Sequence
atgc intronic sequence ATGC exonic sequenceACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcctatgccatgccatgcaaaatccttatgaccgaaaaaatactaatgtttccaatgatgttttgtcag
Basic information
species | Oryza sativa |
transcript | LOC_Os02g35870.2 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G013079_T01 (Zea mays), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgttt--cctatgc-catgccatgcaaaa---tccttatgaccgaaaaaatactaatgtttccaatgatgttttgtcag
|||||||||||||||||||||| || ||||||||||||||||| || ||||||||||| || ||||| ||||| ||||| || || |||||||||||||||||||||| ||| |||| ||| || || || | | || ||||||| | ||| |||| ||| ||||
ACTGGAAATTTGGGGAGGAAGGAAATAAATACTTCCGTCATGCCACGGGGCAGATATATGCCATTTCGAAAGATCTCGCTACTTATATTTCAATCAACCAgtatgtttaattcatgttcatgacatacagaagtgtctgttcatctaaaggggaactaatgatgccagtgatattt-atcag
upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G070708_T02 (Zea mays), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcctatgc---catgccatgcaaaa---------tccttatgaccgaaaaaatactaatgtttccaatgatgttttgtcag
|||||||||||||||||||||| || || ||||||||||||||||| ||||||||||| || ||||| ||||| || ||||| || || |||||||| | |||||||| | | || | ||| ||||| ||| | | | | ||| ||| ||| | | | ||| |||| ||||
ACTGGAAATTTGGGGAGGAAGGAAATAAGTACTTCCGTCATGCTACAGGGCAGATATATGCCATTTCGAAAGATCTGGCGACTTATATCTCAATCAATCGgtatgtttaattcgtgttcacgacatacaaaagggtgcctgtccatctaaagggaaactaactgatgctgcaagcgatatttt-tcag
upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA04G43340.2 (Glycine max), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcctatgc--catgccatgcaaaatc------cttatgaccgaaaaaatactaatgtttccaatg---atgttttgtcag-------------
||||| ||||| || || ||||||||||||||||| ||||| |||||||||||||| || || ||||| || || || || |||||||| |||||||||||||| | || | ||| | | || ||| ||| | | || | ||| | || | | || |||
TTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGATCTGGCCACTTACATTTCCATCAACCAgtatgtatatcatttttcgtgcaacacttaactggctatcttctgatctcggcaccacaactgtgtattttgtacagggattaccagatgagcaattgtt
upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA13G02420.1 (Glycine max), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatg--tttcctatgccatgccatgcaaaa-tccttatgaccgaaaaaatactaatgtttccaatgatgttttgtcag-----------------------
||||||||||| || || ||||||||||||||||| ||||| |||||||||||||| || || || || || || || ||||||||||| ||||||||||||| | || | ||| | | | | | |||| || | || | | | |||| || |
TTTGGAAATTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGATCTGGCCACCTACATTTCCATCAACCAgtatggatacgcttttccaattagtacttagcttcctatggttgagag--tatcagaggggctaatgttgaccccatacaactgtagtgcatgatcaagaat
upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA14G33700.1 (Glycine max), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc--tatgccatgccatgcaaaatcct-tatgaccgaaa----aaatactaatgtt-----tccaatgatgttttgtcag------------
||||| ||||| || || ||||||||||| ||||| ||||| |||||||||||||| || || || || || || || ||||||||||| || |||||||||| | | | | |||||| | | || || | ||| | || | | ||||| || | ||| || || | |
TTTGGAAGTTTGGAGAAGAGGGGAACAAATATTTCCGACATGCAACTGGGCAGATATATGCAATCTCTAAGGATCTAGCCACCTACATTTCCATTAACCAgtatggatacagttttccatgcactactaagtcatctataattgagaccagaggagctaatcttgaccatacaactatattgcatgaatagatttaagta
upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA06G11330.1 (Glycine max), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgt-------ttcctatgccatgccatgcaaaat-ccttatgaccgaaaaaatactaatgt---ttccaatgatgttttgtcag-------------
||||| ||||| || || ||||||||||||||||| ||||| |||||||||||||| || || ||||| || | || || |||||||| |||||| |||| || || | | | | | || ||| ||| | | | | ||| || | | | || |||
