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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcctttattcaagaaatctgttcttccttgcttttccttggtttatctgtccttggggtacggtcatgctgagatggccttgctttacaactcgtgttcacttggcatgataattttcgtattgtaatcgtgccacttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCGGCAGACATTGGATTCAAGGATATGACTAGCCACTGCGAAGCCCTGACGATCGGGAAACAGC

Basic information

species Zea mays
transcript GRMZM2G168449_T03
intron # 17
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|87154189|gb|DY398978.1|DY398978
EST:     CTTCTGTACCTGCATCAGATCTTCTGAGTATCGATCAGCTCCTTGAAACG                         GTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCGGCAGACATTGGA
genomic: CTTCTGTACCTGCATCAGATCTTCTGAGTATCGATCAGCTCCTTGAAACGgtatggcctt ... cttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCGGCAGACATTGGA
EST: gi|78112306|gb|DV530700.1|DV530700
EST:     TCCTTGAAACG                         GTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCGGCAGACATTGGA
genomic: TCCTTGAAACGgtatggcctt ... cttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCGGCAGACATTGGA
EST: gi|211451737|gb|FL033183.1|FL033183
EST:     CTTCTGTACCTGCATCAGATCTTCTGAGTATCGATCAGCTCCTTGAAACG                         GTTGGTGCARAACCAGCACCTCAGGCTGGAGTAGTGTCGGCAGACATTGGA
genomic: CTTCTGTACCTGCATCAGATCTTCTGAGTATCGATCAGCTCCTTGAAACGgtatggcctt ... cttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCGGCAGACATTGGA
EST: gi|78112307|gb|DV530701.1|DV530701
EST:     TCCTTGAAACG                         GTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCGGCAGACATTGGA
genomic: TCCTTGAAACGgtatggcctt ... cttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCGGCAGACATTGGA

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: 39 (upstream exon), 41 (downstream exon)
Score: 4

TGACCATGATGCTTTTGGGGAAGCTTCGGAAGGCGCAGAAGCTCGCACATCTTCTGTACCTGCATCAGATCTTCTGAGTATCGATCAGCTCCTTGAAACGgtatggcctt ... cttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCGGCAGACATTGGATTCAAGGATATGACTAGCCACTGCGAAGCCCTGACGATCGGGAAACAGC


Block sizes: 47 (upstream exon), 24 (downstream exon)
Score: 7

TGACCATGATGCTTTTGGGGAAGCTTCGGAAGGCGCAGAAGCTCGCACATCTTCTGTACCTGCATCAGATCTTCTGAGTATCGATCAGCTCCTTGAAACGgtatggcctt ... cttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCGGCAGACATTGGATTCAAGGATATGACTAGCCACTGCGAAGCCCTGACGATCGGGAAACAGC


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 5

TGACCATGATGCTTTTGGGGAAGCTTCGGAAGGCGCAGAAGCTCGCACATCTTCTGTACCTGCATCAGATCTTCTGAGTATCGATCAGCTCCTTGAAACGgtatggcctt ... cttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCGGCAGACATTGGATTCAAGGATATGACTAGCCACTGCGAAGCCCTGACGATCGGGAAACAGC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 16

TGACCATGATGCTTTTGGGGAAGCTTCGGAAGGCGCAGAAGCTCGCACATCTTCTGTACCTGCATCAGATCTTCTGAGTATCGATCAGCTCCTTGAAACGgtatggcctt ... cttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCGGCAGACATTGGATTCAAGGATATGACTAGCCACTGCGAAGCCCTGACGATCGGGAAACAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgtgttcacttggcatgataattttcgtattgtaatcgtgccacttatttcagGTTGGTGCAGAACCAGCACCTCAGGCTGGAGTAGTGTCGGCAGACATTGGATTCAAGGATATGACTAGCCACTGCGAAGCCCTGACGATCGGGAAACAGC
                                             cttatttc  CT-rich tract
                   ataattttcgtatt  TA-rich tract