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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGAGGCAGGCCCCAATGGCGTTGGCTCGCCTCCGCCTCCTCGACCGCTACGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcactagagccgttcgacggaatgccgctgcggaatggggttgactgctgaccgtgtctcccttgacattggggctgtcgtttctccctacag

Basic information

species Zea mays
transcript GRMZM2G040945_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|71771543|gb|DR969480.1|DR969480
EST:     CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAG                         ACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
genomic: CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
EST: gi|76020827|gb|DT947997.1|DT947997
EST:     CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAG                         ACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
genomic: CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
EST: gi|211297219|gb|FL425381.1|FL425381
EST:     CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAG                         ACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
genomic: CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
EST: gi|76020213|gb|DT947383.1|DT947383
EST:     CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAG                         ACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
genomic: CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
EST: gi|211377248|gb|FL413757.1|FL413757
EST:     CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAG                         ACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
genomic: CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
EST: gi|148971904|gb|EE022679.2|EE022679
EST:     CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAG                         ACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
genomic: CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
EST: gi|76915905|gb|DV166160.1|DV166160
EST:     CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAG                         ACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
genomic: CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
EST: gi|148935914|gb|EC879965.2|EC879965
EST:     CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAG                         ACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
genomic: CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
EST: gi|76925058|gb|DV170275.1|DV170275
EST:     CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAG                         ACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
genomic: CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
EST: gi|211082071|gb|FL392683.1|FL392683
EST:     CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAG                         ACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
genomic: CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
EST: gi|93283038|gb|EB675302.1|EB675302
EST:     CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAG                         ACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
genomic: CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
EST: gi|71417284|gb|DR803998.1|DR803998
EST:     CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAG                         ACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
genomic: CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
EST: gi|78111525|gb|DV529922.1|DV529922
EST:     CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAG                         ACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG
genomic: CGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCG

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: 43 (upstream exon), 45 (downstream exon)
Score: 41

TCGAGGCAGGCCCCAATGGCGTTGGCTCGCCTCCGCCTCCTCGACCGCTACGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCGAGGACGAGATCGAGCGCATCCGCCGCGAGTTCGATGACGCCAAGCGCAA


Block sizes: 25 (upstream exon), 48 (downstream exon)
Score: 4

TCGAGGCAGGCCCCAATGGCGTTGGCTCGCCTCCGCCTCCTCGACCGCTACGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCGAGGACGAGATCGAGCGCATCCGCCGCGAGTTCGATGACGCCAAGCGCAA


Block sizes: 41 (upstream exon), 19 (downstream exon)
Score: 7

TCGAGGCAGGCCCCAATGGCGTTGGCTCGCCTCCGCCTCCTCGACCGCTACGGTCTCCTGTCGCCGGCGCTCTCTGCGACGGCGCTGCGGTCCTTGGGAGgttgttgcac ... ctccctacagACCTGCGCGCGCTCTGCACGCTCTCCACCACGCTGCGGTCCGGCGCCGGCGAGGACGAGATCGAGCGCATCCGCCGCGAGTTCGATGACGCCAAGCGCAA