Sequence
atgc intronic sequence ATGC exonic sequencegtacttctgtttcaattgtataaatgattttaattattccttttcacatgttttcatatttcaatctgttgctatttgatctggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACACTAGTGTTCAATTTGTGAGAGACAGTGTAAAGCTTCTGCGCCCTTCTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G080044_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g11140.1 (Oryza sativa), 3'ss of exon 4
---------------gtacttctgtttcaattgtataaatgatt-ttaattattccttttcacatgttttcatatttcaatctgttgctatttgatctggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACACTAGTGTTCAATTTGTGAGAGACAGTGTAAAGCTTCTGCGCCCTTCTGA
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gtaatgtagtttgaagtataaaaatactgctagtgtatattataatttactggattttatcatatggtttcatgtttttaaatgtgaaactatgatttggtcggcagAAGTGGATGTTTGGGAGATAGCTCCATCATTTACAGAGTTACTGAAGAACACTAGTGTTCAATTCGTGAAGGATAGTGTAAAGCTTCTGCGCCCTTCTGAMapped 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|76934119|gb|DV173742.1|DV173742EST: CGAGCTATTGTCAGGAG AAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACA
genomic: CGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACA
EST:
gi|30306789|gb|CD001462.1|CD001462EST: ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAG AAGTGGATATCTGGGAGATAGCTCCATC
genomic: ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATC
EST:
gi|29543792|gb|CB604172.1|CB604172EST: ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAG AAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACA
genomic: ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACA
EST:
gi|31998276|gb|CD662009.1|CD662009EST: ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAG AAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACA
genomic: ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACA
EST:
gi|211318168|gb|FL216126.1|FL216126EST: ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAG AAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGT
genomic: ATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGT
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:
37 (upstream exon),
48 (downstream exon)
Score:
26GTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACACTAGTGTTCAATTTGTGAGAGACAGTGTAAAGCTTCTGCGCCCTTCTGA
Block sizes:
45 (upstream exon),
38 (downstream exon)
Score:
20GTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACACTAGTGTTCAATTTGTGAGAGACAGTGTAAAGCTTCTGCGCCCTTCTGA
Block sizes:
43 (upstream exon),
41 (downstream exon)
Score:
9GTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACACTAGTGTTCAATTTGTGAGAGACAGTGTAAAGCTTCTGCGCCCTTCTGA
Block sizes:
45 (upstream exon),
48 (downstream exon)
Score:
12GTTCTTCTGGTTGATCAATCTGATAAATTTGTATTTAAACCCATGTTGTACGAGCTATTGTCAGGAGgtacttctgt ... tggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACACTAGTGTTCAATTTGTGAGAGACAGTGTAAAGCTTCTGCGCCCTTCTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccttttcacatgttttcatatttcaatctgttgctatttgatctggttgccagAAGTGGATATCTGGGAGATAGCTCCATCTTTTACAGAGTTGCTGAAAAACACTAGTGTTCAATTTGTGAGAGACAGTGTAAAGCTTCTGCGCCCTTCTGA
atttgat putative branch site (score: 12)
ttttcatatttcaat TA-rich tract