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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttcggtttgctggtcattgtgctcggtatacagcctgcatatatttggctgtagctaacatatgactggtgattattttctccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG

Basic information

species Zea mays
transcript GRMZM2G147256_T02
intron # 2
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|71299596|gb|DR785811.1|DR785811
EST:     CACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCG                         GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
genomic: CACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
EST: gi|76912287|gb|DV164658.1|DV164658
EST:     AGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCG                         GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
genomic: AGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
EST: gi|101397910|gb|EB820832.1|EB820832
EST:     TTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCG                         GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
genomic: TTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
EST: gi|149098292|gb|EE184260.2|EE184260
EST:     CACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCG                         GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
genomic: CACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
EST: gi|89763649|gb|DY690753.1|DY690753
EST:     GTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCG                         GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
genomic: GTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
EST: gi|94474055|gb|EB703013.1|EB703013
EST:     CACTGGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCG                         GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
genomic: CACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
EST: gi|84970143|gb|DW468493.1|DW468493
EST:     CACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCG                         GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
genomic: CACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
EST: gi|78124407|gb|DV542791.1|DV542791
EST:     CACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCG                         GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
genomic: CACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
EST: gi|93284471|gb|EB676735.1|EB676735
EST:     TAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCG                         GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
genomic: TAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
EST: gi|78119582|gb|DV537966.1|DV537966
EST:     CACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCG                         GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
genomic: CACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
EST: gi|78124376|gb|DV542760.1|DV542760
EST:     CACTTAGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCG                         GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
genomic: CACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
EST: gi|71758972|gb|DR956909.1|DR956909
EST:     AC-TGGAGGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCG                         GTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT
genomic: ACTTGGA-GTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGT

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: 20

GCACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 75

GCACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 35

GCACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG


Block sizes: 46 (upstream exon), 32 (downstream exon)
Score: 34

GCACTTGGAGTTCCTGTAGATAGACTCGTGAAAGCTGCTGATTCAGTTTCGgtatgtttcg ... ccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatatatttggctgtagctaacatatgactggtgattattttctccggaactagGTATGCCTATCGAAAGGGTTAGGCGCACCCGTCGGATCAGTGATTGTTGGTTCGAAGGCCTTCATTGACAAG
                agctaac  putative branch site (score: 34)
                                    ttattttctcc  putative PPT
                                 tgattatttt  TA-rich tract