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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctgattcacccataagattaaatttttacataacagctgctttactccgcatctctgtagcttttgtagcttgtgtgctgataatgcttactgcttgtcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTATTTTTGGGGCTATTTTTAATTGTCTGGATCCCATATTAACCATAGTTTC

Basic information

species Zea mays
transcript GRMZM2G373175_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 7
gtacctgattcacccataagattaaatttttacataacagctgctttactccgcatc-tctgtagcttttgtagcttgtgtgctgataatgcttactgcttgtcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTATTTTTGGGGCTATTTTTAATTGTCTGGATCCCATATTAACCATAGTTTC
||| | ||| || || | | || |    ||||        |||||||| |  | ||| |||  ||| ||||||||   |||||| |  || |  || | ||| ||||  ||||||||||||| || |||||||||||||| ||||| || || |||||||| |||||||| |||||||||||||| || ||||||||||||||||| |||||
gtatcagatccatccttcaaatcatccgtttatc-----actgctttatt--gaatcatcttgagcatttgtagc--atgtgctaactatacccacggattggcattaccagGAAAGCACTTATCCATGCTTCCAGTTGAGCCTAAATTGGGGAAGATGCTGATTTTTGGTGCTATTTTTAATTGCCTTGATCCCATATTAACCATTGTTTC

upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA09G18490.1 (Glycine max), 3'ss of exon 8
gtacctgattcacccataagattaaatttttacataacagctgctttactccgcatctctgtagcttttgtagcttgtgtgctgataatgcttactgcttgtcatttt-cagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTATTTTTGGGGCTATTTTTAATTGTCTGGATCCCATATTAACCATAGTTTC
     || || |||      ||||   |    ||| | |      |||||    || |      ||| |  ||  |     |  ||| |       |  ||||| ||  ||||  |  ||||| | ||||||||  | ||||| ||  | || ||||||||||| ||||| | ||| || ||||| ||||||||||||||||| || ||| |
---gttggttgacc------atta---tccggcatgaaaatctgcttactgattattttc----cttataaagtataaagcccaatagt-----tggtctgtcaattgacagGGCACAACTTGACAATGCTTCCCATGGAACCCAAACTTGGCAAGATGCTTATATTTGGTGTTATCTTCAATTGCCTGGATCCCATATTAACTATTGTTGC

upper sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA20G25800.1 (Glycine max), 3'ss of exon 16
gtacctgattcacccataagattaaatttttacataacagctgctttactccgcatctctg---tagcttttgtagcttgtgtgctgataatgcttact---gcttgtcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTATTTTTGGGGCTATTTTTAATTGTCTGGATCCCATATTAACCATAGTTTC
                             ||   | |   || ||   |   | |  | ||   || |||||     |    || |||  |    || |   || |   |||  ||||      | || | ||||||||  | ||||| ||  | || |||||||| || || || |||||||| ||||| |||||||||||||||||  | ||| |
----------------------------gttggttgatcccttctagtcctggaaaatttggcttatcttttcctcttgaaatgatgaagacttgtatttgggccttcaattgacagGGCGCTGCCTGACAATGCTTCCTATGGAACCCAAACTTGGCAAGATGCTAATATTAGGTGCTATTTTCAATTGCCTGGATCCCATATTAACTGTGGTTGC

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|37416592|gb|CF645948.1|CF645948
EST:     TCTTAAAGTCATTGGAGCATTTGATCAGAATGAAGAATTGACGGTTCTTG                         GAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTA
genomic: TCTTAAAGTCATTGGAGCATTTGATCAGAATGAAGAATTGACGGTTCTTGgtacctgatt ... tcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTA
EST: gi|6021234|gb|AW066162.1|AW066162
EST:     TCTTAAAGTCATTGGAGCATTTGATCAGAATGAAGAATTGACGGTTCTTG                         GAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTA
genomic: TCTTAAAGTCATTGGAGCATTTGATCAGAATGAAGAATTGACGGTTCTTGgtacctgatt ... tcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTA

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: 46

GTACAAAATGCCATTGAATATCTTAAAGTCATTGGAGCATTTGATCAGAATGAAGAATTGACGGTTCTTGgtacctgatt ... tcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTATTTTTGGGGCTATTTTTAATTGTCTGGATCCCATATTAACCATAGTTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 13

GTACAAAATGCCATTGAATATCTTAAAGTCATTGGAGCATTTGATCAGAATGAAGAATTGACGGTTCTTGgtacctgatt ... tcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTATTTTTGGGGCTATTTTTAATTGTCTGGATCCCATATTAACCATAGTTTC


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 13

GTACAAAATGCCATTGAATATCTTAAAGTCATTGGAGCATTTGATCAGAATGAAGAATTGACGGTTCTTGgtacctgatt ... tcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTATTTTTGGGGCTATTTTTAATTGTCTGGATCCCATATTAACCATAGTTTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 42

GTACAAAATGCCATTGAATATCTTAAAGTCATTGGAGCATTTGATCAGAATGAAGAATTGACGGTTCTTGgtacctgatt ... tcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTATTTTTGGGGCTATTTTTAATTGTCTGGATCCCATATTAACCATAGTTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgtagcttttgtagcttgtgtgctgataatgcttactgcttgtcattttcagGAAAGCACTTGTCTATGCTTCCAGTTGAACCTAAGTTAGGAAAGATGCTTATTTTTGGGGCTATTTTTAATTGTCTGGATCCCATATTAACCATAGTTTC
                                tgcttac  putative branch site (score: 42)
                                             tcattttc  putative PPT
         ttttgta  TA-rich tract