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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtggtgttcagttatgttcttgaaatgtatctgttgttttcttgtttattaacaacttccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG

Basic information

species Zea mays
transcript GRMZM2G057576_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 18
gtttgtggtgttcagttatgttcttgaaatgtatctgttgttttc--------ttgtttattaacaacttccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG
||||||  | || ||||||| | |||     | ||| || ||           | ||  ||| ||| | |  ||| ||||||||||||||||||||||||||| |||||||| ||||||||  | |||||||||||||||||||| ||||| ||||| || || |||||||| |||||||
gtttgttatcttaagttatgct-ttgttgcctgtctattattactggctggggtggtccatttacaccattattgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 18
gtttgtggtgttcagttatgttcttgaaatgtatctgttgttttc--------ttgtttattaacaacttccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG
||||||  | || ||||||| | |||     | ||| || ||           | || |||| ||| | |  ||| ||||||||||||||||||||||||||| |||||||| ||||||||  | |||||||||||||||||||| ||||| ||||| || || |||||||| |||||||
gtttgttatcttaagttatgct-ttgttgcctgtctattattactggctggggtggtctatttacaccattattgaacagGCACTTGTTGAGTTCTTTGGCACTCTTTCAAGAGAGTGGGCTTTGGAGTGCATGAAGGACCTTCTGCTGGTCAATCTAAGAGGGAATCTTCAAATTGTTG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 16
gtttgtggtgttcagt--tatgttcttgaaatgtatctg----ttgttttct-tgtttattaacaacttccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG
|||||   | |  |||  ||   |      || |||||     ||||| | | |  |||| |  || |   || ||  ||| || |||||||||||||| ||||||||||  || ||||| |||||||||||||| || ||| ||||||| || || ||||| || ||||| ||  |||
gtttg-aatttcaagtgctaaagtgactggatctatctaaaaattgttatttattcttatcatgaaatgattttca--gGCTCTAGTTGAGTTCTTTGGAACCCTTTCAAAAGAATGGGCGCTAGAGTGCATGAAAGATCTTTTACTGGTCAACCTTAGGGGCAACCTTCAAATAATTG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 18
---------------gtttg--tggtgttcagttatgttcttgaa---atgtatctgttgttttcttgtttattaacaacttccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG
               | |    ||    ||  |||| |   |  |   || ||| | |||| |||||      | |  |     |    ||||   | |||||||||||||| ||||||||  | || |||||||| ||||| ||||| || ||| |||| || ||||| ||||| |||||||| ||  |||
gttttgattgcaactgctcaaatgacaatctattatatatatatatatatatatatattgtattcttacaatatgattataatgtatttcagGGTTTAGTTGAGTTCTTTGGAACCCTTTCTCGAGAATGGGCACTTGAGTGTATGAAAGATCTTTTACTTGTCAATCTTAGGGGCAATCTTCAAATAATTG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 18
gtttgtggtgttcagttatgttcttgaaatgtatctgttgttttcttgtttattaacaactt----ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG
|||||          | | ||   || | | |||||    |||| || ||||||   | | |       |   ||||| || |||||||||||||| || |||||||  || ||||| |||||||||||||| || ||| ||||||| || || ||||| || ||||| ||  |||
gtttgaatcaagtgctaaagtgactgga-tctatctaa-atttttttatttattcttatcatgaaatgattttcagGCTCTAGTTGAGTTCTTTGGAACTCTTTCAAAAGAATGGGCGCTAGAGTGCATGAAAGATCTTTTACTGGTCAACCTTAGGGGCAACCTTCAAATAATTG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 18
------gtttgtggtgttcagtt---atgttct-tgaaatgtatctgttgttttcttgtttattaacaacttccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG
       ||     |  |||  |   |   ||| |   |  | | | || | |||||  |   | |  |     |    |||||  | |||||||||||||| ||||||||  | || |||||||| ||||| ||||| || ||| |||| || ||||| ||||| |||||||| ||  |||
gttttgattccaactactcaaatgacacaatctatcgtaaatttgttttatattcttactatatgattatgatgtatttcagGCTTTAGTTGAGTTCTTTGGAACCCTTTCTCGAGAATGGGCACTCGAGTGTATGAAAGATCTTTTACTTGTCAATCTTAGGGGCAATCTTCAAATAATTG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 16
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 18
-----gtttgtggtgttcagttatgttcttgaaatgtatctgttgttttcttgtttattaacaacttcct---tgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG
     |  | ||   |  | ||  ||| || ||     |  || ||    |||||   |||||   | ||   |   ||||| ||||||||||| |||||||| ||||| || ||||||||  | |||||||||||||| ||  | ||||| || ||||| || ||||| |||||  |||
gtagtgcctctgaaatatattttggttgttaaacctactaagtggtcaagttgttgcataacactctgctccatatgcagGCTCTTGTTGAGTTTTTTGGCACTCTTTCTAGCGAGTGGGCTATGGAGTGCATGAAGGATCTGTTGCTGGTCAACCTGAGAGGCAATCTGCAGATAATTG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 16
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 18
-------gtttgtggtgttcagttatgttcttgaaatgtatctgttgttttcttgtttattaacaacttccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG
       | |    |||||   | |  |  |  |  || || |  | |||| || |   |  |     |  ||   ||||| ||||||||||||||||| || |||||||| || ||||| || ||||| ||||| ||||||||||| || |||||  | |  |||||||||||  |||
gttagatgctcaaagtgttacataacttgttctatttgaatgtagtatttttttctaactatatggtatattt---cagGCTCTTGTTGAGTTCTTTGGAACTCTTTCAAGAGAATGGGCTCTTGAGTGTATGAAAGACCTTCTACTTGTCAATCTTCGTGCCAATCTTCAGATAATTG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 16
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
gtttgtggtgttcagttatgttcttgaaatgtatctgttgtttt---cttgtttattaacaacttccttgca-cagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG
|||| |    ||||  | ||||  |    |   |  |  ||| |   |||| |  | || |  |   |  |  ||||||||||| ||||||||||| || |||||| | || |||||  | |||||||||||||||||||| ||||| ||||| || || || ||||||||  |||
gtttttatacttcaactgtgtttcttggttcactaggaggttgtaaacttgctattgaatacgtggttctcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG

