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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtctaatcacattttcaacagtgccaatactcatagaaacacagttagtgattaagcaattatctctatagATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAG

Basic information

species Zea mays
transcript GRMZM5G871572_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871572_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g45350.3 (Oryza sativa), 3'ss of exon 5
-------gtttgtc-taatcacattttcaacagtgccaatactcatagaaacacagttagtgattaagcaattatctctatagATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAG
        || ||    ||  |||||| |  | ||  ||| ||  ||| |  |   ||  || ||||| ||| ||   | |||||||| ||||| ||  |||||||||||||||||||||||||||  |||||||| ||||||||||||
gttagtacttagtaacgattgcatttttattaatgtaaatgcttgtagtagtattattcatgtttaagaaataatgcttgtagATGCTTGGAGTCAAGAGAACTGAAAGGGTTCTTCCAACTGGAACTTCATTGACTGTTGTTGGTGAG
















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|78114655|gb|DV533043.1|DV533043
EST:     CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAG                         ATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCCACTGGAATCTCCTTG
genomic: CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAGgtttgtctaa ... atctctatagATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTG
EST: gi|93012428|gb|EB637948.1|EB637948
EST:     CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAG                         ATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTG
genomic: CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAGgtttgtctaa ... atctctatagATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTG
EST: gi|56691676|gb|CX129579.1|CX129579
EST:     GTACGTGGAACTCTAGATTATTTACAGGGGTTGAAG                         ATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTG
genomic: GTACGTGGAACTCTAGATTATTTACAAGGGTTGAAGgtttgtctaa ... atctctatagATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTG
EST: gi|94474067|gb|EB703025.1|EB703025
EST:     CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAG                         ATGCTGGGAATAAAA
genomic: CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAGgtttgtctaa ... atctctatagATGCTGGGAGTAAAA
EST: gi|149055712|gb|EE156420.2|EE156420
EST:     CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAG                         ATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTG
genomic: CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAGgtttgtctaa ... atctctatagATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTG
EST: gi|71432571|gb|DR813621.1|DR813621
EST:     CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAG                         ATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTG
genomic: CAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAGgtttgtctaa ... atctctatagATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTG

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), 48 (downstream exon)
Score: 209

TTCTGCAGCTGGTTTAATTTTAACTGTTGCCAGTGAGGTTTTTGAGGAGTCAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAGgtttgtctaa ... atctctatagATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 167

TTCTGCAGCTGGTTTAATTTTAACTGTTGCCAGTGAGGTTTTTGAGGAGTCAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAGgtttgtctaa ... atctctatagATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 179

TTCTGCAGCTGGTTTAATTTTAACTGTTGCCAGTGAGGTTTTTGAGGAGTCAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAGgtttgtctaa ... atctctatagATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 185

TTCTGCAGCTGGTTTAATTTTAACTGTTGCCAGTGAGGTTTTTGAGGAGTCAGGGAGGACACTTGTACGTGGAACTCTAGATTATTTACAAGGGTTGAAGgtttgtctaa ... atctctatagATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacagtgccaatactcatagaaacacagttagtgattaagcaattatctctatagATGCTGGGAGTAAAACGAACTGAAAGGGTTCTTCCAACTGGAATCTCATTGACAGTTGTTGGTGAG
                                           ttatctct  CT-rich tract
                                         aattatct  TA-rich tract