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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgggcattccttttcccaggcagcgaggtgttttgtgtatatgcaccgcgtttggtgcctttggtgtcctaactgcctgtgaatgttaccagATCATACCATACTACCATGTGAATTGCATTGCACCGCTCAACGCTCATTGAGGGCCATGTTTCGATATGCTCCTGCCAATGCCATTCGCATGATATTTAT

Basic information

species Zea mays
transcript GRMZM2G046418_T01
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|149111411|gb|EE294913.2|EE294913
EST:     GGAGCAGTTCGACTAGGCTCAGCTGAAGCTGTTGATGTATCGTGAGATCG                         ATCATACCATACTACCATGTGAATTGCATTGCACCGCTCAACGCTCATTGA
genomic: GGAGCAGTTCGACTAGGCTCAGCTGAAGCTGTTGATGTATCGTGAGATCGgtatgggcat ... atgttaccagATCATACCATACTACCATGTGAATTGCATTGCACCGCTCAACGCTCATTGA




















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), 49 (downstream exon)
Score: 130

TTCAGCGCTCCCCCGCCCCACGTTCCTTCAGAGCAAGTTAACACTGACTGGGAGCAGTTCGACTAGGCTCAGCTGAAGCTGTTGATGTATCGTGAGATCGgtatgggcat ... atgttaccagATCATACCATACTACCATGTGAATTGCATTGCACCGCTCAACGCTCATTGAGGGCCATGTTTCGATATGCTCCTGCCAATGCCATTCGCATGATATTTAT


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

TTCAGCGCTCCCCCGCCCCACGTTCCTTCAGAGCAAGTTAACACTGACTGGGAGCAGTTCGACTAGGCTCAGCTGAAGCTGTTGATGTATCGTGAGATCGgtatgggcat ... atgttaccagATCATACCATACTACCATGTGAATTGCATTGCACCGCTCAACGCTCATTGAGGGCCATGTTTCGATATGCTCCTGCCAATGCCATTCGCATGATATTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 46

TTCAGCGCTCCCCCGCCCCACGTTCCTTCAGAGCAAGTTAACACTGACTGGGAGCAGTTCGACTAGGCTCAGCTGAAGCTGTTGATGTATCGTGAGATCGgtatgggcat ... atgttaccagATCATACCATACTACCATGTGAATTGCATTGCACCGCTCAACGCTCATTGAGGGCCATGTTTCGATATGCTCCTGCCAATGCCATTCGCATGATATTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 335

TTCAGCGCTCCCCCGCCCCACGTTCCTTCAGAGCAAGTTAACACTGACTGGGAGCAGTTCGACTAGGCTCAGCTGAAGCTGTTGATGTATCGTGAGATCGgtatgggcat ... atgttaccagATCATACCATACTACCATGTGAATTGCATTGCACCGCTCAACGCTCATTGAGGGCCATGTTTCGATATGCTCCTGCCAATGCCATTCGCATGATATTTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgcaccgcgtttggtgcctttggtgtcctaactgcctgtgaatgttaccagATCATACCATACTACCATGTGAATTGCATTGCACCGCTCAACGCTCATTGAGGGCCATGTTTCGATATGCTCCTGCCAATGCCATTCGCATGATATTTAT
                             tcctaac  putative branch site (score: 335)
                                            aatgtta  TA-rich tract