TTTGGAAGTTTGGAGAAGAGGGGAACAAATACTTCCGACATGCAACTGGGCAGATATATGCAATCTCAAAGGATTTGGCCACTTACATTTCCATCAACAAgtacgtatatcatttttcgtccactacttaactggatatcttctgatctcggtaccataactgtgtatttcgcacagggattaccagattagcaattgtt
upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G77810.2 (Arabidopsis thaliana), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgt-ttcctatgccatgccatgcaaaatccttatgaccgaaaaaatact----aatgtttccaatgatgttttgtcag
| ||||||||||| ||||| || ||||||||||| || |||||||| || ||||| || || || || || || || || | ||||| || ||||||||||| || | || | | ||| | | | | || | || |||| ||| ||| | |||
ATTGGAAATTTGGAGAGGATGGTAACAAATACTTTCGACATGCTACAGGACAGATCTATGCCATCTCCAAGGATCTTGCTAATTACATATCCATCAACCAgtacgtacttctgcatcctttt-cataaagagccttccatcaaatgtttgtcctaaaaggtttacaactttgtatg--cag
upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G22015.1 (Arabidopsis thaliana), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcctatgccatgccatgcaaaatccttatgaccgaaaaaatact--aatgtttccaatgatgttttgtcag----------------------------
||||||||||| || ||||| |||||||| ||||| |||||||| || ||||| || || || ||||| || || || || ||||| || | ||||||||| || || | ||| | | | | | || | || | | ||||| | ||
TTTGGAAATTTGGAGAAGAAGGTAACAAATATTTCCGACATGCTACGGGACAGATTTATGCCATATCAAAGGATCTTGCCACATACATATCTAACAACCAgtaagtgaccaactttatggtttttggattttcgacaaggtaagatatgttttaccaagggaaatgagtatcaaccaaacataacatttgatgtttgacttcgcag
upper sequence: LOC_Os02g35870.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv18s0001g04150.t01 (Vitis vinifera), 5'ss of exon 9
ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcctatgccatgccatgcaaaatccttatgaccgaaaaaatactaatgtttccaat---gatgttttgtcag----------------------
||||||| ||||| ||||| |||||||| || ||||| ||||| ||||||||||| || || || |||||||| || || || ||||| || ||||||||||| | | | | || ||| || | | | || | | | || | || ||| |
ACTGGAAGTTTGGAGAGGAGGGGAACAAGTATTTCCGGCATGCAACTGGGCAGATTTATGCAATCTCAAAAGATCTGGCCACATACATCTCGATCAACCAgtaagaattgagt-tttttttatatggaattagcctgtttggccattttctgagctaccatatcaaaaggtcttgcaattcatcccctgggcatgattttcMapped 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|58666495|gb|CK055181.1|CK055181EST: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCA GCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
genomic: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc ... gttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
EST:
gi|163922994|gb|EG712767.1|EG712767EST: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCA GCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
genomic: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc ... gttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
EST:
gi|29682555|gb|CB678830.1|CB678830EST: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCA GCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
genomic: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc ... gttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
EST:
gi|58666808|gb|CK055494.1|CK055494EST: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCA GCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
genomic: CAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc ... gttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTT
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:
49 (upstream exon),
73 (downstream exon)
Score:
14ACTGGAAATTTGGGGAGGAAGGGAACAAATACTTCCGTCATGCTACTGGGCAGATATACGCGATTTCAAAAGACCTCGCGACCTACATTTCAATCAACCAgtatgtttcc ... gttttgtcagGCCTATCTTACACAAATTTGCGAACGAAGATGTATCACTTGGTTCATGGTTTATTGGTTTAGAAGTGAATCATATCGATGAAAGAAACATGTGCTGCGGG
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