Sequence
atgc intronic sequence ATGC exonic sequence...gggcgcagttctcctgcgctttcgagattttttttttgtcacagaccaatatcattctgatttctgagtatctatgtattaaggtggttttctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGATTGTGAAGTTCGTCTCTGGGATGCTAAAACATCTCGCTGCACAGCAGAAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G167886_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 5
gggcgcagttctcctgcgctttcgagattttttttttgtcacagaccaata-------tcattctgatttctgagtatctat-gtattaaggtggttttctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGATTGTGAAGTTCGTCTCTGGGATGCTAAAACATCTCGCTGCACAGCAGAAC
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--------caaactgttaattcagaaaaatgttttacaaaaaaaaacaatgttgaattttgtttcacttttttattacttgccataagaaattattgttgcaatgtagGTTAGATATCATCCATTACATCCTGATATCGTTGCTAGCGGAAGTTTGGATAATGAAGTTTGTCTATGGGATGCTAAAACCTCCCGTTGCATTGGATCACMapped 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|18385319|gb|BM418518.1|BM418518EST: CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG GTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT
genomic: CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT
EST:
gi|18384882|gb|BM418081.1|BM418081EST: CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG GTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGT
genomic: CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGT
EST:
gi|76015702|gb|DT942872.1|DT942872EST: CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGT- -T-AGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT
genomic: CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT
EST:
gi|22489334|gb|BU049257.1|BU049257EST: CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG GTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT
genomic: CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT
EST:
gi|87298785|gb|DY470788.1|DY470788EST: CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG GTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT
genomic: CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT
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:
48 (upstream exon),
41 (downstream exon)
Score:
48TGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGATTGTGAAGTTCGTCTCTGGGATGCTAAAACATCTCGCTGCACAGCAGAAC
Block sizes:
46 (upstream exon),
48 (downstream exon)
Score:
24TGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGATTGTGAAGTTCGTCTCTGGGATGCTAAAACATCTCGCTGCACAGCAGAAC
Block sizes:
48 (upstream exon),
45 (downstream exon)
Score:
31TGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGATTGTGAAGTTCGTCTCTGGGATGCTAAAACATCTCGCTGCACAGCAGAAC
Block sizes:
48 (upstream exon),
43 (downstream exon)
Score:
36TGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGATTGTGAAGTTCGTCTCTGGGATGCTAAAACATCTCGCTGCACAGCAGAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaatatcattctgatttctgagtatctatgtattaaggtggttttctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGATTGTGAAGTTCGTCTCTGGGATGCTAAAACATCTCGCTGCACAGCAGAAC
ttctgat putative branch site (score: 36)
ttttctgtt putative PPT
tatctatgtattaa TA-rich tract