACTGTGTTTTTCTGTGGTATCGTAATGTCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCAAgtaagtagcttcataccttctgtatggacatttgcttttgatcatgcattctttggtaatgcttatgctaatgtactattggatggatcacag------------------------------
|  || ||||||||||||||||||| || ||||||||||| || |||||||| || || || ||||| ||||| ||||| ||||| || ||||| |||||||| |||  ||| |     |  |  | ||||||  |  | |  ||  ||  |||  || | |  |   ||    | || ||| || ||  | |                              
TATTCTATTTGAGTGGCATTCTCACGGTATTTTTCTGTGGGATTGTAATGTCCCATTACACGTGGCACAATGTTACAGAGAGTTCAAGAGTCACTACCAAgtatgtattttcctgaaagcaattggaacattttttggtcaggatttatatttt--tatttcaaaaaataggtcattactggctgtatgcctgttttaatttctgtctataaaatttccacag

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|211189601|gb|FL054040.1|FL054040
EST:     TCACACTATACTTGGCACAATGTAACAGAAAGTTCGAGGGTCACAACCAA                         GCATGCCTTTGCAACATTGTCGTTTATCTCCGAGACTTTTCTGTTTCTTTA
genomic: TCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCAAgtaagtagct ... tggatcacagGCATGCCTTTGCAACATTGTCGTTTATCTTCGAGACTTTTCTGTTTCTTTA
EST: gi|211187216|gb|FL054038.1|FL054038
EST:     TCACACTATACTTGGCACAATGTAACAGAAAGTTCGAGGGTCACAACCAA                         GCATGCCTTTGCAACATTGTCGTTTATCTCCGAGACTTTTCTGTTTCTTTA
genomic: TCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCAAgtaagtagct ... tggatcacagGCATGCCTTTGCAACATTGTCGTTTATCTTCGAGACTTTTCTGTTTCTTTA