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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccattgaacaatagcattgcaatgcagaattgcagatattggtgatgcgaggacaaccaggcagtgctcatagtataatgttgcttgctacattctgcagGGACGAGGAACTTATGTCGCAGGGGCTCACACTGAATGATGATTTGCAGCGTGTTCTAGCAAAACATGATGCAATAGCAGCAGGCATTGCAGTCCGAGTG

Basic information

species Zea mays
transcript GRMZM2G062953_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062953_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 7
ccattgaacaatagcattgcaatgcagaattgcagatattggtgatg-cgaggacaaccag-----gcagtgctcatagtataatgttgcttgctacattctgcagGGACGAGGAACTTATGTCGCAGGGGCTCACACTGAATGATGATTTGCAGCGTGTTCTAGCAAAACATGATGCAATAGCAGCAGGCATTGCAGTCCGAGTG
   |  ||   | |||    | |      | || |  ||  ||  |  |      ||| |      |||      ||| || |||  || ||    |||| | |||||| |||||||||||||| || |||||  ||||||||||||| ||||| |||||||| |||||||| |||||||| || |||||||||||||| ||||||
---tgaaaagctggca--aaagtagcccttggctggcatctgtattatctcatttaactatttattgcaacatatatactaaaattctggtttggccatt-tacagGGATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGACTTGCAACGTGTTCTCGCAAAACACGATGCAATTGCTGCAGGCATTGCAGTTCGAGTG
















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|22490527|gb|BU050450.1|BU050450
EST:     CAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCAC                         GGACGAGGAACTTATGTCGCAGGGGCTCACACTGAATGATGATTTGCAGCG
genomic: CAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgctc ... cattctgcagGGACGAGGAACTTATGTCGCAGGGGCTCACACTGAATGATGATTTGCAGCG
EST: gi|20300238|gb|BQ163181.1|BQ163181
EST:     CAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCAC                         GGACGAGGAACTTATGTCGCAGGGGCTCACACTGAATGATGATTTGCAGCG
genomic: CAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgctc ... cattctgcagGGACGAGGAACTTATGTCGCAGGGGCTCACACTGAATGATGATTTGCAGCG
EST: gi|87153881|gb|DY398670.1|DY398670
EST:     CAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCAC                         GGACGAGGAACTTATGTCGCAGGGGCTCACACTGAATGATGATTTGCAGCG
genomic: CAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgctc ... cattctgcagGGACGAGGAACTTATGTCGCAGGGGCTCACACTGAATGATGATTTGCAGCG

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: 110

GGGCTAAGGCAGGAGGTAATTGTGGAACTTGTGGATCAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgctc ... cattctgcagGGACGAGGAACTTATGTCGCAGGGGCTCACACTGAATGATGATTTGCAGCGTGTTCTAGCAAAACATGATGCAATAGCAGCAGGCATTGCAGTCCGAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 434

GGGCTAAGGCAGGAGGTAATTGTGGAACTTGTGGATCAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgctc ... cattctgcagGGACGAGGAACTTATGTCGCAGGGGCTCACACTGAATGATGATTTGCAGCGTGTTCTAGCAAAACATGATGCAATAGCAGCAGGCATTGCAGTCCGAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 402

GGGCTAAGGCAGGAGGTAATTGTGGAACTTGTGGATCAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgctc ... cattctgcagGGACGAGGAACTTATGTCGCAGGGGCTCACACTGAATGATGATTTGCAGCGTGTTCTAGCAAAACATGATGCAATAGCAGCAGGCATTGCAGTCCGAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 292

GGGCTAAGGCAGGAGGTAATTGTGGAACTTGTGGATCAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgctc ... cattctgcagGGACGAGGAACTTATGTCGCAGGGGCTCACACTGAATGATGATTTGCAGCGTGTTCTAGCAAAACATGATGCAATAGCAGCAGGCATTGCAGTCCGAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcgaggacaaccaggcagtgctcatagtataatgttgcttgctacattctgcagGGACGAGGAACTTATGTCGCAGGGGCTCACACTGAATGATGATTTGCAGCGTGTTCTAGCAAAACATGATGCAATAGCAGCAGGCATTGCAGTCCGAGTG
                        atagtataat  TA-rich tract