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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGTgtaagcataagcatccacaaagacatgcacttgaatatatatgggaaaattaatcaccatattatgataacacccttgaaaggttgcaagaccttttacctttgtttttccttgaaacag

Basic information

species Zea mays
transcript GRMZM2G110289_T01
intron # 6
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|18384842|gb|BM418041.1|BM418041
EST:     ATAACTCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGT                         GGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAGC
genomic: ATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGTgtaagcataa ... cttgaaacagGGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAGC
EST: gi|18384843|gb|BM418042.1|BM418042
EST:     ATAACTCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGT                         GGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAGC
genomic: ATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGTgtaagcataa ... cttgaaacagGGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAGC
EST: gi|16746087|gb|BM032517.1|BM032517
EST:     ATAACTCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGT                         GGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAGC
genomic: ATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGTgtaagcataa ... cttgaaacagGGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAGC
EST: gi|18384685|gb|BM417884.1|BM417884
EST:     ATAACTCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGT                         GGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAGC
genomic: ATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGTgtaagcataa ... cttgaaacagGGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAGC
EST: gi|18384684|gb|BM417883.1|BM417883
EST:     ATAACTCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGT                         GGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAG
genomic: ATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGTgtaagcataa ... cttgaaacagGGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAG
EST: gi|18384683|gb|BM417882.1|BM417882
EST:     ATAACTCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGT                         GGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAGC
genomic: ATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGTgtaagcataa ... cttgaaacagGGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAGC
EST: gi|16745974|gb|BM032404.1|BM032404
EST:     TAACTCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAAT-CAGNT                         GGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAG
genomic: TAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAG-Tgtaagcataa ... cttgaaacagGGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAG

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: 110

GGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGTgtaagcataa ... cttgaaacagGGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAGCTTGTATCTCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 70

GGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGTgtaagcataa ... cttgaaacagGGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAGCTTGTATCTCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 57

GGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGTgtaagcataa ... cttgaaacagGGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAGCTTGTATCTCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 85

GGTGCCAAGGCACTTTCGAACATGCTGAAAAAGAATAAATCAATACGTATTCTACAGTTCAGCAATAATGCAATTGAATACAGTgtaagcataa ... cttgaaacagGGTTTTGCAAGTATTGCAGAAGCCCTTTTAGAGAATAATACGATACGGAGCTTGTATCTCAA