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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcaataattttattgttgtgacttgtgacacatgttccaagacctccatcaattgtctgatggcttacatcttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTGTGGGATAAAGTTCTTCAGCCTGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCCACTGCA

Basic information

species Zea mays
transcript GRMZM5G873600_T01
intron # 1
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|32796693|gb|CD948929.1|CD948929
EST:     GAACTTATTATTGTCACCAACAAAAACTCATTATTCAAGCTGCAAGCTAG                         GTATGTGGTTGAGAGAATGGATGGTGATCTGTGGGATAAAGTTCTTCAGCC
genomic: GAACTTATTATTGTCACCAACAAAAACTCATTATTCAAGCTGCAAGCTAGgtattcaata ... aaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTGTGGGATAAAGTTCTTCAGCC




















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: 49 (upstream exon), 48 (downstream exon)
Score: 403

GATCCTACACTTGCTGTTGTTGCTTACAGACGTGGACAGTGTGATGATGAACTTATTATTGTCACCAACAAAAACTCATTATTCAAGCTGCAAGCTAGgtattcaata ... aaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTGTGGGATAAAGTTCTTCAGCCTGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCCACTGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 285

GATCCTACACTTGCTGTTGTTGCTTACAGACGTGGACAGTGTGATGATGAACTTATTATTGTCACCAACAAAAACTCATTATTCAAGCTGCAAGCTAGgtattcaata ... aaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTGTGGGATAAAGTTCTTCAGCCTGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCCACTGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 237

GATCCTACACTTGCTGTTGTTGCTTACAGACGTGGACAGTGTGATGATGAACTTATTATTGTCACCAACAAAAACTCATTATTCAAGCTGCAAGCTAGgtattcaata ... aaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTGTGGGATAAAGTTCTTCAGCCTGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCCACTGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 326

GATCCTACACTTGCTGTTGTTGCTTACAGACGTGGACAGTGTGATGATGAACTTATTATTGTCACCAACAAAAACTCATTATTCAAGCTGCAAGCTAGgtattcaata ... aaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTGTGGGATAAAGTTCTTCAGCCTGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCCACTGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatcaattgtctgatggcttacatcttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTGTGGGATAAAGTTCTTCAGCCTGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCCACTGCA
                 ggcttac  putative branch site (score: 326)
                           ttcatattgcatttat  TA-rich tract