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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctactgcattgttatttctctaaactagcttgactaaattgaagtgtattttctaagcttgtttaccaaagaagatattgtaacatcatattctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG

Basic information

species Zea mays
transcript GRMZM2G145029_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145029_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g34180.1 (Oryza sativa), 3'ss of exon 3
ctactgcattgttatttctctaaactagcttgactaaattgaagtgtattttctaagcttgtttaccaaagaagatattgtaacatcata-------ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG
    |    | ||||||     |  |||||| |  ||||  || |  |  |  |||  |  | |  || |||   | || ||| || |||       | |||| |||||||||||||| ||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||| ||| | ||||| || ||  |  
----tcatctattattttctacacttagctt-atcaaat--aaatagaagtattaacttgttctgtcatagattttcttttaatattatagtcttgatcctttccagCAAAGGTCTGCTACAAAAGTGACATTTCCACTTGTCTGGACAAACACTTGCTGTAGCCACCCTCTATACCGCGAGTCCGAGCTCATTGAAGATAAAAGCC

upper sequence: GRMZM2G145029_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G38550.1 (Glycine max), 3'ss of exon 3
ctactgcattgttatttctctaaactagcttgactaaattgaagtgtattttctaagcttgtttaccaaagaagatattgtaacatcatattctttac-----agCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG
    |   |    | |||||||   | || ||  ||  || |||| | |       | ||   |            | ||  |     | |||||||      ||||| | ||||||||||| || || || || ||||| |||||||||||||| |||||||||||||| ||||| || || ||| | ||||| || |||    
----ttggtgaaaaattctctatgtt-gcatgtgtattttcaagtctttgactcgtgttttaatttggtctgtttgactgagattctttgttctttatgatgaagCAACGATCTGCAACAAAGGTAACTTTCCCTCTTGTGTGGACAAACACCTGTTGTAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCC

upper sequence: GRMZM2G145029_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 3
ctactgcattgttatttctctaaactagcttgactaaattgaagtgtattttctaagcttgtttaccaaagaagatattgtaacatcatattctttac-----agCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG-
    ||  | |  |||||||||   || | ||  ||  || | || |         ||||   |            | ||  |   | | |||||||      ||||| | |||||||| || || ||||| || ||||| |||||||||||||| || |||||||| || ||||| || || ||| | ||||| || |||     
----tg-gtggaaatttctctatg-tatcatgtgtattttcatgtcttggactcgtgctttaatttggtctctttgactgagattccttgttctttatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT

upper sequence: GRMZM2G145029_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv11s0206g00020.t01 (Vitis vinifera), 3'ss of exon 1
ctactgcattgttatttctctaaa-ctagcttgactaaattgaag--tgtattttctaagcttgtt----taccaaagaagatattgtaacatcatattctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCA--GAGTTGATTGAGGAAAATTGTG
        | |     |  | |   ||  |||  |    ||| ||  |  | |    |  | ||||    |   | |    || | |  |||  | |     | |||| |   |||  | |   | | | || |  | |  |  | |    |      ||  |  || ||    |  |  ||  |  | ||  | |  | |    ||  
------tttcggaggctgacgagggcttactttgcagtcttggaggtttcactcaacagccgtgttattcttttatattgaatctggatacaa-acacctgctgcagCCATCCTCTTTACCGTGAATCAGATCTT-ATTAATGAGAATGTGCTTGGAGTGCGGA-ATGCTGCACAAAGAAAGCTATTGGGTGAACTCGGCATTCCTGCT

upper sequence: GRMZM2G145029_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0023g00600.t01 (Vitis vinifera), 3'ss of exon 3
ctactgcattgttatttctctaaactagcttgactaaattgaagtgtattttctaagcttgtttaccaaagaagatattgtaacatcatattcttt--acagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG-
 |  | ||   | |||     ||  ||  | |  |   ||| |         |  |  |||   | || |     | || |  |  ||| ||  ||  ||||||||||||||| ||||| |||||||| ||  | || ||||||||||||||||| ||||||||||| ||||| || |||||| | ||||| || ||| | | 
ttgtttcaccctgattctatcaagata--tagcattctttgtaaacatcagccagaatttgagaatcacatgctgtgttctttctgcatgtttcttgtacagCAAAGGTCTGCCACAAAGGTGACATTCCCTTTGGTGTGGACAAACACCTGCTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATTGATGAGAAT-GCGC

upper sequence: GRMZM2G145029_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S28_399V6.1 (Physcomitrella patens), 3'ss of exon 3
ctac--tgcattgttatttctctaaactagcttgactaaattgaag---tgtattttctaagcttgtttaccaaagaagat--attgtaacatcatattctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG
| ||  || || ||||    | |  | |||  ||| | | ||| ||   ||| |  | ||  |   |  || |||    ||  ||  | | || |||||     ||| || | || || || |||||||| ||||||||||| ||||| ||||| || || |||||||| || ||||| ||||| ||  | |||||||| || |   
ccaccgtgtatggttagagat-tggattag--tgagtgacttgcagggatgtctcctttagacccatggacaaaatcttatttatgttgatattatattt----cagAAACGTTCGGCTACGAAAGTGACCTTTCCACTTGTGTGGACCAACACTTGTTGCAGCCATCCACTGTACCGTGAGTCTGAACTTATTGAGGATAAATACC

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|60355106|gb|DN222079.1|DN222079
EST:     CTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: CTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|148948633|gb|EC898545.2|EC898545
EST:     GAGCTTTCAGTGTTTTCTTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|211100857|gb|FL320689.1|FL320689
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|211043409|gb|FL322272.1|FL322272
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|211523188|gb|FL353428.1|FL353428
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|211514701|gb|FL326221.1|FL326221
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|148948634|gb|EC898546.2|EC898546
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|15313313|gb|BI478657.1|BI478657
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|148930170|gb|EC872550.2|EC872550
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|211410145|gb|FL360134.1|FL360134
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|8318714|gb|BE025279.1|BE025279
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattttctaagcttgtttaccaaagaagatattgtaacatcatattctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG
                                ttgtaac  putative branch site (score: 2)
                                           tattcttt  putative PPT
                                          atattcttta  TA-rich tract