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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCTGATGTTAGTGACATCTTTGAACCCTgtaagtaaaatgaaaatttaccttttttaaatatctgtttgtggttgtaaaaagtagtgagccatgcttactttttgaacgattgcag

Basic information

species Zea mays
transcript GRMZM2G010823_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 15
TCTCTGATGTTAGTGACATCTTTGAACCCTgtaagtaaaatgaa--aatttaccttttttaaatatctgtttgtggttgtaaaaagt--agtgagc-catgcttacttt--ttgaacgattgcag
||| ||||||| |||||||||||||||||||||||| ||||  |   ||||       ||| || | | |||    ||  |     |   |||||  ||| |||| ||   || ||  | |||||
TCTTTGATGTTGGTGACATCTTTGAACCCTgtaagtgaaattcatccattttgtagccttacatttatcttttctattacatctgctttcgtgagtgcatacttaattctatttaataaatgcag
















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|60342181|gb|DN209154.1|DN209154
EST:     TCTCTGATGTTAGTGACATCTTTGAACCCT                         AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
genomic: TCTCTGATGTTAGTGACATCTTTGAACCCTgtaagtaaaa ... acgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
EST: gi|60357469|gb|DN224442.1|DN224442
EST:     TCTCTGATGTTAGTGACATCTTTGAACCCT                         AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
genomic: TCTCTGATGTTAGTGACATCTTTGAACCCTgtaagtaaaa ... acgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
EST: gi|149081506|gb|EE170642.2|EE170642
EST:     TCTCTGATGTTAGTGACATCTTTGAACCCT                         AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
genomic: TCTCTGATGTTAGTGACATCTTTGAACCCTgtaagtaaaa ... acgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
EST: gi|91868642|gb|EB400097.1|EB400097
EST:     TGTTAGTGACATCTGTGAACCCT                         AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
genomic: TGTTAGTGACATCTTTGAACCCTgtaagtaaaa ... acgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
EST: gi|149089383|gb|EE178622.2|EE178622
EST:     TCTCTGATGTTAGTGACATCTTTGAACCCT                         AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
genomic: TCTCTGATGTTAGTGACATCTTTGAACCCTgtaagtaaaa ... acgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
EST: gi|6022572|gb|AW067384.1|AW067384
EST:     TCTCTGATGTTAGTGACATCTTTGAACCCT                         AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
genomic: TCTCTGATGTTAGTGACATCTTTGAACCCTgtaagtaaaa ... acgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
EST: gi|5901092|gb|AW042192.1|AW042192
EST:     TCTCTGATGTTAGTGACATCTTTGAACCCT                         AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
genomic: TCTCTGATGTTAGTGACATCTTTGAACCCTgtaagtaaaa ... acgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
EST: gi|78022604|gb|DV490991.1|DV490991
EST:     TCTCTGATGTTAGTGACATCTTTGAACCCT                         AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
genomic: TCTCTGATGTTAGTGACATCTTTGAACCCTgtaagtaaaa ... acgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
EST: gi|211208053|gb|FL436834.1|FL436834
EST:     TTTCTGATGTTAGTGACATCTTTGAACCCT                         AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
genomic: TCTCTGATGTTAGTGACATCTTTGAACCCTgtaagtaaaa ... acgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
EST: gi|8930245|gb|BE225009.1|BE225009
EST:     TCTCTGATGTTAGTGACATCTTTGAACCCT                         AAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA
genomic: TCTCTGATGTTAGTGACATCTTTGAACCCTgtaagtaaaa ... acgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAA

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: 30 (upstream exon), 49 (downstream exon)
Score: 231

TCTCTGATGTTAGTGACATCTTTGAACCCTgtaagtaaaa ... acgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 372

TCTCTGATGTTAGTGACATCTTTGAACCCTgtaagtaaaa ... acgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 446

TCTCTGATGTTAGTGACATCTTTGAACCCTgtaagtaaaa ... acgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG


Block sizes: 30 (upstream exon), 49 (downstream exon)
Score: 378

TCTCTGATGTTAGTGACATCTTTGAACCCTgtaagtaaaa ... acgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG