Sequence
atgc intronic sequence ATGC exonic sequencegtatttatcagttggatataagctgtaaataaattatttctctgttattgatatctaatccacctggtcatcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 6
gtatttatc--agttggatataagctgtaaataaat---tatt-----tctctgttattgatatctaatccacctggtcatctttt--------ctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA
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gtatttatcttggatccacactagtcgagaaacaatggatattgctgttcttggttctcgtgctctgatccatttggcaaaattttactgtgttctagTGTTGGCTTAGCACATAGGGAAGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCTGA
upper sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 6
---gtatttatcagttggat-ataagct--gtaaataaattatt--tctctgttattgatat-ctaatccacctggtcatcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA
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gtaatatttgtaacctgcattatctttttggttaaagaaatattgatcttgacgacctatttgctgatttatcca-ccgtattttc-agTATCGGCCTGACAGAGAGAGAGGAAGGCGACCTTGGACCTGTATACGGATTTCAATGGCGACACTTTGGTGCTAA
upper sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatttatcagttggatataagctgtaaataaattatttctctgttattgatatctaatccacctggtcatcttt---tctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA
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gtaaactttaattcagcatttttctttcacaacttgaagctttgtggccattacactgataaattgaaagtttttaatttcagTATTGGACTGACTGAGAGAGAGGAAGGTGACCTTGGACCCGTTTATGGATTTCAGTGGAGACACTTTGGTGCTAAMapped 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|84980638|gb|DW530987.1|DW530987EST: AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGATCG TATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT
genomic: AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT
EST:
gi|32838087|gb|CD977765.1|CD977765EST: AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCG TATTGACTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT
genomic: AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT
EST:
gi|67012996|gb|CO441745.1|CO441745EST: AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCG TATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT
genomic: AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT
EST:
gi|32930437|gb|CF035249.1|CF035249EST: AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCG TATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT
genomic: AAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATT
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),
49 (downstream exon)
Score:
114GTTTTGCAAGAAAAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
62GTTTTGCAAGAAAAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA
Block sizes:
47 (upstream exon),
49 (downstream exon)
Score:
45GTTTTGCAAGAAAAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
37GTTTTGCAAGAAAAGGGTATTCATATCTGGGATGGCAATGCTTCAAGAGAGTATCTTGACCGgtatttatca ... tcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaataaattatttctctgttattgatatctaatccacctggtcatcttttctagTATTGGCTTGGCACACAGGGAGGAAGGTGATCTAGGTCCAGTTTATGGATTTCAATGGCGACACTTTGGTGCCGA
atctaat putative branch site (score: 37)
tcatcttttct putative PPT
ttattgatatctaat TA-rich tract