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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctatttctgtccttgatgtccttttacttctgtagttctgtattgtaaaggttttagatttttttgatcccttcacttacatgacactgtttggtttccattcataaaactcaatttgatttgtatttattgtgcagGATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTTAATGATTGGGAGAACCATCTAACAACAATTTTTCCTGAG

Basic information

species Zea mays
transcript GRMZM2G020096_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 10
gtctatttctgtccttgatgtccttttacttctgtagttctgtattgtaaaggttttagatttttttgatcccttcacttacatgacactgtttggtttccattcataaaactcaatttgatttgtatttattgtgcagGATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTTAATGATTGGGAGAACCATCTAACAACAATTTTTCCTGAG
|||| || ||||   || |  | |  | ||| ||  ||| | |   ||| || |||               |  |    ||||  ||     ||||||   ||| |  | ||| || | ||||| ||||| || ||||||||||||||  |||||| |||| ||||||||| |||||| |||||||| | ||||| ||||||||||||||||||||||| |||||||||
gtctcttcctgtttctgttaccttagtgcttgtgctgttatatgcagtagagctttgg-------------ctatagaatacagaac-----ttggtt---attaactagact-aactggatttatatttgttttgcagGATTTTATGGTAGGAAAACTCCCACAAGCTCCGGGGGAGCTGCCTACTTTGAATGACTGGGAGAACCATCTAACAACAATATTTCCTGAG

upper sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 3'ss of exon 10
gtctatttctgtccttgatgtccttttacttctgtagttctgtattgtaaaggttttagatttttttgatcccttcacttacatgacactgtttggtttccattcataaaactcaatttgatttgtatttattgtgcagGATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTTAATGATTGGGAGAACCATCTAACAACAATTTTTCCTGAG
|||| || ||||   || |  | |  | ||| |   ||| | |   ||| || |||               |  |    ||||  ||     ||||||   ||| |  | ||| || ||||||| ||||| || ||||||||||||||  |||||| |||| ||||||||| |||||| |||||||| | ||||| |||||||||||||||||||| || |||||||||
gtctcttcctgtttgtgttaccttagtgcttgttctgttatatgcagtagagctttgg-------------ctatagaatacagaac-----ttggtt---attaactagact-aacttgatttatatttgttttgcagGATTTTATGGTAGGAAAACTCCCACAAGCTCCCGGGGAGCTGCCTACTTTGAATGACTGGGAGAACCATCTAACAACGATATTTCCTGAG
















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|211306283|gb|FL001396.1|FL001396
EST:     TTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGG                         GATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTT
genomic: TTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGGgtctatttct ... tattgtgcagGATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTT
EST: gi|211306281|gb|FL001394.1|FL001394
EST:     TTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGG                         GATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTT
genomic: TTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGGgtctatttct ... tattgtgcagGATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTT
EST: gi|89251366|gb|DY623152.1|DY623152
EST:     TTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGG                         GATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTT
genomic: TTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGGgtctatttct ... tattgtgcagGATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTT
EST: gi|211306280|gb|FL001393.1|FL001393
EST:     TTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGG                         GATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTT
genomic: TTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGGgtctatttct ... tattgtgcagGATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTT
EST: gi|211304264|gb|FL001390.1|FL001390
EST:     TTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGG                         GATTTTATGCAATGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTT
genomic: TTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGGgtctatttct ... tattgtgcagGATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTT
EST: gi|211306282|gb|FL001395.1|FL001395
EST:     TTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGG                         GATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTT
genomic: TTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGGgtctatttct ... tattgtgcagGATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTT

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: 235

GTTTGAGCAATATGTGGATTATGCATTAGATGTCCCCATGTATTTTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGGgtctatttct ... tattgtgcagGATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTTAATGATTGGGAGAACCATCTAACAACAATTTTTCCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 498

GTTTGAGCAATATGTGGATTATGCATTAGATGTCCCCATGTATTTTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGGgtctatttct ... tattgtgcagGATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTTAATGATTGGGAGAACCATCTAACAACAATTTTTCCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1717

GTTTGAGCAATATGTGGATTATGCATTAGATGTCCCCATGTATTTTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGGgtctatttct ... tattgtgcagGATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTTAATGATTGGGAGAACCATCTAACAACAATTTTTCCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

GTTTGAGCAATATGTGGATTATGCATTAGATGTCCCCATGTATTTTGTGTACCGAAATAATAAGTATATTGACTGCACCGGAATGTCATTTCGGgtctatttct ... tattgtgcagGATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTTAATGATTGGGAGAACCATCTAACAACAATTTTTCCTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacactgtttggtttccattcataaaactcaatttgatttgtatttattgtgcagGATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTTAATGATTGGGAGAACCATCTAACAACAATTTTTCCTGAG
                               atttgat  putative branch site (score: 139)
                     ataaaactcaatttga  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctatttctgtccttgatgtccttttacttctgtagttctgtattgtaaaggttttagatttttttgatcccttcacttacatgacactgtttggtttccattcataaaactcaatttgatttgtatttattgtgcagGATTTTATGCAAGGAAAGCTCCGACAAGCTCCTGGGGAGTTGCCTACTCTTAATGATTGGGAGAACCATCTAACAACAATTTTTCCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA