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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttagaatatattcattttgagaaggcttcgttcacctttcttctctaattgatcgcacattaattcatacttgtgtgcatttttctcttatgtagGCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATTTTGGGCTCACTAAGCGCATATCTGAATCTATGAGGCAGGCACTAGCAAA

Basic information

species Zea mays
transcript GRMZM2G140917_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140917_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g48770.2 (Oryza sativa), 3'ss of exon 8
gtatttagaatatattcattttgagaagg-cttcgttcacct--------ttcttctctaattga-----tcgcacattaattcatacttgtg-tgcatttttctcttatgtagGCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATTTTGGGCTCACTAAGCGCATATCTGAATCTATGAGGCAGGCACTAGCAAA
||||||  | | |||     ||||  ||  ||||  ||||||        || ||||| |  ||      | ||| ||| |||  | ||     |||||| || |  |  ||||||||||||||||| ||||||||||||||||| || ||||||||||||||||||||||| ||||| ||||||||| |||| ||||||||||||||||||||
gtatttcaattttatgtgccttgaagagatcttctgtcacctcaatttttttattctccatctgtaattcttgcaaattcatttgtgctgacaatgcattatttttct--gtagGCAATTTTCTTGTTAGCAAGGAACCTCCACACAAGCCGATTCTCCTTGATTTTGGGCTTACTAAACGCATATCTCAATCAATGAGGCAGGCACTAGCAAA

upper sequence: GRMZM2G140917_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA14G20110.1 (Glycine max), 3'ss of exon 8
-----------------------gtatttaga---atatattcattttgagaaggcttcgttcacctttcttctctaattgatcgcacattaattcatacttgtgtgcatttttctcttatgtagGCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATTTTGGGCTCACTAAGCGCATATCTGAATCTATGAGGCAGGCACTAGCAAA
                          |||      || ||| ||| |  | | |   |    |  |    |  || |  || ||    | || ||      | |    | |    || |   |||| ||||||||||||||||||||| ||||||||   || ||| | ||||| ||||| || || |||    ||||     | || | ||| ||||| |||||
gtactctctctctctctccctctacgtttgtgcttatgtatgcatgtgcatatgatgtaacacttccgattgttccatgtgctcatgaactattttggctctct---tactggaatcat-catagGAAATTTTCTTGTGAGCAAGGAATCTCCACATCGTCCTATTTTACTTGACTTTGGCCTTACAAAGAAACTATCAAGCACCATTAAGCAAGCACTTGCAAA

upper sequence: GRMZM2G140917_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv04s0008g02740.t01 (Vitis vinifera), 3'ss of exon 7
gtatttagaatatattcattttgagaaggc--ttcgttc-acctttcttctctaattgatcgcacattaattca-----tacttgtgtgcatttttctcttatgtagGCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATTTTGGGCTCACTAAGCGCATATCTGAATCTATGAGGCAGGCACTAGCAAA
     || | |   | | |  || |       | | ||| ||||||    | | | || |   | ||||||| |     | |||     |||  ||||||   | ||| ||||||||||| ||||||||||||||||||   ||  || | ||||| |||||||| || |||    ||||    |||||||  || |||||||| ||
----gtaaatttgctacctgatgggctattcatccattctaccttttagttatgactgctaaaaaattaattgaataaatgctttcccacatgattctct---gcagGAAATTTTCTTGTCAGCAAGGAACCTCCACATCGTCCAGTTTTGCTTGACTTTGGGCTTACAAAGTCACTATCAAGCTCTATGAAACAAGCACTAGCGAA

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|211144291|gb|FL032433.1|FL032433
EST:     CGCTCATCAAATATACATTGATGGCTTCTTTAACGGCGACCCTCATCCTG                         GCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATT
genomic: CGCTCATCAAATATACATTGATGGCTTCTTTAACGGCGACCCTCATCCTGgtatttagaa ... tcttatgtagGCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATT
EST: gi|211144284|gb|FL032426.1|FL032426
EST:     CGCTCATCAAATATACATTGATGGCTTCTTTAACGGCGACCCTCATCCTG                         GCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATT
genomic: CGCTCATCAAATATACATTGATGGCTTCTTTAACGGCGACCCTCATCCTGgtatttagaa ... tcttatgtagGCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATT
EST: gi|211144280|gb|FL032422.1|FL032422
EST:     CGCTCATCAAATATACATTGATGGCTTCTTTAACGGCGACCCTCATCCTG                         GCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATT
genomic: CGCTCATCAAATATACATTGATGGCTTCTTTAACGGCGACCCTCATCCTGgtatttagaa ... tcttatgtagGCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATT
EST: gi|211142860|gb|FL032421.1|FL032421
EST:     CGCTCATCAAATATACATTGATGGCTTCTTTAACGGCGACCCTCATCCTG                         GCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATT
genomic: CGCTCATCAAATATACATTGATGGCTTCTTTAACGGCGACCCTCATCCTGgtatttagaa ... tcttatgtagGCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATT

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), 40 (downstream exon)
Score: 24

GCATATGGTGTTGACAAGCAAAAACTGGTCGAAGAGATAACCCGTGCATACGCTCATCAAATATACATTGATGGCTTCTTTAACGGCGACCCTCATCCTGgtatttagaa ... tcttatgtagGCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATTTTGGGCTCACTAAGCGCATATCTGAATCTATGAGGCAGGCACTAGCAAA


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

GCATATGGTGTTGACAAGCAAAAACTGGTCGAAGAGATAACCCGTGCATACGCTCATCAAATATACATTGATGGCTTCTTTAACGGCGACCCTCATCCTGgtatttagaa ... tcttatgtagGCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATTTTGGGCTCACTAAGCGCATATCTGAATCTATGAGGCAGGCACTAGCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

GCATATGGTGTTGACAAGCAAAAACTGGTCGAAGAGATAACCCGTGCATACGCTCATCAAATATACATTGATGGCTTCTTTAACGGCGACCCTCATCCTGgtatttagaa ... tcttatgtagGCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATTTTGGGCTCACTAAGCGCATATCTGAATCTATGAGGCAGGCACTAGCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 145

GCATATGGTGTTGACAAGCAAAAACTGGTCGAAGAGATAACCCGTGCATACGCTCATCAAATATACATTGATGGCTTCTTTAACGGCGACCCTCATCCTGgtatttagaa ... tcttatgtagGCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATTTTGGGCTCACTAAGCGCATATCTGAATCTATGAGGCAGGCACTAGCAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctctaattgatcgcacattaattcatacttgtgtgcatttttctcttatgtagGCAATTTTCTTGTGAGCAAGGAACCTCCACATAAACCGATTCTCCTTGATTTTGGGCTCACTAAGCGCATATCTGAATCTATGAGGCAGGCACTAGCAAA
                 cattaat  putative branch site (score: 145)
                                   tgcatttttctctt  putative PPT
                  attaattcatactt  TA-rich tract