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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatttttgcctcattgctttgatacatactctctgcagaacttgttccggttagatagctttgtagacctgatctcatgcatgtgctccgtagtcctagcatggcaggctggccttttgatgttgttggtcatatttatgtagttatgataaaatatgttgatttacagCTATTGGCCTACATATCCACCAATGGACGTGAAACTCCCACACGAACTGAATGTGTATCAG

Basic information

species Zea mays
transcript GRMZM2G704093_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G704093_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 10
gtaaatatttttgcctcattgctttgatacatactctctgcagaacttgttccggttagatagctttgtagacctgatctcatgcatgtgctccgtagtcctagcatggcaggctggccttttgatgttgttggtcatatttatgtagttatgataaaatatgttgatttacagCTATTGGCCTACATATCCACCAATGGACGTGAAACTCCCACACGAACTGAATGTGTATCAG
                                                       ||| ||| |||| ||           | || | ||||  | | |  || ||||  |          ||||| || |   |||||  | || | || |||| ||||||||||  || |||||||||||| ||||||||||||||||| ||||||||||| || ||||| ||||| ||||||
-------------------------------------------------------ttatataactttataa---------taggcgtttgctgagca-tgttaacatgcaa---------cttgatattttctatcataaatgtgcatttctgattaaatatgttgcattgcagCTATTGGCCAACATATCCACCAATGGATGTGAAACTCCCCCATGAACTTAATGTCTATCAG

upper sequence: GRMZM2G704093_T01 (Zea mays), 3'ss of exon 9
lower sequence: PP1S70_181V6.1 (Physcomitrella patens), 3'ss of exon 10
---gtaaatatttttgc---ctcattgctttgatacatactctctgcagaacttgttccggttagatagctttgtagacctgatctcatgcatgtgctccgtagtcctagcatggcaggctggccttttgatgttgttggtcatatttatgtagttatgataaaatatgttgatttacagCTATTGGCCTACATATCCACCAATGGACGTGAAACTCCCACACGAACTGAATGTGTATCAG---------------------------------------
    ||||  |||||     |||   ||| |  |    | ||| |  |    |||| ||      |||  | || |  |||  |||  |      |||   ||     || || |     ||         |     | |  || |  ||    |  |  ||   | || ||  ||  ||||||||||||||||||||||| ||||| || |  || |||| ||| || ||||||||||||                                       
gtaataaacctttttagtcactcgaagctctcttgttgattcttttaatggtttgtgcc------atacttctggatgcct--tcttgt---caagctttatatgtgaagtattgtgtagtgat-------taacacttgcaatctgcattctatcttattattttttggtg--ttgtagCTATTGGCCTACATATCCACCCATGGAGGTTAGGCTTCCACGCGAGCTCAATGTGTATCAGGACATATTCAAGGAGTTTTATCTAAGTAAGCACAGTGGG
















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|32809761|gb|CD961995.1|CD961995
EST:     ACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTACAACAGG                         CTATTGGCCTACATATCCACCAATGGACGTGAAACTCCCACACGAACTGAA
genomic: ACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTACAACAGGgtaaatattt ... tgatttacagCTATTGGCCTACATATCCACCAATGGACGTGAAACTCCCACACGAACTGAA
EST: gi|31357483|gb|CD441840.1|CD441840
EST:     ACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTACAACAGG                         CTATTGGCCTACATATCCACCAATGGACGTGAAACTCCCACACGAACTGAA
genomic: ACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTACAACAGGgtaaatattt ... tgatttacagCTATTGGCCTACATATCCACCAATGGACGTGAAACTCCCACACGAACTGAA

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), 47 (downstream exon)
Score: 165

AATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTACAACAGGgtaaatattt ... tgatttacagCTATTGGCCTACATATCCACCAATGGACGTGAAACTCCCACACGAACTGAATGTGTATCAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 140

AATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTACAACAGGgtaaatattt ... tgatttacagCTATTGGCCTACATATCCACCAATGGACGTGAAACTCCCACACGAACTGAATGTGTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

AATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTACAACAGGgtaaatattt ... tgatttacagCTATTGGCCTACATATCCACCAATGGACGTGAAACTCCCACACGAACTGAATGTGTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

AATTATCCAAAGAAATAAACGATTCATTCAGGCAATCATCTCAAGCTAGGACAAAGCTTCCCTCAGGCATTGAAATGAGTGTTCATGTGCTTACAACAGGgtaaatattt ... tgatttacagCTATTGGCCTACATATCCACCAATGGACGTGAAACTCCCACACGAACTGAATGTGTATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgatgttgttggtcatatttatgtagttatgataaaatatgttgatttacagCTATTGGCCTACATATCCACCAATGGACGTGAAACTCCCACACGAACTGAATGTGTATCAG
                                          tgttgat  putative branch site (score: 155)
                 atatttatgtagttat  TA-rich tract