Sequence
atgc intronic sequence ATGC exonic sequencegtcagcattgctagagctagtacatatattgctccctccctgatatttttcttttcgtaaatttcatagtaacaacaagttacctttttcagGGGTATGTCCAGTGCACATGCGATCTTTATCACAGCTATATCATTATATCTTGTCATGTCTACAGATCTTTTCTCTGATCGCCTTAAGGGGCCTATCACA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g46410.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g46410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G132084_T04 (Zea mays), 3'ss of exon 4
gtcagcat----tgctagagctagtacatatattgctccctccctgatatttttcttttcgtaaatttcatagtaacaacaagtta--cctttttcagGGGTATGTCCAGTGCACATGCGATCTTTATCACAGCTATATCATTATATCTTGTCATGTCTACAGATCTTTTCTCTGATCGCCTTAAGGGGCCTATCACA
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gtaagtatattgtgtcagagctagtatacctatacacatgttcc----atctttcatttcagaaacttcatgctgatgacgaattatacttgttttagGGGTATGTCCAGCGCACATGCAATTTTTATCACGGCTGTATCATTATATATTGTCACGTCGACTGATCTTTTCTCCGATTGTGTCAAGGGGCCTATTACA
upper sequence: LOC_Os03g46410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G016184_T02 (Zea mays), 3'ss of exon 3
gtcagcattgc--tagagctagtacatatattgctccctccctgatatttttcttttcgtaaatttcatagtaacaacaagtt---acct-ttttcagGGGTATGTCCAGTGCACATGCGATCTTTATCACAGCTATATCATTATATCTTGTCATGTCTACAGATCTTTTCTCTGATCGCCTTAAGGGGCCTATCACA
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gtcagtattgtgtcagaactagtacacctatactcatgttcc----attttccatttcagaaacttcacactgatgaccaatttatacatgtttttagGGGTATGTCCAGCGCTCATGCAATTTTTATCACGGCTGTATCATTATATCTTGTCATGTCAACTGATCTTTTCTCCGACCGCGTCAAGGGACCTATTACA
upper sequence: LOC_Os03g46410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G016184_T01 (Zea mays), 3'ss of exon 3
gtcagcattgc--tagagctagtacatatattgctccctccctgatatttttcttttcgtaaatttcatagtaacaacaagtt---acct-ttttcagGGGTATGTCCAGTGCACATGCGATCTTTATCACAGCTATATCATTATATCTTGTCATGTCTACAGATCTTTTCTCTGATCGCCTTAAGGGGCCTATCACA------------------------------------
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gtcagtattgtgtcagaactagtacacctatactcatgttcc----attttccatttcagaaacttcacactgatgaccaatttatacatgtttttaggggtatgtccagcgctcatgcaatttttatcacggctgtatcattatatcttgtcatgtcaactgatcttttctccgaccgcgtcaaGGGACCTATTACATTCCGTTATTCGATAATATCCACCTCTGCGTTGGGG
upper sequence: LOC_Os03g46410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G132084_T01 (Zea mays), 3'ss of exon 3
---gtcagcattgctagagctagtacatatattgctccctccctgatatttttcttttcgtaaatttcatagtaacaacaagtta--cctttttcagGGGTATGTCCAGTGCACATGCGATCTTTATCACAGCTATATCATTATATCTTGTCATGTCTACAGATCTTTTCTCTGATCGCCTTAAGGGGCCTATCACA------------------------------------
|| || |||||||||| | ||| | || || |||| |||| ||| ||||| | | || | ||| | | ||| |||||||||||||| |||||||| || |||||||| ||| ||||||||||| |||||| ||| || ||||||||||| ||| | | ||||||||||| |||
