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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatataagttttcatatttttggaatgtgaatacattgtcagcaagtttctgtgagtgaagcttgtgtgagtttaactgtttgttctaaaagtacacctttttactgtctcacatgacatagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG

Basic information

species Zea mays
transcript GRMZM2G081682_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 13
---------------------------------------------------------gtaatataagttttcatatttttggaatgtgaatacattgtcagcaagtttctgtgagtgaagcttgtgtgagtttaactgtttgttctaaaagtac---acctttttactgtctcacatgacatagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG
                                                         | | |  | |  ||||| | ||   |   | | |   |||  | ||| ||| | | | ||  |  ||| ||   ||||| || | || | |||  |    |  |   | || | ||||   | | |||||| |||||||| |||||||| |||||||| ||||||||||||||||| ||
gtacatatgtagtttgttattgggtttacagtgatttcgaaagttgaactgttatttggatttcaggaattcatgtattaacaccattagtgttttg--aacaattttattt-actgctgtctgtctggagttaaccgtgtattgtgaaataatctaaagtacattctttttcaccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG
















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|31349785|gb|CD434142.1|CD434142
EST:     CTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCTTACAG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACA
genomic: CTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCTTACAGgtaatataag ... catgacatagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACA
EST: gi|5846747|gb|AI999830.1|AI999830
EST:     CTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCTTACAG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACA
genomic: CTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCTTACAGgtaatataag ... catgacatagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACA
EST: gi|5296207|gb|AI782887.1|AI782887
EST:     CTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCTTACAG                         GAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACA
genomic: CTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCTTACAGgtaatataag ... catgacatagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACA

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: 47 (upstream exon), 49 (downstream exon)
Score: 308

GTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCTTACAGgtaatataag ... catgacatagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 337

GTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCTTACAGgtaatataag ... catgacatagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 295

GTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCTTACAGgtaatataag ... catgacatagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 398

GTATGACTGGGATGTTGCGACTACGTTTGCTTTTCTACAGAAGTACGGTCTTACAGgtaatataag ... catgacatagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtttaactgtttgttctaaaagtacacctttttactgtctcacatgacatagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG
                ttctaaaa  TA-rich tract