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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactctcatttctttcaggatactttccatcaatattaataaaagtttttagtacatgtttgtttttgaagttatccattccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAAGAATGGCTTGCAATAACACGAAAATTCAACAGTGTTTTCCCTTTAGCAC

Basic information

species Zea mays
transcript GRMZM2G461145_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G461145_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g51540.1 (Oryza sativa), 3'ss of exon 6
gtactctc----atttctttcaggat-actttccatcaatattaataaa------agtttttagtacatgtttgtttttgaag-ttatccattccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAAGAATGGCTTGCAATAACACGAAAATTCAACAGTGTTTTCCCTTTAGCAC
|| | ||     |  |  |||||||| | ||   |||  | | | ||||      | |||   |||||  ||||||| ||| |  |  ||| |||||||||||| |||||||||||||||  |||||||||| |||| ||||||||||||||||||||||||||||||||||| |||||||||| ||||||| | ||| | |
gtgccctttattacctgattcaggattatttcttatccttgtaattaaattttgcattttgctgtacacatttgtttctgagggcttgccaatccattttagGTAATAGACATTCCATCCGGTCCAGGACCACATGAGATCCAGTATGATGAAGAATGGCTTGCAATAACACGGAAATTCAACAATGTTTTCTCCTTAACTC

upper sequence: GRMZM2G461145_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA04G06310.1 (Glycine max), 3'ss of exon 4
--------gtactctcatttctttcaggat-actttccatcaatattaataaaagtttttagtacatgtttgtttttgaagttatccattccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAAGAATGGCTTGCAATAACACGAAAATTCAACAGTGTTTTCCCTTTAGCAC
         || |   ||   || |||| | | | | |    |||    |   ||||  |  ||||    ||  ||    |||  |  | ||  ||||| || | || |||  |||  || ||||||| ||||| || |||||||||||||||||| | ||||||||||| || ||||||  | | ||||||||  |  
gtataggcatagttctataatttgcagggttaatcttctgtgatagctgtttgagttagtgatacaatcatggctt----gtt--ctgtgcc--tttagATTGTGGAAATTGAATCAGATGCAGGACCTTATGAGATTCAGTATGATGAAGAATGGTTAGCAATAACACGGAAGTTCAACCCTATATTCCCTTTGACTT

upper sequence: GRMZM2G461145_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv18s0001g08180.t01 (Vitis vinifera), 3'ss of exon 6
gta-ctctcatttctttcaggatactttccatcaatattaataaaa--gtttttagtacatgtttgttt---ttgaagttatccattccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAAGAATGGCTTGCAATAACACGAAAATTCAACAGTGTTTTCCCTTTAGCAC
||| | ||  ||  |||||      |||  |    | |||||  |    ||  | | |  |   ||  |   |||  | ||   |     |||||| || | || ||   | |    |||||||| ||||| || |||||||||||||||||| | ||||||||||| || ||||||  | | || |||||| |  
gtagcccttgttattttcatttatgttttaagggcttttaatgtagtcattgctggaaattaaatgcctcaattggtggtactgagcgagttttagATTGTTGAAATAGAAACAGTGCCAGGACCTTATGAGATTCAGTATGATGAAGAATGGTTGGCAATAACACGGAAGTTCAACTCTATCTTTCCTTTAACCA

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|67037524|gb|CO464338.1|CO464338
EST:     CGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAG                         GTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA
genomic: CGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAGgtactctcat ... tccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA
EST: gi|32834976|gb|CD974654.1|CD974654
EST:     CGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAG                         GTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA
genomic: CGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAGgtactctcat ... tccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA
EST: gi|83279349|gb|DV943357.1|DV943357
EST:     CGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAG                         GTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA
genomic: CGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAGgtactctcat ... tccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA
EST: gi|32930289|gb|CF035101.1|CF035101
EST:     CGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAG                         GTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA
genomic: CGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAGgtactctcat ... tccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA
EST: gi|32930245|gb|CF035057.1|CF035057
EST:     CGAAGTTTCTTGCACTAGATAAGTGCATTCCTGGGCGCAATTTTTTGCAG                         GTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA
genomic: CGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAGgtactctcat ... tccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA
EST: gi|32833267|gb|CD972945.1|CD972945
EST:     CGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAG                         GTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA
genomic: CGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAGgtactctcat ... tccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA
EST: gi|17931921|gb|BM268881.1|BM268881
EST:     CGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAG                         GTTATATACCTTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA
genomic: CGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAGgtactctcat ... tccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA
EST: gi|17931886|gb|BM268846.1|BM268846
EST:     CGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAG                         GTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA
genomic: CGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAGgtactctcat ... tccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAA

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: 48 (upstream exon), 47 (downstream exon)
Score: 103

TCACTGTAAGTTTCCTGCTGTTATCCAGCATGGCAAGAATGGACCTACAACGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAGgtactctcat ... tccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAAGAATGGCTTGCAATAACACGAAAATTCAACAGTGTTTTCCCTTTAGCAC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 62

TCACTGTAAGTTTCCTGCTGTTATCCAGCATGGCAAGAATGGACCTACAACGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAGgtactctcat ... tccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAAGAATGGCTTGCAATAACACGAAAATTCAACAGTGTTTTCCCTTTAGCAC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 47

TCACTGTAAGTTTCCTGCTGTTATCCAGCATGGCAAGAATGGACCTACAACGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAGgtactctcat ... tccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAAGAATGGCTTGCAATAACACGAAAATTCAACAGTGTTTTCCCTTTAGCAC


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 58

TCACTGTAAGTTTCCTGCTGTTATCCAGCATGGCAAGAATGGACCTACAACGAAGTTTCTTGCACTTGATAAGTGCATTCCTGGGCGCAATTTTTTGCAGgtactctcat ... tccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAAGAATGGCTTGCAATAACACGAAAATTCAACAGTGTTTTCCCTTTAGCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaataaaagtttttagtacatgtttgtttttgaagttatccattccattttagGTTATAGACATTCCATCCAATCCAGGACCATATGAAATCCAGTATGATGAAGAATGGCTTGCAATAACACGAAAATTCAACAGTGTTTTCCCTTTAGCAC
 tattaat  putative branch site (score: 58)
                                            ttccatttt  putative PPT
     taaaagtttttagta  TA-rich tract