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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggcaataaactaattgcttgaggtttattttatttttctggacacgttacatgttatttctcaccagGACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCG

Basic information

species Zea mays
transcript GRMZM2G173777_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173777_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g07070.1 (Oryza sativa), 3'ss of exon 11
gtgggcaataaactaattgct--tgaggttta-----ttttatttttctggacacg-ttacatgttatttctcaccagGACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCG
||||| || || || ||  ||  |||  |||      ||   ||| | | || |   | ||||| | ||  |   |||||||| |||||||||||||||||||||||||||||||| ||||||||||| ||| | ||||| ||||| 
gtggg-aagaagcttatgactcttgaaatttgcagtgttccgtttctgttgagagaatgacatgctgttgttgtgcagGACATTCGCCTTGTTCGGGATAAGTTTACTCATGTGTCCAGAGGTTTTGCTTTCATCCATTTTCATTCA
















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|211224726|gb|FL222444.1|FL222444
EST:     CTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG                         GACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCC
genomic: CTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAGgtgggcaata ... ttctcaccagGACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCC
EST: gi|18661711|gb|BM501540.1|BM501540
EST:     CTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG                         GACATCCGCCTTGTGTCGGGATAAG
genomic: CTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAGgtgggcaata ... ttctcaccagGACATCCGCCTTGT-TCGGGATAAG
EST: gi|211344311|gb|FL081282.1|FL081282
EST:     CTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG                         GACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCC
genomic: CTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAGgtgggcaata ... ttctcaccagGACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCC
EST: gi|13490949|gb|BG517713.1|BG517713
EST:     CTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG                         GACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCC
genomic: CTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAGgtgggcaata ... ttctcaccagGACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCC

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: 131

GTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAGgtgggcaata ... ttctcaccagGACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

GTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAGgtgggcaata ... ttctcaccagGACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

GTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAGgtgggcaata ... ttctcaccagGACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 99

GTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAGgtgggcaata ... ttctcaccagGACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcttgaggtttattttatttttctggacacgttacatgttatttctcaccagGACATCCGCCTTGTTCGGGATAAGTTTACTCATGTGTCTAGAGGTTTTGCCTTCGTTCATTTCCATTCG
 aactaat  putative branch site (score: 99)
                                         ttatttctc  putative PPT
           tttattttatttttct  TA-rich tract