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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACTGCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtaccaagcagtttaacactatctgccctttcgaaaatcgtaagcaccatcttcggattgccttggggctttctttggcaattgctcatgctgatg...

Basic information

species Zea mays
transcript GRMZM2G019812_T02
intron # 9
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|18180597|gb|BM381807.1|BM381807
EST:     GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAG--ACA                         --CA-GAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCC
genomic: GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... ggttacgaagTGCAGGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCC
EST: gi|148956071|gb|EC901822.2|EC901822
EST:     GCATGTCAAGCCAGCAGTTGGTGGATTTCATCCGCGAGCATATAGACACA                         -G-AGGA--AA-GCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCC
genomic: GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... ggttacgaagTGCAGGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCC
EST: gi|14244484|gb|BG842495.2|BG842495
EST:     GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAG--ACA                         --CA-GAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCC
genomic: GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... ggttacgaagTGCAGGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCC
EST: gi|3157148|gb|AA979770.1|AA979770
EST:     GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACA                         -G-AGGA--AA-GCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCC
genomic: GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... ggttacgaagTGCAGGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCC
EST: gi|9742960|gb|BE519108.1|BE519108
EST:     GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACA                         TGCAGGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCC
genomic: GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... ggttacgaagTGCAGGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCC

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: 100

GGACTGCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... ggttacgaagTGCAGGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCTCCGTCGACCATGGGCGGCGAGGGATGCGATAACATGACGATGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

GGACTGCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... ggttacgaagTGCAGGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCTCCGTCGACCATGGGCGGCGAGGGATGCGATAACATGACGATGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

GGACTGCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... ggttacgaagTGCAGGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCTCCGTCGACCATGGGCGGCGAGGGATGCGATAACATGACGATGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

GGACTGCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... ggttacgaagTGCAGGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCTCCGTCGACCATGGGCGGCGAGGGATGCGATAACATGACGATGAT