Sequence
atgc intronic sequence ATGC exonic sequencegtatgttccatcaaaatttatcgtaaaataactgagctacagaatttcttgcatgactgaaaccttggcaaatatactcgaaacgatctgccatgattcttaatccaaccatttcatcccctggttgagtgttcactcatgcttttgatagGTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G040247_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os04g11880.3 (Oryza sativa), 3'ss of exon 15
gtatgttccatcaaaatttatcgtaaaataactgagctacagaatttcttgcatgactgaaaccttggcaa-atatactcgaaacgatctgccatgattcttaatccaaccatttcatcccctggtt-gagtgttcact-------catgcttttgatagGTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAG------------------
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----------------------------------------------------------gctatattgacactgtagaatagagatg--ctacaactttatttaatccaatccttctcttccctggttcaagtgttcattgaaatattacgcttttgatagGTTGCGGGATCGCCTTGTGAAAATTGTGACAGACTATCGAACAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAGGTTAATATTCAAGAAAAA
upper sequence: GRMZM2G040247_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os04g11880.1 (Oryza sativa), 3'ss of exon 17
gtatgttccatcaaaatttatcgtaaaataactgagctacagaatttcttgcatgactgaaaccttggcaa-atatactcgaaacgatctgccatgattcttaatccaaccatttcatcccctggtt-gagtgttcact-------catgcttttgatagGTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAG
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----------------------------------------------------------gctatattgacactgtagaatagagatg--ctacaactttatttaatccaatccttctcttccctggttcaagtgttcattgaaatattacgcttttgatagGTTGCGGGATCGCCTTGTGAAAATTGTGACAGACTATCGAACAGAAACTTCATTAAGACATGGGTGCAATGATATACTTAAGMapped 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|211348416|gb|FL045968.1|FL045968EST: GATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCG GTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTC
genomic: GATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCGgtatgttcca ... cttttgatagGTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTC
EST:
gi|71445370|gb|DR826420.1|DR826420EST: ATCCTCTGTACA-TGTTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCG GTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTC
genomic: ATCCTCTGTACATTG-TCAGTTTGGTTCCTGATGGCTTAGAAATACCTCGgtatgttcca ... cttttgatagGTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTC
EST:
gi|40303669|gb|CK348056.1|CK348056EST: TGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCG GTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTC
genomic: TGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCGgtatgttcca ... cttttgatagGTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTC
EST:
gi|74239642|gb|DT647556.1|DT647556EST: GATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCG GTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTC
genomic: GATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCGgtatgttcca ... cttttgatagGTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTC
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),
48 (downstream exon)
Score:
54GTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCGgtatgttcca ... cttttgatagGTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAG
Block sizes:
49 (upstream exon),
47 (downstream exon)
Score:
62GTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCGgtatgttcca ... cttttgatagGTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAG
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
124GTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCGgtatgttcca ... cttttgatagGTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAG
Block sizes:
46 (upstream exon),
48 (downstream exon)
Score:
92GTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCGgtatgttcca ... cttttgatagGTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttaatccaaccatttcatcccctggttgagtgttcactcatgcttttgatagGTTGCGGGATCGTCTTGTGAAAATTGTGACGGATTACCGGACAGAAACTTCATTGCGAAATGGATGCAACGATATACTTAAG
tcttaat putative branch site (score: 92)
tgctttt putative PPT
ttttgata TA-rich tract