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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTACCCACCACAACCATATGAGCGATCTTACCCACCGCAACCATATGGGCAACAACCATACCCACCCCCGCCAGCAGCAGAGTCGCCGTACCCACCAGgtgagatgcaattcagcagagaaaattccatcttttttcatgatgttagtcaatgctctaactggatcgcctccctttgcctcgtttgatcttatgcag

Basic information

species Zea mays
transcript GRMZM2G704277_T01
intron # 5
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|213183073|gb|FM191381.1|FM191381
EST:     GCAACAACCATACCCGCCCCCGCCAGCAGCAGAGTCGCCGTACCCACCAG                         CGCCTTACCCTGGTACTTATCCACCAAGACCCTATTGATATAGCAGCGTCA
genomic: GCAACAACCATACCCACCCCCGCCAGCAGCAGAGTCGCCGTACCCACCAGgtgagatgca ... tcttatgcagCGCCTTACCCTGGTACTTATCCACCAAGACCCTATTGATATAGCAGCGTCA
EST: gi|32793577|gb|CD945813.1|CD945813
EST:     GCAACAACCATACCCGCCCCCGCCAGCAGCAGAGTCGCCGTACCCACCAG                         CGCCTTACCCTGGTACTTATCCACCAAGACCCTATTGATATAGCAGCGTCA
genomic: GCAACAACCATACCCACCCCCGCCAGCAGCAGAGTCGCCGTACCCACCAGgtgagatgca ... tcttatgcagCGCCTTACCCTGGTACTTATCCACCAAGACCCTATTGATATAGCAGCGTCA
EST: gi|94477275|gb|EB706233.1|EB706233
EST:     GCAACAACCATACCCACCCCCGCCAGCAGCAGAGTCGCCGTACCCACCAG                         CGCCTTACCCTGGTACTTATCCACCAAGACCCTATTGATATAGCAGCGTCA
genomic: GCAACAACCATACCCACCCCCGCCAGCAGCAGAGTCGCCGTACCCACCAGgtgagatgca ... tcttatgcagCGCCTTACCCTGGTACTTATCCACCAAGACCCTATTGATATAGCAGCGTCA
EST: gi|89251013|gb|DY622799.1|DY622799
EST:     GCAACAACCATACCCACCCCCGCCAGCAGCAGAGTCGCCGTACCCACCAG                         CGCCTTACCCTGGTACTTATCCACCAAGACCCTATTGATATAGCAGCGTCA
genomic: GCAACAACCATACCCACCCCCGCCAGCAGCAGAGTCGCCGTACCCACCAGgtgagatgca ... tcttatgcagCGCCTTACCCTGGTACTTATCCACCAAGACCCTATTGATATAGCAGCGTCA

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: 41

TCTTACCCACCACAACCATATGAGCGATCTTACCCACCGCAACCATATGGGCAACAACCATACCCACCCCCGCCAGCAGCAGAGTCGCCGTACCCACCAGgtgagatgca ... tcttatgcagCGCCTTACCCTGGTACTTATCCACCAAGACCCTATTGATATAGCAGCGTCAGTAATGATCTCAGGTAGAGGCATCAAAAGCAACAAACAACAGCCTTGAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 43

TCTTACCCACCACAACCATATGAGCGATCTTACCCACCGCAACCATATGGGCAACAACCATACCCACCCCCGCCAGCAGCAGAGTCGCCGTACCCACCAGgtgagatgca ... tcttatgcagCGCCTTACCCTGGTACTTATCCACCAAGACCCTATTGATATAGCAGCGTCAGTAATGATCTCAGGTAGAGGCATCAAAAGCAACAAACAACAGCCTTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54

TCTTACCCACCACAACCATATGAGCGATCTTACCCACCGCAACCATATGGGCAACAACCATACCCACCCCCGCCAGCAGCAGAGTCGCCGTACCCACCAGgtgagatgca ... tcttatgcagCGCCTTACCCTGGTACTTATCCACCAAGACCCTATTGATATAGCAGCGTCAGTAATGATCTCAGGTAGAGGCATCAAAAGCAACAAACAACAGCCTTGAT


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 33

TCTTACCCACCACAACCATATGAGCGATCTTACCCACCGCAACCATATGGGCAACAACCATACCCACCCCCGCCAGCAGCAGAGTCGCCGTACCCACCAGgtgagatgca ... tcttatgcagCGCCTTACCCTGGTACTTATCCACCAAGACCCTATTGATATAGCAGCGTCAGTAATGATCTCAGGTAGAGGCATCAAAAGCAACAAACAACAGCCTTGAT