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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcctatttggagacctgttatttatacctgattatttattatgaagcatgaatatgccttttcttatactacctaccgccactaatattctgcagGTTCATCAAGAAACAGTGGGTCAAGTGAATAGCTGCCGTGTGTAGAGTGATCAGGTAATTACTGATCAACAACACCCCAGCACCACCATTTTGCAGCATT

Basic information

species Zea mays
transcript GRMZM2G081359_T03
intron # 8
splice site 3'
intron type U2

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|78084539|gb|DV512932.1|DV512932
EST:     TCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAG                         GTTCATCAAGAAACAGTGGGTCAAGTGAATAGCTGCCGTGTGTAGAGTGAT
genomic: TCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcctatttg ... tattctgcagGTTCATCAAGAAACAGTGGGTCAAGTGAATAGCTGCCGTGTGTAGAGTGAT
EST: gi|211396319|gb|FL436139.1|FL436139
EST:     GAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAG                         GTTCATCAAGAAACAGTGGGTCAAGTGAATAGCTGCCGTGTGTAGAGTGAT
genomic: GAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcctatttg ... tattctgcagGTTCATCAAGAAACAGTGGGTCAAGTGAATAGCTGCCGTGTGTAGAGTGAT

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

TCATCAGAACCTGGGAGCTTGCGTCGCTGGGATGGTCCATTCCTTTGCCAGAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcctatttg ... tattctgcagGTTCATCAAGAAACAGTGGGTCAAGTGAATAGCTGCCGTGTGTAGAGTGATCAGGTAATTACTGATCAACAACACCCCAGCACCACCATTTTGCAGCATT


Block sizes: 46 (upstream exon), 40 (downstream exon)
Score: 11

TCATCAGAACCTGGGAGCTTGCGTCGCTGGGATGGTCCATTCCTTTGCCAGAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcctatttg ... tattctgcagGTTCATCAAGAAACAGTGGGTCAAGTGAATAGCTGCCGTGTGTAGAGTGATCAGGTAATTACTGATCAACAACACCCCAGCACCACCATTTTGCAGCATT


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 10

TCATCAGAACCTGGGAGCTTGCGTCGCTGGGATGGTCCATTCCTTTGCCAGAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcctatttg ... tattctgcagGTTCATCAAGAAACAGTGGGTCAAGTGAATAGCTGCCGTGTGTAGAGTGATCAGGTAATTACTGATCAACAACACCCCAGCACCACCATTTTGCAGCATT


Block sizes: 46 (upstream exon), 23 (downstream exon)
Score: 11

TCATCAGAACCTGGGAGCTTGCGTCGCTGGGATGGTCCATTCCTTTGCCAGAGCTGTCAGGAAAAGAAAGAAGCAATGGAGGGAAAGCGTCGTTCACGAGgtcctatttg ... tattctgcagGTTCATCAAGAAACAGTGGGTCAAGTGAATAGCTGCCGTGTGTAGAGTGATCAGGTAATTACTGATCAACAACACCCCAGCACCACCATTTTGCAGCATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaagcatgaatatgccttttcttatactacctaccgccactaatattctgcagGTTCATCAAGAAACAGTGGGTCAAGTGAATAGCTGCCGTGTGTAGAGTGATCAGGTAATTACTGATCAACAACACCCCAGCACCACCATTTTGCAGCATT
                                       cactaat  putative branch site (score: 11)
                  ttttcttata  TA-rich tract