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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCACCCTCACGGCAAGCCCTGATCACATCATCCTGCTTGTCTCTCCCCAACCTAGCTCCATCTCTCTTTCATCTACTCTTCCATCGATCGATCCATCGgtaagaacatgcgatgccctctgtgtgcgtgtgaatctatgcatgcatggatctgccctcgttccttttcctgtccattttcccgtttctttcctgcttg...

Basic information

species Zea mays
transcript GRMZM2G018589_T01
intron # 1
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|78108882|gb|DV527299.1|DV527299
EST:     AACCTAGCTCCATCTCTCTTTCATCTACTCTTCCATCGATCGATCCATCG                         TACTGCGTGAGGATGGGGAGGGGAAAGATTGAGATCAAGAGGATCGAGAAC
genomic: AACCTAGCTCCATCTCTCTTTCATCTACTCTTCCATCGATCGATCCATCGgtaagaacat ... actgttacagTACTGCGTGAGGATGGGGAGGGGAAAGATTGAGATCAAGAGGATCGAGAAC
EST: gi|37418627|gb|CF646984.1|CF646984
EST:     AACCTAGCTCCATCTCTCTTTCATCTACTCTTCCATCGATCGATCCATCG                         TACTGCGTGAGGATGGGGAGGGGAAAGATTGAGATCAA
genomic: AACCTAGCTCCATCTCTCTTTCATCTACTCTTCCATCGATCGATCCATCGgtaagaacat ... actgttacagTACTGCGTGAGGATGGGGAGGGGAAAGATTGAGATCAA
EST: gi|37418613|gb|CF646976.1|CF646976
EST:     AACCTAGCTCCATCTCTCTTTCATCTACTCTTCCATCGATCGATCCATCG                         TACTGCGTGAGGATGGGGAGGGGAAAGATTGAGATCAAGAGGATCGAGAAC
genomic: AACCTAGCTCCATCTCTCTTTCATCTACTCTTCCATCGATCGATCCATCGgtaagaacat ... actgttacagTACTGCGTGAGGATGGGGAGGGGAAAGATTGAGATCAAGAGGATCGAGAAC

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 1 RNA-Seqlibrary.


Block sizes: 30 (upstream exon), 42 (downstream exon)
Score: 7

CATCACCCTCACGGCAAGCCCTGATCACATCATCCTGCTTGTCTCTCCCCAACCTAGCTCCATCTCTCTTTCATCTACTCTTCCATCGATCGATCCATCGgtaagaacat ... actgttacagTACTGCGTGAGGATGGGGAGGGGAAAGATTGAGATCAAGAGGATCGAGAACACCACCAGCCGCCAGGTGACCTTCTGCAAGCGCAGGAATGGGCTGCTGA




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