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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgccaccctaaccaatccatggtagccggtgctcattgtgtcagtcagtaatggcttgattgcgtcttcgtctgatgttcgtcagGTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCATCAAGCGCCAGATCGACTCTTGCATCACCGACCTCCCCTGCCTCGACGAG

Basic information

species Zea mays
transcript GRMZM2G112072_T02
intron # 4
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|22133591|gb|BQ833790.1|BQ833790
EST:     GAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGG                         GTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGG
genomic: GAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGGgtgcgccacc ... tgttcgtcagGTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGG
EST: gi|76285399|gb|DV024967.1|DV024967
EST:     GAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGG                         GTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGGgtgcgccacc ... tgttcgtcagGTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCAT
EST: gi|26558570|gb|CA830805.1|CA830805
EST:     GAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGG                         GTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGGgtgcgccacc ... tgttcgtcagGTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCAT
EST: gi|94479774|gb|EB708732.1|EB708732
EST:     GAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGG                         GTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGGgtgcgccacc ... tgttcgtcagGTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCAT
EST: gi|28909485|gb|CB331838.1|CB331838
EST:     GAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGG                         GTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGG
genomic: GAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGGgtgcgccacc ... tgttcgtcagGTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGG
EST: gi|87155656|gb|DY400445.1|DY400445
EST:     GAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGG                         GTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGGgtgcgccacc ... tgttcgtcagGTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCAT
EST: gi|76937083|gb|DV175029.1|DV175029
EST:     GAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGG                         GTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGGgtgcgccacc ... tgttcgtcagGTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCAT

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), 47 (downstream exon)
Score: 67

TGCAGGGGATCGTGATGGTCATAATGAGCAAGGCCACCAGCGAGGTGATCGAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGGgtgcgccacc ... tgttcgtcagGTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCATCAAGCGCCAGATCGACTCTTGCATCACCGACCTCCCCTGCCTCGACGAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 8

TGCAGGGGATCGTGATGGTCATAATGAGCAAGGCCACCAGCGAGGTGATCGAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGGgtgcgccacc ... tgttcgtcagGTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCATCAAGCGCCAGATCGACTCTTGCATCACCGACCTCCCCTGCCTCGACGAG


Block sizes: 46 (upstream exon), 38 (downstream exon)
Score: 11

TGCAGGGGATCGTGATGGTCATAATGAGCAAGGCCACCAGCGAGGTGATCGAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGGgtgcgccacc ... tgttcgtcagGTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCATCAAGCGCCAGATCGACTCTTGCATCACCGACCTCCCCTGCCTCGACGAG


Block sizes: 25 (upstream exon), 25 (downstream exon)
Score: 1

TGCAGGGGATCGTGATGGTCATAATGAGCAAGGCCACCAGCGAGGTGATCGAGCGCTGGAACTTCAACATCGACACCTACCCCGAGGTCGTCGAGAAGGGgtgcgccacc ... tgttcgtcagGTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCATCAAGCGCCAGATCGACTCTTGCATCACCGACCTCCCCTGCCTCGACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcattgtgtcagtcagtaatggcttgattgcgtcttcgtctgatgttcgtcagGTCTATCAAGGAGAAGAGCGACAAAAAGATCATGAGGGAGATTCGGGCCATCAAGCGCCAGATCGACTCTTGCATCACCGACCTCCCCTGCCTCGACGAG
                                       gtctgat  putative branch site (score: 1)