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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAACAGCAAACAAGTTGCTCGAACACCCATTTATCCAAACTTTGAACCACTACAGCCCACATAGCGTTGTACATTCATTTTCGGGAATTAAATCTCCAgtaagctttctgactttctccttatgacatgtgatatccaaagtttcaacttaaagctttatgcatatgtataattggcttgttggtgtcag

Basic information

species Zea mays
transcript GRMZM2G156800_T01
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|211137994|gb|FL439623.1|FL439623
EST:     ACTACAGCCCACATAGCGTTGTACATTCATTTTCGGGAATTAAATCTCCA                         GATACTGTGCMCAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCA
genomic: ACTACAGCCCACATAGCGTTGTACATTCATTTTCGGGAATTAAATCTCCAgtaagctttc ... ttggtgtcagGATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCA
EST: gi|33094498|gb|CF054492.1|CF054492
EST:     GTACATTCATTTTCGGCAATTAAATCTCCA                         GATACTGTGCACAGCAGTGCAAGAGATAAAGTAACCTGGAAAAGTGATTCA
genomic: GTACATTCATTTTCGGGAATTAAATCTCCAgtaagctttc ... ttggtgtcagGATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCA
EST: gi|166573023|gb|EG319912.1|EG319912
EST:     CGGGAATTAAATCTCCA                         GATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCA
genomic: CGGGAATTAAATCTCCAgtaagctttc ... ttggtgtcagGATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCA
EST: gi|33095640|gb|CF055634.1|CF055634
EST:     ACATTCATTTTCGGGAATTAAATCTCCC                         GATACTGTGCACAGCAGTGCAAGAGATAAAGTAACCTGGAAAAGTGATTCA
genomic: ACATTCATTTTCGGGAATTAAATCTCCAgtaagctttc ... ttggtgtcagGATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCA
EST: gi|71427641|gb|DR808691.1|DR808691
EST:     ATAGCGTTGTACATTCATTTTCGGGAATTAAATCTCCA                         GATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCA
genomic: ATAGCGTTGTACATTCATTTTCGGGAATTAAATCTCCAgtaagctttc ... ttggtgtcagGATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCA
EST: gi|60345120|gb|DN212093.1|DN212093
EST:     ACTACAGCCCACATAGCGTTGTACATTCATTTTCGGGAATTAAATCTCCA                         GATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCA
genomic: ACTACAGCCCACATAGCGTTGTACATTCATTTTCGGGAATTAAATCTCCAgtaagctttc ... ttggtgtcagGATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCA

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), 47 (downstream exon)
Score: 79

ACCAACAGCAAACAAGTTGCTCGAACACCCATTTATCCAAACTTTGAACCACTACAGCCCACATAGCGTTGTACATTCATTTTCGGGAATTAAATCTCCAgtaagctttc ... ttggtgtcagGATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 73

ACCAACAGCAAACAAGTTGCTCGAACACCCATTTATCCAAACTTTGAACCACTACAGCCCACATAGCGTTGTACATTCATTTTCGGGAATTAAATCTCCAgtaagctttc ... ttggtgtcagGATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 126

ACCAACAGCAAACAAGTTGCTCGAACACCCATTTATCCAAACTTTGAACCACTACAGCCCACATAGCGTTGTACATTCATTTTCGGGAATTAAATCTCCAgtaagctttc ... ttggtgtcagGATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 73

ACCAACAGCAAACAAGTTGCTCGAACACCCATTTATCCAAACTTTGAACCACTACAGCCCACATAGCGTTGTACATTCATTTTCGGGAATTAAATCTCCAgtaagctttc ... ttggtgtcagGATACTGTGCACAGCAGTGCAAGAGATAAAGTACCCTGGAAAAGTGATTCATATATGAGAGGGAAACATGCAAATGG