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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCCAGCATTTTCACTATTGCTCACCCATCCTCCTATGATGCATGGTACAATGTCATCATCCATGAGCAATACAACTGTTTCTACGCAGCCCCAAGAGgtatgaacatttcacttaatcatgcaaattcaactccatctgtgctttccagtgaagcaacaatgtatttctctctttcttgccaacttggtacattctg...

Basic information

species Zea mays
transcript GRMZM2G163888_T01
intron # 8
splice site 5'
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|32942842|gb|CF047661.1|CF047661
EST:     CAATGTCATCATCCATGAGCAATACAACTGTTTCTACGCAGCCCCAAGAG                         AATGCCAATCCAGTTGGTTTACCCAACCCTCAATTGACTCAATCTCAGCAA
genomic: CAATGTCATCATCCATGAGCAATACAACTGTTTCTACGCAGCCCCAAGAGgtatgaacat ... attctcgcagAATGCCAATCCAGTTGGTTTACCCAACCCTCAATTGACTCAATCTCAGCAA
EST: gi|32850553|gb|CD990234.1|CD990234
EST:     CAATGTCATCATCCATGAGCAATACAACTGTTTCTACGCAGCCCCAAGAG                         AATGCCAATCCAGTTAGTTTACCCAACCCTCAATTGACTCAATCTCAGCAA
genomic: CAATGTCATCATCCATGAGCAATACAACTGTTTCTACGCAGCCCCAAGAGgtatgaacat ... attctcgcagAATGCCAATCCAGTTGGTTTACCCAACCCTCAATTGACTCAATCTCAGCAA
EST: gi|211270098|gb|FL340192.1|FL340192
EST:     CAATGTCATCATCCATGAGCARWACAACTGTTTCTACACAGCCCCAAGAG                         AATGCCAATCCAGTTGGTTTACCCAACCCTCAATTGACTCAATCTCAGCAA
genomic: CAATGTCATCATCCATGAGCAATACAACTGTTTCTACGCAGCCCCAAGAGgtatgaacat ... attctcgcagAATGCCAATCCAGTTGGTTTACCCAACCCTCAATTGACTCAATCTCAGCAA
EST: gi|95107690|gb|EB739919.1|EB739919
EST:     CATGAGCAATACAACTGTTTCTACGCAGCCCCAAGAG                         AATGCCAATCCAGTTGGTTTACCCAACCCTCAATTGACTCAATCTCAGCAA
genomic: CATGAGCAATACAACTGTTTCTACGCAGCCCCAAGAGgtatgaacat ... attctcgcagAATGCCAATCCAGTTGGTTTACCCAACCCTCAATTGACTCAATCTCAGCAA
EST: gi|32944594|gb|CF049413.1|CF049413
EST:     CAATGTCATCATCCATGAGCAATACAACTGTTTCTACGCAGCCCCAAGAG                         AATGCCAATCCAGTTGGTTTACCCAACCCTCAATTGACTCAATCTCAGCAA
genomic: CAATGTCATCATCCATGAGCAATACAACTGTTTCTACGCAGCCCCAAGAGgtatgaacat ... attctcgcagAATGCCAATCCAGTTGGTTTACCCAACCCTCAATTGACTCAATCTCAGCAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 259

TGATCCAGCATTTTCACTATTGCTCACCCATCCTCCTATGATGCATGGTACAATGTCATCATCCATGAGCAATACAACTGTTTCTACGCAGCCCCAAGAGgtatgaacat ... attctcgcagAATGCCAATCCAGTTGGTTTACCCAACCCTCAATTGACTCAATCTCAGCAAAGCACCAGCATTGCTTCAGGGCCTCCACTCCCTCAGCATCTTCTTCATC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 239

TGATCCAGCATTTTCACTATTGCTCACCCATCCTCCTATGATGCATGGTACAATGTCATCATCCATGAGCAATACAACTGTTTCTACGCAGCCCCAAGAGgtatgaacat ... attctcgcagAATGCCAATCCAGTTGGTTTACCCAACCCTCAATTGACTCAATCTCAGCAAAGCACCAGCATTGCTTCAGGGCCTCCACTCCCTCAGCATCTTCTTCATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

TGATCCAGCATTTTCACTATTGCTCACCCATCCTCCTATGATGCATGGTACAATGTCATCATCCATGAGCAATACAACTGTTTCTACGCAGCCCCAAGAGgtatgaacat ... attctcgcagAATGCCAATCCAGTTGGTTTACCCAACCCTCAATTGACTCAATCTCAGCAAAGCACCAGCATTGCTTCAGGGCCTCCACTCCCTCAGCATCTTCTTCATC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 255

TGATCCAGCATTTTCACTATTGCTCACCCATCCTCCTATGATGCATGGTACAATGTCATCATCCATGAGCAATACAACTGTTTCTACGCAGCCCCAAGAGgtatgaacat ... attctcgcagAATGCCAATCCAGTTGGTTTACCCAACCCTCAATTGACTCAATCTCAGCAAAGCACCAGCATTGCTTCAGGGCCTCCACTCCCTCAGCATCTTCTTCATC