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|16137384|gb|BI894249.1|BI894249
EST:     TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCAATGAGCCCCAG                         GCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
genomic: TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
EST: gi|18384990|gb|BM418189.1|BM418189
EST:     TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG                         GCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
genomic: TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
EST: gi|15188223|gb|BI417200.1|BI417200
EST:     TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG                         GCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
genomic: TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
EST: gi|18385023|gb|BM418222.1|BM418222
EST:     TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG                         GCACT-GTTGAGTTCTTTGGCACCCTTTCA-GGGAGTGGGCACTAGAGTGC
genomic: TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
EST: gi|22489541|gb|BU049464.1|BU049464
EST:     TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG                         GCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGTTTTCTAGAGTGC
genomic: TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
EST: gi|18053133|gb|BM318791.1|BM318791
EST:     TGCCTGATATCAAGCGTGTCATTGTAAATACTTATGCCATTGATTCCCAG                         GCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
genomic: TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
EST: gi|15313673|gb|BI478897.1|BI478897
EST:     TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG                         GCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
genomic: TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
EST: gi|15313671|gb|BI478896.1|BI478896
EST:     TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG                         GCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
genomic: TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
EST: gi|15177612|gb|BI398551.1|BI398551
EST:     TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG                         GCACTTGTT-AGTTCTTTGGC-CCCTTTCA-GGGAGTGGG
genomic: TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGG
EST: gi|32928656|gb|CF033468.1|CF033468
EST:     TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG                         GCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
genomic: TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
EST: gi|88758497|gb|DY542866.1|DY542866
EST:     TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG                         GCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
genomic: TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
EST: gi|32929052|gb|CF033864.1|CF033864
EST:     TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG                         GCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC
genomic: TGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttcttgaaatgtatctgttgttttcttgtttattaacaacttccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG
                                 tattaac  putative branch site (score: 1)
                                          cttccttgc  putative PPT
                       ttttcttgtttattaa  TA-rich tract