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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatgccatttgcttctctattcagtgaaggggaaatatcattaaatttatgtgcaacgatgatttcagATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAG

Basic information

species Zea mays
transcript GRMZM5G824405_T02
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os03g18310.2 (Oryza sativa), 3'ss of exon 16
gtaagtatgccatttgcttctc-tattcagtgaaggggaaatatcattaaatttatgtgcaacgatgatttcagATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAG
||||||||||  |||    ||  || |     |||        |  || || || ||||   |  |   ||||||||||||||||||||||||||||  ||||||||||||| || || |||||||| |||||||||
gtaagtatgctttttatcacttgtaattgagaaagaaacttctttcttgaacttgtgtgtggcatttgattcagATATGGACTAGCACACTCCAGAGGTCAATATTAACAGCGCAGCCTATCATTGGATTTCCAAAG

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 15
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 17
------------------------gtaagtatgccatttgcttctctattcagtgaaggggaaatatcattaa-atttatgtg---caacgatgatttcagATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAG
                         | | |||         |  | | |  | |  |   ||| | | || |  |||  ||||      |  || ||| ||||||||||||||||||| ||||||||||| ||||| |||  ||| ||  |||| || ||||||
taatgctttatactattctactagttgaatatatatggaagtcatgtgtaaattttaacagaattctaataagcattcttgtgattttgctgtggttt-agATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTTGGGTTCCCAAAG
















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|84980594|gb|DW530943.1|DW530943
EST:     AGCTTGCGAGCTTTGTGGAGAAGCGACTGAAATCCGAGCGGACTGCCTCT                         ATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATT
genomic: AGCTTGCGAGCTTTGTGGAGAAGCGACTGAAATCCGAGCGGACTGCCTCTgtaagtatgc ... atgatttcagATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATT
EST: gi|211189269|gb|FL030572.1|FL030572
EST:     AGCTTGCGAGCTTTGTGGAGAAGCGACTGAAATCCGAGCGGACTGCCTCT                         ATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATT
genomic: AGCTTGCGAGCTTTGTGGAGAAGCGACTGAAATCCGAGCGGACTGCCTCTgtaagtatgc ... atgatttcagATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATT
EST: gi|67015674|gb|CO444423.1|CO444423
EST:     AGCTTGCGAGCTTTGTGGAGAAGCGACTGAAATCCGAGCGGACTGCCTCT                         ATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATT
genomic: AGCTTGCGAGCTTTGTGGAGAAGCGACTGAAATCCGAGCGGACTGCCTCTgtaagtatgc ... atgatttcagATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATT
EST: gi|67010650|gb|CO439399.1|CO439399
EST:     AGCTTGCGAGCTTTGTGGAGAAGCGACTGAAATCCGAGCGGACTGCCTCT                         ATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATT
genomic: AGCTTGCGAGCTTTGTGGAGAAGCGACTGAAATCCGAGCGGACTGCCTCTgtaagtatgc ... atgatttcagATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATT

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), 46 (downstream exon)
Score: 142

TGAGGCCGGTGAGCTTTATTCAAGGAAGCTTGCGAGCTTTGTGGAGAAGCGACTGAAATCCGAGCGGACTGCCTCTgtaagtatgc ... atgatttcagATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

TGAGGCCGGTGAGCTTTATTCAAGGAAGCTTGCGAGCTTTGTGGAGAAGCGACTGAAATCCGAGCGGACTGCCTCTgtaagtatgc ... atgatttcagATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 160

TGAGGCCGGTGAGCTTTATTCAAGGAAGCTTGCGAGCTTTGTGGAGAAGCGACTGAAATCCGAGCGGACTGCCTCTgtaagtatgc ... atgatttcagATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 446

TGAGGCCGGTGAGCTTTATTCAAGGAAGCTTGCGAGCTTTGTGGAGAAGCGACTGAAATCCGAGCGGACTGCCTCTgtaagtatgc ... atgatttcagATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctattcagtgaaggggaaatatcattaaatttatgtgcaacgatgatttcagATATGGACTAGCACACTCCAGAGAACAATATTAACAGCACATCCGATCATTGGTTTTCCAAAG
                   aaatatcattaaattt  TA-rich tract