taagtatattgtgtcagagctagtatacctatacacatgttcc----atctttcatttcagaaacttcatgctgatgacgaattatacttgttttaggggtatgtccagcgcacatgcaatttttatcacggctgtatcattatatattgtcacgtcgactgatcttttctccgattgtgtcaaGGGGCCTATTACATTCCGTAATTCGATAATATCCACTTCTGCATTGGGG
upper sequence: LOC_Os03g46410.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G016184_T03 (Zea mays), 3'ss of exon 1
gtcagcattgc--tagagctagtacatatattgctccctccctgatatttttcttttcgtaaatttcatagtaacaacaagtt---acct-ttttcagGGGTATGTCCAGTGCACATGCGATCTTTATCACAGCTATATCATTATATCTTGTCATGTCTACAGATCTTTTCTCTGATCGCCTTAAGGGGCCTATCACA------------
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gtcagtattgtgtcagaactagtacacctatactcatgttcc----attttccatttcagaaacttcacactgatgaccaatttatacatgtttttaggggtatgtccagCGCTCATGCAATTTTTATCACGGCTGTATCATTATATCTTGTCATGTCAACTGATCTTTTCTCCGACCGCGTCAAGGGACCTATTACATTCCGTTATTCGMapped 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|33655919|gb|CF278533.1|CF278533EST: AAGGGATATTCTTCACTGACAAAGATACAACGTGTTGAATGGAACAACAG GGNGTATGTCCAGTGCACATGCGATCTTTATCACAGCTATATCATTATATC
genomic: AAGGGATATTCTTCACTGACAAAGATACAACGTGTTGAATGGAACAACAGgtcagcattg ... cctttttcagGG-GTATGTCCAGTGCACATGCGATCTTTATCACAGCTATATCATTATATC
EST:
gi|86847432|gb|CI287010.1|CI287010EST: AAGGGATATTCTTCACTGACAAAGATACAACGTGTTGAATGGAACAACAG GGGTATGTCCAGTGCACATGCGATCTT
genomic: AAGGGATATTCTTCACTGACAAAGATACAACGTGTTGAATGGAACAACAGgtcagcattg ... cctttttcagGGGTATGTCCAGTGCACATGCGATCTT
EST:
gi|88362926|gb|CI614282.1|CI614282EST: AAGGGATATTCTTCACTGACAAAGATACAACGTGTTGAATGGAACAACAG GGGTATGTCCAGTGCACATGCGATCT
genomic: AAGGGATATTCTTCACTGACAAAGATACAACGTGTTGAATGGAACAACAGgtcagcattg ... cctttttcagGGGTATGTCCAGTGCACATGCGATCT
EST:
gi|33681071|gb|CF309310.1|CF309310EST: AAGGGATATTCTTCACTGACAAAGATACAACGTGTTGAATGGAACAACAG GG-TATGTCCAGTGCACATGCGATCTTTATCACAGCTATATCATTATATCT
genomic: AAGGGATATTCTTCACTGACAAAGATACAACGTGTTGAATGGAACAACAGgtcagcattg ... cctttttcagGGGTATGTCCAGTGCACATGCGATCTTTATCACAGCTATATCATTATATCT
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:
68 (upstream exon),
75 (downstream exon)
Score:
16GCATATGATCTCACAAGGGTACTGAGCTCATTTTACTTCAAGGGATATTCTTCACTGACAAAGATACAACGTGTTGAATGGAACAACAGgtcagcattg ... cctttttcagGGGTATGTCCAGTGCACATGCGATCTTTATCACAGCTATATCATTATATCTTGTCATGTCTACAGATCTTTTCTCTGATCGCCTTAAGGGGCCTATCACA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctgatatttttcttttcgtaaatttcatagtaacaacaagttacctttttcagGGGTATGTCCAGTGCACATGCGATCTTTATCACAGCTATATCATTATATCTTGTCATGTCTACAGATCTTTTCTCTGATCGCCTTAAGGGGCCTATCACA
tagtaac putative branch site (score: 16)
ttacctttttc putative PPT
atatttttcttttcgt TA-rich tract