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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCGCATACTACGCAGCGGGCGCCTTGGGAGGCGCCGCGGCCTGCGGGTTCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAGgtgcgtgcagtgcctgagttcacgggaaccatcgctttctttgcccgtccgactactgccaaattccgggaccccggtttcgatcacaccagtgttctaacaaacgccacatgatatctcggtcgtcgcag

Basic information

species Zea mays
transcript GRMZM2G009045_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|148932947|gb|EE285780.2|EE285780
EST:     TCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAG                         ATCGACCCCGCCAAGTACAAGAACACCTCGTCGGCGTTCAGCGTGGTGATG
genomic: TCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAGgtgcgtgcag ... gtcgtcgcagATCGACCCCGCCAAGTACAAGAACACCTCGTCGGCGTTCAGCGTGGTGATG
EST: gi|91051907|gb|EB162325.1|EB162325
EST:     TCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAG                         ATCGACCCCGCCAAGTACAAGAACACCTCGTCGGCGTTCAGCGTGGTGATG
genomic: TCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAGgtgcgtgcag ... gtcgtcgcagATCGACCCCGCCAAGTACAAGAACACCTCGTCGGCGTTCAGCGTGGTGATG
EST: gi|13150488|gb|BG320810.1|BG320810
EST:     TCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAG                         ATCGACCCCGCCAAGTACAAGAACACCTCGTCGGCGTTCAGCGTGTGTGAT
genomic: TCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAGgtgcgtgcag ... gtcgtcgcagATCGACCCCGCCAAGTACAAGAACACCTCGTCGGCGTTCAGCGTG-GTGAT
EST: gi|211020550|gb|FL192315.1|FL192315
EST:     TCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAG                         ATCGACCCCGCCAAGTACAAGAACACCTCGTCGGCGTTCAGCGTGGTGATG
genomic: TCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAGgtgcgtgcag ... gtcgtcgcagATCGACCCCGCCAAGTACAAGAACACCTCGTCGGCGTTCAGCGTGGTGATG
EST: gi|149096561|gb|EE182315.2|EE182315
EST:     TCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAG                         ATCGACCCCGCCAAGTACAAGAACACCTCGTCGGCGTTCAGCGTGGTGATG
genomic: TCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAGgtgcgtgcag ... gtcgtcgcagATCGACCCCGCCAAGTACAAGAACACCTCGTCGGCGTTCAGCGTGGTGATG
EST: gi|149104489|gb|EE289936.2|EE289936
EST:     TCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAG                         ATCGACCCCGCCAAGTACAAGAACACCTCGTCGGCGTTCAGCGTGGTGATG
genomic: TCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAGgtgcgtgcag ... gtcgtcgcagATCGACCCCGCCAAGTACAAGAACACCTCGTCGGCGTTCAGCGTGGTGATG

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 407

GCCCGCATACTACGCAGCGGGCGCCTTGGGAGGCGCCGCGGCCTGCGGGTTCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAGgtgcgtgcag ... gtcgtcgcagATCGACCCCGCCAAGTACAAGAACACCTCGTCGGCGTTCAGCGTGGTGATGAGGGAGCAGGGCCTCCGGGGCTTCTACAGGGGGTGGGCGCCGACGTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 279

GCCCGCATACTACGCAGCGGGCGCCTTGGGAGGCGCCGCGGCCTGCGGGTTCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAGgtgcgtgcag ... gtcgtcgcagATCGACCCCGCCAAGTACAAGAACACCTCGTCGGCGTTCAGCGTGGTGATGAGGGAGCAGGGCCTCCGGGGCTTCTACAGGGGGTGGGCGCCGACGTTCG


Block sizes: 46 (upstream exon), 11 (downstream exon)
Score: 3

GCCCGCATACTACGCAGCGGGCGCCTTGGGAGGCGCCGCGGCCTGCGGGTTCACGCACGCCGCCGTCACGCCGCTCGACGTCATCAAGTGCAATATCCAGgtgcgtgcag ... gtcgtcgcagATCGACCCCGCCAAGTACAAGAACACCTCGTCGGCGTTCAGCGTGGTGATGAGGGAGCAGGGCCTCCGGGGCTTCTACAGGGGGTGGGCGCCGACGTTCG