Sequence
atgc intronic sequence ATGC exonic sequence...gttgtgtccaacaagatttatgggctgctcctcaacatacacatacttcatttgtatgataatggatgccatgtaactgactgtgttttgtattttgcagCCACAACATTAACTGGTCTTCATTTTGTGACAACCACCTTGATGACTATCGTGTTTCGGTGGTTAGGCCTCAGCCAGCCCTCCCACTTACCAATACCAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os12g05780.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g05780.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G014610_T01 (Zea mays), 3'ss of exon 2
-------------------------------------gttgtgtccaacaagatttatgggctgctcctcaacatacacatacttcatttgtatgataatggatgccatgtaactgactgtgttttgtattttgcagCCACAACATTAACTGGTCTTCATTTTGTGACAACCACCTTGATGACTATCGTGTTTCGGTGGTTAGGCCTCAGCCAGCCCTCCCACTTACCAATACCAGA
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gtgcgtgcatgtgttgtgtgcttgcttacctggggggatctcatctcacgcctctta-attttgactgtcattatttattaaccgcgctctcttcttcttgcttgcttcttgtgtggctccgtggcgtgtgctgcagCCACGACGTTAACGGGGCTGCATTTCGCGACCACCACCGTGATGACCCTCGTGTTCCGGTGGGTCGGCCTCAGCCAGCCGTCGCAGCTGCCGTTACCGGA
upper sequence: LOC_Os12g05780.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G147446_T01 (Zea mays), 3'ss of exon 2
gttgtgtccaacaagatttatgggc-tgctcctcaacatacacat--acttcatttgtatgataatggatgccatgtaactgactgtgttttg----tattttgcagCCACAACATTAACTGGTCTTCATTTTGTGACAACCACCTTGATGACTATCGTGTTTCGGTGGTTAGGCCTCAGCCAGCCCTCCCACTTACCAATACCAGA
| || |||| ||| | | ||| ||| | ||| | | | | ||| || ||||| | | | | |||| | |||| |||||||||||||||| || |||||||||||||| || ||||||||||||||| | ||||| ||||||||||| || ||||| ||||||||||| || ||||
-------tctaccgtatttctggacattctcaacaaagtgtgcatcgatgtgaacttggatatatctcctgtcatgtcattaattaccttttcctcttttttttcagCCACAACATTAACCGGGCTTCATTTTGTGACTACTACCTTGATGACTATCTTATTTCGTTGGTTAGGCCTGAGTCAGCCATCCCACTTACCCCTAGCAGA
upper sequence: LOC_Os12g05780.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G071378_T02 (Zea mays), 3'ss of exon 2
gttgtgtccaacaagatttatgggc-tgctc--ctcaacatacacatacttcatttgtatgataatggatgccatgtaactgactgtgttttgtat-------tttgcagCCACAACATTAACTGGTCTTCATTTTGTGACAACCACCTTGATGACTATCGTGTTTCGGTGGTTAGGCCTCAGCCAGCCCTCCCACTTACCAATACCAGA
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----------accatatttctgcgcattctcagctaaatatgcatggatgtgaacttggatatatctcctgtcatgtcgttgattaccttttctctctctttttttccagCCACGACATTAACTGGGCTTCATTTTGTGACCACTACCTTGATGACTATTGTATTTCGATGGTTAGGCCTGAGCCAGCCATCCCACTTACCCCTAGCAGAMapped 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|218493260|gb|FG949071.1|FG949071EST: AATCATCATGGTCAACAAGGCTCTGATGGCTACACATGGATTCAGTTTCG CCACAACATTAACTGGTCTTCATTTTGTGACAACCACCTTGATGACTATCG
genomic: AATCATCATGGTCAACAAGGCTCTGATGGCTACACATGGATTCAGTTTCGgtatgttttt ... tattttgcagCCACAACATTAACTGGTCTTCATTTTGTGACAACCACCTTGATGACTATCG
EST:
gi|44674789|gb|CR288223.1|CR288223EST: AATCATCATGGTCAACAAGGCTCTGATGGCTACACATGGATTCAGTTTCG CCACAACATTAACTGGTCTTCATTTTGTGACAACCACCTTGATGACTATCG
genomic: AATCATCATGGTCAACAAGGCTCTGATGGCTACACATGGATTCAGTTTCGgtatgttttt ... tattttgcagCCACAACATTAACTGGTCTTCATTTTGTGACAACCACCTTGATGACTATCG
EST:
gi|58595545|gb|CK006073.1|CK006073EST: AATCATCATGGTCAACAAGGCTCTGATGGCTACACATGGATTCAGTTTCG CCACGACATTAACTGGTCTTCATTTTGTGACAACCACCTTGATGACTATCG
genomic: AATCATCATGGTCAACAAGGCTCTGATGGCTACACATGGATTCAGTTTCGgtatgttttt ... tattttgcagCCACAACATTAACTGGTCTTCATTTTGTGACAACCACCTTGATGACTATCG
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 1 RNA-Seqlibrary.
Block sizes:
34 (upstream exon),
42 (downstream exon)
Score:
1AAGGTGCTAGATTTTGCGGCATGGAGTTTCAACATCACCACATCCGTTGGAATCATCATGGTCAACAAGGCTCTGATGGCTACACATGGATTCAGTTTCGgtatgttttt ... tattttgcagCCACAACATTAACTGGTCTTCATTTTGTGACAACCACCTTGATGACTATCGTGTTTCGGTGGTTAGGCCTCAGCCAGCCCTCCCACTTACCAATACCAGA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcatttgtatgataatggatgccatgtaactgactgtgttttgtattttgcagCCACAACATTAACTGGTCTTCATTTTGTGACAACCACCTTGATGACTATCGTGTTTCGGTGGTTAGGCCTCAGCCAGCCCTCCCACTTACCAATACCAGA
aactgac putative branch site (score: 1)
ttttgtatttt TA-rich tract