Sequence
atgc intronic sequence ATGC exonic sequencegtttaaaaccttatctagcttaattgtgattgccttgattatgccattatagaacttaatatttggatgtattatgcgactaagacatattacctttcttctctgttgaaaagGCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCATGGTTTTGTTCCTCCATTCTTGGCACGTCCTTATCTGCAAACAAATGTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G080930_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g54770.1 (Oryza sativa), 3'ss of exon 6
gtttaaaaccttatctagcttaat-tgtgattgccttgattatgccattatagaacttaatatttggatgtattatgcgactaagacatattacctttcttctctgt--tgaaaagGCAT-GTTCTGCTTAAACGACTCGGCCAACTAC-GGCTCTCAGTTAGTCTTCATGGTTTTGTTC------CTCCATTCTTGGCACGTCCTTATCTGCAAACAAATGTC
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gtttactactttatctgccttgatatttcagcctcttatttctgacgttaaaaaacttatgggatggatgtaatatgcaactaagacatattacctttctactatgtgctaaagAGGGATCATTCTGCTTAAGCGACTCAGCCAACTACCGGCTCT------GTCTGCATGGTTTTGTTCTGCACTCTTCATTCCTCGAGCGTG-TTGCCTGCTT-CATGTG--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|93284594|gb|EB676858.1|EB676858EST: CAACTGCATGACTTCAGTTCAG GCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCA
genomic: CAACTGCATGACTTCAGTTCAGgtttaaaacc ... tgttgaaaagGCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCA
EST:
gi|6102005|gb|AW126475.1|AW126475EST: CATGACTTCAGTTCAG GCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCA
genomic: CATGACTTCAGTTCAGgtttaaaacc ... tgttgaaaagGCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCA
EST:
gi|60342272|gb|DN209245.1|DN209245EST: TCAGGAACAAATTTGGAACTGTCGTCAACTGCATGACTTCAGTTCAG GCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCA
genomic: TCAGGAACAAATTTGGAACTGTCGTCAACTGCATGACTTCAGTTCAGgtttaaaacc ... tgttgaaaagGCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCA
EST:
gi|67013664|gb|CO442413.1|CO442413EST: CTGTCAGGAACAAATTTGGAACTGTCGTCAACTGCATGACTTCAGTTCAG GCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCA
genomic: CTGTCAGGAACAAATTTGGAACTGTCGTCAACTGCATGACTTCAGTTCAGgtttaaaacc ... tgttgaaaagGCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCA
EST:
gi|76911951|gb|DV164503.1|DV164503EST: CTGTCAGGAACAAATTTGGAACTGTCGTCAACTGCATGACTTCAGTTCAG GCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCA
genomic: CTGTCAGGAACAAATTTGGAACTGTCGTCAACTGCATGACTTCAGTTCAGgtttaaaacc ... tgttgaaaagGCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCA
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:
47 (upstream exon),
39 (downstream exon)
Score:
10GAAGCCCGTGCCTGATACTTCTTGGTGTGAGAACTTAGTCCTTGGTTTGGCTGTCAGGAACAAATTTGGAACTGTCGTCAACTGCATGACTTCAGTTCAGgtttaaaacc ... tgttgaaaagGCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCATGGTTTTGTTCCTCCATTCTTGGCACGTCCTTATCTGCAAACAAATGTC
Block sizes:
20 (upstream exon),
30 (downstream exon)
Score:
2GAAGCCCGTGCCTGATACTTCTTGGTGTGAGAACTTAGTCCTTGGTTTGGCTGTCAGGAACAAATTTGGAACTGTCGTCAACTGCATGACTTCAGTTCAGgtttaaaacc ... tgttgaaaagGCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCATGGTTTTGTTCCTCCATTCTTGGCACGTCCTTATCTGCAAACAAATGTC
Block sizes:
49 (upstream exon),
40 (downstream exon)
Score:
5GAAGCCCGTGCCTGATACTTCTTGGTGTGAGAACTTAGTCCTTGGTTTGGCTGTCAGGAACAAATTTGGAACTGTCGTCAACTGCATGACTTCAGTTCAGgtttaaaacc ... tgttgaaaagGCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCATGGTTTTGTTCCTCCATTCTTGGCACGTCCTTATCTGCAAACAAATGTC
Block sizes:
46 (upstream exon),
42 (downstream exon)
Score:
6GAAGCCCGTGCCTGATACTTCTTGGTGTGAGAACTTAGTCCTTGGTTTGGCTGTCAGGAACAAATTTGGAACTGTCGTCAACTGCATGACTTCAGTTCAGgtttaaaacc ... tgttgaaaagGCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCATGGTTTTGTTCCTCCATTCTTGGCACGTCCTTATCTGCAAACAAATGTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatttggatgtattatgcgactaagacatattacctttcttctctgttgaaaagGCATGTTCTGCTTAAACGACTCGGCCAACTACGGCTCTCAGTTAGTCTTCATGGTTTTGTTCCTCCATTCTTGGCACGTCCTTATCTGCAAACAAATGTC
acttaat putative branch site (score: 6)
ttacctttcttctctg putative PPT
atgtattat TA-rich tract