Sequence
atgc intronic sequence ATGC exonic sequencegtaatgctttaacctcaactttccgaataatgggtgcaaatcaactaaaattgctcctctaagctttactgttgtctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACTCGACGTGGTCAGCCTTGTTGGTTTCGGGTGCCTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g46580.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g46580.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G168681_T01 (Zea mays), 3'ss of exon 3
----gtaatgctttaacctcaactttccgaataatgggtgcaaatcaactaa-----aattgctcctctaagctttactgttgtctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACTCGACGTGGTCAGCCTTGTTGGTTTCGGGTGCCTCAG
| | ||| || | ||| | | | ||| | |||| || | | |||| |||||| | || || | | ||||||| |||| |||||| ||||||||||||||||||||||| ||||||||||| || || |||||||| ||||| |||||||||||
gtatttttttttttgtcccccactgttgccaggaaaaatgccagtcaaggaactgagagtggctcatctaagttcgctcgtcgtattt-cagCTTCAGGCTTTCTTTCTTGTGCTTGATGATATCATGGATGACTCTCACACTCGTCGCGGCCAGCCTTGCTGGTTCAGGGTGCCTCAG
upper sequence: LOC_Os05g46580.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 3
---------------------------------gtaatgctttaac-----ctcaactttccgaataatgggtgcaaatcaactaaaattgctcctctaagc-tttactgttgt-ctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACTCGACGTGGTCAGCCTTGTTGGTTTCGGGTGCCTCAG
|||| || ||| || | | || | || | || | | | | || | | | | | || || | || ||||||| || || ||||| || |||||||| || |||||| | |||||||| || ||||||||||| || |||||| | ||||| ||
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagatgtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG
upper sequence: LOC_Os05g46580.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatgctttaacctcaactttccgaataatgggtgcaaatcaactaaaattgctcctctaagctttactgttgtctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACTCGACGTGGTCAGCCTTGTTGGTTTCGGGTGCCTCAG-------------
||||| | | | || | | || | ||| || || ||||| | | ||| | ||| | || ||||||||||||| || || ||||||||||| |||||||| | ||| ||| || ||||| ||||||||||||||| | ||| ||
gtaattcctcttttacttctcttcttatctt---------tcatctcaa--tgctcattttgtatttgc--ttgcatttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG
upper sequence: LOC_Os05g46580.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------gtaatgctttaacctc---aactttccgaataatgggtgcaaa--------tcaactaaaattgct-cctctaagctttactgttgtctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACTCGACGTGGTCAGCCTTGTTGGTTTCGGGTGCCTCAG
||| | ||| ||| | || | | |||| | | | || | | | ||| | || | | | || ||| || |||| |||||||| || || |||||||||||||| |||||| | ||| |||||| |||||||| ||||| ||||| | || ||||||
gtataccaatgataaagacttatcctttcaatctctattagtaatagatactctcctctctctctctttatgtcgctatcactcatcatattcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG
upper sequence: LOC_Os05g46580.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ10874 (Selaginella moellendorffii), 3'ss of exon 4
gtaatgctttaacctcaactttccgaataatgggtgcaaatcaactaaaat-tgctcct--ctaagctttactgttgtctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACTCGACGTGGTCAGCCTTGTTGGTTTCGGGTGCCTCAG
| || | || | | || | | | || || ||| | |||| ||||| || || || | | |||||||||||||||||||| ||||| || | |||||||||||||||||| | ||| ||
-----------------------------gtaggcgttcttctgtagagacgtgttagaaacgagttttaacatttgcttgcacagCTCCAAGCGTATTTCCTAATCTTAGATGATATCATGGATGATTCACACACGAGAAGGGGTCAGCCTTGTTGGTTTAGACAGCCAAAG
upper sequence: LOC_Os05g46580.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ25934 (Selaginella moellendorffii), 3'ss of exon 4
gtaatgctttaacctcaactttccgaataatgggtgcaaatcaactaaaattgctcctctaagctttactgttgtctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACTCGACGTGGTCAGCCTTGTTGGTTTCGGGTGCCTCAG
| | | || | | | || || | | || || ||| | |||| ||||| || || || || | |||||||||||||||||||| ||||| || | |||||||||||||||||| | ||| ||
-------------------gtaggcattcttgtttagagacgtgttagaaacg-------agttttaacatttgcttgcacagCTCCAAGCGTATTTCCTGGTCTTAGATGATATCATGGATGATTCACACACGAGAAGGGGTCAGCCTTGTTGGTTTAGACAGCCAAAGMapped 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|32948182|gb|BP184754.1|BP184754EST: GTCAGGAAGACATGTTTCTCGCGAGCACTCTTGGTTGGTGCGTTGAATGG CTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACT
genomic: GTCAGGAAGACATGTTTCTCGCGAGCACTCTTGGTTGGTGCGTTGAATGGgtaatgcttt ... gtctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACT
EST:
gi|41884200|gb|BX929031.1|BX929031EST: GTCAGGAAGACATGTTTCTCGCGAGCACTCTTGGTTGGTGCGTTGAATGG CTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACT
genomic: GTCAGGAAGACATGTTTCTCGCGAGCACTCTTGGTTGGTGCGTTGAATGGgtaatgcttt ... gtctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACT
EST:
gi|58603777|gb|CK014305.1|CK014305EST: GTTTCTCGCGAGCACTCTTGGTTGGTGCGTTGAATGG CTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACT
genomic: GTTTCTCGCGAGCACTCTTGGTTGGTGCGTTGAATGGgtaatgcttt ... gtctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACT
EST:
gi|58608132|gb|CK036165.1|CK036165EST: GTCAGGAAGACATGTTTCTCGCGAGCACTCTTGGTTGGTGCGTTGAATGG CTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACT
genomic: GTCAGGAAGACATGTTTCTCGCGAGCACTCTTGGTTGGTGCGTTGAATGGgtaatgcttt ... gtctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACT
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:
72 (upstream exon),
45 (downstream exon)
Score:
29TCTCTCTGTGGTCGATAGCTATAAGCTGTTGAAGGGCACCAATGTTCTAAGTCAGGAAGACATGTTTCTCGCGAGCACTCTTGGTTGGTGCGTTGAATGGgtaatgcttt ... gtctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACTCGACGTGGTCAGCCTTGTTGGTTTCGGGTGCCTCAG
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgggtgcaaatcaactaaaattgctcctctaagctttactgttgtctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACTCGACGTGGTCAGCCTTGTTGGTTTCGGGTGCCTCAG
aactaaa putative branch site (score: 29)
aaatcaactaaaatt TA-rich tract