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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTCAATTCCCTTGTTCCCGTCACTCACGGGAGACACAAACAGCGGCTCTGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAGgtaagccttgtttttctttttggtatagaatgcactagcgttatgtgagttatcttgacatcgttagaagcgtctcattcataccgttgtccactgaaccag

Basic information

species Zea mays
transcript GRMZM2G153754_T01
intron # 10
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|19769452|gb|BQ034173.1|BQ034173
EST:     TGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAG                         GACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTG
genomic: TGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAGgtaagccttg ... actgaaccagGACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTG
EST: gi|32939282|gb|CF044101.1|CF044101
EST:     TGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAG                         GACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTG
genomic: TGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAGgtaagccttg ... actgaaccagGACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTG
EST: gi|19769852|gb|BQ034573.1|BQ034573
EST:     TGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAG                         GACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTG
genomic: TGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAGgtaagccttg ... actgaaccagGACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTG
EST: gi|26455740|gb|CA827323.1|CA827323
EST:     TGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAG                         GACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACG
genomic: TGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAGgtaagccttg ... actgaaccagGACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACG
EST: gi|19769954|gb|BQ034675.1|BQ034675
EST:     TGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAG                         GACCATATTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTG
genomic: TGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAGgtaagccttg ... actgaaccagGACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTG
EST: gi|211458168|gb|FL127580.1|FL127580
EST:     TGCAATGAACATCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAG                         GACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGTAGTACGACTTG
genomic: TGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAGgtaagccttg ... actgaaccagGACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTG
EST: gi|32940347|gb|CF045166.1|CF045166
EST:     TGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAG                         GACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTG
genomic: TGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAGgtaagccttg ... actgaaccagGACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTG
EST: gi|32938400|gb|CF043219.1|CF043219
EST:     TGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAG                         GACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTG
genomic: TGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAGgtaagccttg ... actgaaccagGACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTG

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 3 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 59

AAGTCAATTCCCTTGTTCCCGTCACTCACGGGAGACACAAACAGCGGCTCTGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAGgtaagccttg ... actgaaccagGACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTGTAGTCCGAACACGTGTGCCTCGTATCCTACGGCAAGGCTCGAGGTACTG


Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 3

AAGTCAATTCCCTTGTTCCCGTCACTCACGGGAGACACAAACAGCGGCTCTGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAGgtaagccttg ... actgaaccagGACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTGTAGTCCGAACACGTGTGCCTCGTATCCTACGGCAAGGCTCGAGGTACTG


Block sizes: 47 (upstream exon), 27 (downstream exon)
Score: 6

AAGTCAATTCCCTTGTTCCCGTCACTCACGGGAGACACAAACAGCGGCTCTGCAATGAACAGCACTGATAGCGCATTCTGCGCGTCACCTCTCACTTTAGgtaagccttg ... actgaaccagGACCATCTTAAAGCTGTGAAGTTGGTGGCCATGGGACCGGAGTACGACTTGTAGTCCGAACACGTGTGCCTCGTATCCTACGGCAAGGCTCGAGGTACTG