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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_T02
intron # 16
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 129

CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 97

CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 167

CATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAGgtttgtggtg ... ccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttcttgaaatgtatctgttgttttcttgtttattaacaacttccttgcacagGCACTTGTTGAGTTCTTTGGCACCCTTTCAAGGGAGTGGGCACTAGAGTGCATGAAGGACCTTCTACTGGTAAATCTGAGGGGAAATCTTCAGATTGTTG
                                 tattaac  putative branch site (score: 167)
                                          cttccttgc  putative PPT
                       ttttcttgtttattaa  TA-rich tract