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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agacctgctagggcatgccttgaaaacaagacaattataaagccatattttggaaatttaaatgttttgtctacattatactaatgaggaaaaattccagGTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCG

Basic information

species Zea mays
transcript GRMZM2G059671_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059671_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 7
agacctgctagggcatgccttgaaaacaag---acaattataaagccatat-tttggaaatttaaatgttttgtctacattatactaatgaggaaaaattccagGTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCG
    | |  |   ||     ||||||  |    |  || || ||||    | |||  | ||||  || |||| | ||   |  ||||||   |||||||  |||| || ||||| || ||||||||||||||||||||||| |||
---tccgtgacctcacattgtgaaaattaatgaatgatcatgaagctgcctatttccagattttgatatttt-tgtagtgtgcactaattgagaaaaatgacagGCTCATTTGGAACCGTGCACCGTGCGGATTGGAATGGCTCG

upper sequence: GRMZM2G059671_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 6
----agacctgctagggc--atgccttgaaaacaagacaattataaagccatattttggaaatttaaatgttttgtctacattatactaatgaggaaaaattccagGTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCG
    || ||   | |||   |    ||    | || | ||| |||     | |||||| |   ||   |  ||   ||  ||| |  |  ||      | |||||||||||||||| ||||| || ||||| ||||||||||| |||
ttcaagtcccaatggggacaaaagtttacctataaaataataatagtaata-attttgtaggattttgttcttaaactgaattgtcttggtgc-----atttccagGTTCTTTTGGGACTGTTCATCGTGCTGATTGGAATGGATCG
















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|76284241|gb|DV023809.1|DV023809
EST:     CTTGATTATCCCATGGAGTGAGCTTGTTCTGAAAGAGAAAATTGGTGCAG                         GTTCTTTTGGTACTGTGCACCGTGCGGATTGAAATGGTTCG
genomic: CTTGATTATCCCATGGAGTGAGCTTGTTCTGAAAGAGAAAATTGGTGCAGgtgtgtttcc ... aaaattccagGTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCG
EST: gi|211082601|gb|FL182313.1|FL182313
EST:     CTTGATTATCCCATGGAGTGAGCTTGTTCTGAAAGAGAAAATTGGTGCAG                         GTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCG
genomic: CTTGATTATCCCATGGAGTGAGCTTGTTCTGAAAGAGAAAATTGGTGCAGgtgtgtttcc ... aaaattccagGTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCG

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: 76

CAATCTGGACTAAGTGATCCCTTTAGCGATATGTCCCTTGAGATAGAAGACTTGATTATCCCATGGAGTGAGCTTGTTCTGAAAGAGAAAATTGGTGCAGgtgtgtttcc ... aaaattccagGTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

CAATCTGGACTAAGTGATCCCTTTAGCGATATGTCCCTTGAGATAGAAGACTTGATTATCCCATGGAGTGAGCTTGTTCTGAAAGAGAAAATTGGTGCAGgtgtgtttcc ... aaaattccagGTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

CAATCTGGACTAAGTGATCCCTTTAGCGATATGTCCCTTGAGATAGAAGACTTGATTATCCCATGGAGTGAGCTTGTTCTGAAAGAGAAAATTGGTGCAGgtgtgtttcc ... aaaattccagGTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 43

CAATCTGGACTAAGTGATCCCTTTAGCGATATGTCCCTTGAGATAGAAGACTTGATTATCCCATGGAGTGAGCTTGTTCTGAAAGAGAAAATTGGTGCAGgtgtgtttcc ... aaaattccagGTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttggaaatttaaatgttttgtctacattatactaatgaggaaaaattccagGTTCTTTTGGTACTGTGCACCGTGCGGATTGGAATGGTTCG
                                 tactaat  putative branch site (score: 43)
        aaatttaaatgttttg  TA-rich tract