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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttttctaaaaatgaacatttcttaaagtttcttattggtattcccatcatatcatttgttagtacatctaaatgtgtcttcttcttttggcatagGTCATTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAATTGTACCAAGTTGCAACAACT

Basic information

species Zea mays
transcript GRMZM2G479243_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G479243_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g16010.1 (Oryza sativa), 3'ss of exon 4
gtaagtgttttctaaaaatgaacatttcttaaagtttcttattggtattcccatcatatcatttgttagtacatctaaatgtgtcttcttcttttggcatagGTCATTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAATTGTACCAAGTTGCAACAACT
                  | |   | | || |       ||  | | ||  | | |  || ||  ||    ||||| ||  |    | || | |     ||| ||| |||| ||||| || |||||||| ||||||||||| ||| |||| |||||||||||||| ||||||||
-----------------gtaagtgtgtgttga-------tagcgttctttgcttaacctctttcttttcagcatctgaaattactattttatgtcat--tagATCACTGCAAGGGAATAGCTTGTATGGCTCACTCCCTCCAGAATTGGGAAATTGTACCAAGTTACAACAACT
















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|7031287|gb|AW461025.1|AW461025
EST:     GTTGGGCCCATACCACCAGAAATTGGAAGGTTAAATCAGTTGCAAACCTT                         GTCATTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA
genomic: GTTGGGCCCATACCACCAGAAATTGGAAGGTTAAATCAGTTGCAAACCTTgtaagtgttt ... tttggcatagGTCATTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA
EST: gi|78180135|gb|DV550508.1|DV550508
EST:     GTTGGGCCCATACCACCAGAAATTGGAAGGTTAAATCAGTTGCAAACCTT                         GTCATTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA
genomic: GTTGGGCCCATACCACCAGAAATTGGAAGGTTAAATCAGTTGCAAACCTTgtaagtgttt ... tttggcatagGTCATTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA
EST: gi|12046680|gb|BF728819.1|BF728819
EST:     GTTGGGCCCATACCACCAGAAATTGGAAGGTTAAATCAGTTGCAAACCTT                         GTCATTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA
genomic: GTTGGGCCCATACCACCAGAAATTGGAAGGTTAAATCAGTTGCAAACCTTgtaagtgttt ... tttggcatagGTCATTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAA

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), 49 (downstream exon)
Score: 62

GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCAGAAATTGGAAGGTTAAATCAGTTGCAAACCTTgtaagtgttt ... tttggcatagGTCATTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAATTGTACCAAGTTGCAACAACT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 33

GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCAGAAATTGGAAGGTTAAATCAGTTGCAAACCTTgtaagtgttt ... tttggcatagGTCATTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAATTGTACCAAGTTGCAACAACT


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 39

GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCAGAAATTGGAAGGTTAAATCAGTTGCAAACCTTgtaagtgttt ... tttggcatagGTCATTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAATTGTACCAAGTTGCAACAACT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 46

GATTCTTGCATACCACAGATTAGTTGGGCCCATACCACCAGAAATTGGAAGGTTAAATCAGTTGCAAACCTTgtaagtgttt ... tttggcatagGTCATTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAATTGTACCAAGTTGCAACAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcccatcatatcatttgttagtacatctaaatgtgtcttcttcttttggcatagGTCATTGCAGGGGAACAGTTTGTATGGTTCACTCCCTCCTGAACTGGGGAATTGTACCAAGTTGCAACAACT
                         atctaaa  putative branch site (score: 46)
                                tgtgtcttcttctttt  CT-rich tract
        atatcattt  TA-rich tract