Sequence
atgc intronic sequence ATGC exonic sequencegttttttttcccttcaaaatatgcaatgacgagtccaaatactgctatgttctcttggactattagacatgataattttcctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCCGCCCGAAGGGGCATCCCAAAACCTGACTCATCTATTGCAAGCA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g55230.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G086030_T01 (Zea mays), 3'ss of exon 20
gttttttttcccttcaaaatatgcaatgacg-agtccaaatactgctatgttctcttggactattagacatgataattttcctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCCGCCCGAAGGGGCATCCCAAAACCTGACTCATCTATTGCAAGCA
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----gttcttttttcagggcatataaaaatataggatatatactctgatcttctcttgaatta--acacattattgtt-----gttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA
upper sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM5G892758_T01 (Zea mays), 3'ss of exon 3
gttttttttcccttcaaaatatgcaatgacg-agtccaaatactgctatgttctcttggactattagacatgataattttcctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCCGCCCGAAGGGGCATCCCAAAACCTGACTCATCTATTGCAAGCA
||| |||||| | | | ||| || || | ||||| | ||||||||||| | || ||| || ||||| | |||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||| |||||||| ||||| ||||||||||| |||||||||||||| |
gttctttttctc-----agcgtacaaaaacataggatatatactccgatgttctcttgaatta----acacattacttttc--gatgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCTGCCCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA
upper sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA08G22850.1 (Glycine max), 3'ss of exon 19
-------------------------------------------gttttttttcccttcaaaatatgcaatgacgagtc-caaatactgctatgttctcttgg--actattaga-----catgataatttt---cctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCCGCCCGAAGGGGCATCCCAAAACCTGACTCATCTATTGCAAGCA
|| | | | || || ||| || | | | || || || ||| | | ||| ||||| | |||| || |||||||||||||||||||||||||||||||||| |||||||| |||| || ||||| || || || || | ||||| ||||| |||| |||||||| |
gtcatttccttttctgatagtagtgctagaatacgtcaaagaatattggtctaggattgaactacgcattggcaaactatggggattgatagattgatttgtttaatgttaccattttcatgaaagttttttccccaatgcagGATGCTGCTGCATGGCTTGAGTATTTTGAATCAAAAGCCCTAGAGCAGCAAGAAGCAGCTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA
upper sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA07G03250.1 (Glycine max), 3'ss of exon 21
-------------------------------gttttttttcccttcaaaatatgcaatgacgag-tccaaatactgctatgttctcttgg--------actattagacatgataa-----ttttcctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCCGCCCGAAGGGGCATCCCAAAACCTGACTCATCTATTGCAAGCA
| | | | | || || ||| || | | | || || | | |||| || ||| ||||| | |||| | ||||||||||||| || |||||||| |||||||| |||||||| |||| || ||||| || | || || | ||||| ||||| |||| |||||||| |
gtcatttccttttctgattgtagtactagaattctggtctaggattgaactaagcattggcaaaatatgggggttgatagatggttttggctaatgttaccatttttcatgaaaggtttttttttccaatgcagGATGCTGCCGCGTGGCTTGAATATTTTGAATCAAAAGCCATAGAGCAGCAAGAAGCAACTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA
upper sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 20
lower sequence: AT1G15290.1 (Arabidopsis thaliana), 3'ss of exon 18
---------------------------------------------gttttttttcccttcaaaatatgcaatgacgagtccaaatactgctatgttctcttggactattagacatgataattttcctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCCGCCCGAAGGGGCATCCCAAAACCTGACTCATCTATTGCAAGCA
| || || | | | | | | || | ||| | | || | | | || | | |||| || |||||||||||||||||||| || |||||||| |||| ||| |||| || || || || | ||||| || |||||||| ||||| | || || || ||||
gtgattgatttgcttctggttcattcgcatacaaatctcagacgaatattaatttcttactagcaaagtaacaa--agtgaacgttttgaactctgagacatacatgtttgttttctccatttgtctctcacagGATGCTGCTGCATGGCTCGAATATTTTGAATCAAGAGCCATAGAGCAGCAGGAAGCAGGCCGAAATGGAATCCCAAAGCCTGATGCTTCCATCGCGAGCA
upper sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 20
lower sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 20
--------------gttttttttcccttcaaaatatgcaatgacgagtccaaatac-tgctatgttctcttggactattagacatgataattttcctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCCGCCCGAAGGGGCATCCCAAAACCTGACTCATCTATTGCAAGCA
| | || | || ||||| | | | | |||| | ||| || | | | | | || || || | |||||||||||||||||||||||| |||||||| |||||||| ||||| || ||||| || || ||| || | ||||| || || |||||||||||||||
atgcgaccaattgagctaagggcatgtttagctaatacaatgtc-actatagatacataaaatggagtcatcaattgacgggcgtgtgtgttctcat---gcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA
upper sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 20
lower sequence: EFJ08067 (Selaginella moellendorffii), 3'ss of exon 20
gttttttttcccttcaaaatatgcaatgacgagtccaaatactgct-atgttctcttggactattagacatgataattttcctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCCGCCCGAAGGGGCATCCCAAAACCTGACTCATCTATTGCAAGCA
|| | || | || | | || | | ||||||| | | || | |||||||||||||| |||||||| |||||||| || |||||| | || |||||||| ||| | | | || || || ||||| | ||| |||||||||
----------------------------gttgatcgactccctcttgattgtgaaacagtctctcatgcatgatatgtgttct-ttacagGATGCTGCTGCCTGGCTTGATTATTTTGATTCTAAAGCAGTTGAGCAACAAGAAGCCACAAGGACAGGGGCACCTAAGCCTGATCCTTCTGTTGCAAGCA
upper sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 20
lower sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 20
gttttttttcccttcaaaatatgcaatgacgagtccaaatactgct-atgttctcttggactattagacatgataattttcctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCCGCCCGAAGGGGCATCCCAAAACCTGACTCATCTATTGCAAGCA
|| | || | || | | || | | ||||||| | | || | |||||||||||||| |||||||| |||||||| || |||||| | || || ||||| ||| | | | || || || ||||| | ||| |||||||||
----------------------------gttgatcgactccctcttgattgtgaaacagtctctcatgcatgatatgtgttct-ttacagGATGCTGCTGCCTGGCTTGATTATTTTGATTCTAAAGCAGTTGAGCAGCAAGAAGCCACAAGGACAGGGGCACCTAAGCCTGATCCTTCTGTTGCAAGCAMapped 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|29688141|gb|CB684416.1|CB684416EST: CCTTACAGATACTTCAGGAGAAACTAGGACAAGATGACCTTCGAACTCAG GATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAA
genomic: CCTTACAGATACTTCAGGAGAAACTAGGACAAGATGACCTTCGAACTCAGgttttttttc ... cctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAA
EST:
gi|58695540|gb|CK084227.1|CK084227EST: CCTTACAGATACTTCAGGAGAAACTAGGACAAGATGACCTTCGAACTCAG GATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAA
genomic: CCTTACAGATACTTCAGGAGAAACTAGGACAAGATGACCTTCGAACTCAGgttttttttc ... cctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAA
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:
75 (upstream exon),
75 (downstream exon)
Score:
77CCTCTCAATGATGGATGCATACTCCTTGAGTGTTCAGCATGAACAGACCACCTTACAGATACTTCAGGAGAAACTAGGACAAGATGACCTTCGAACTCAGgttttttttc ... cctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCCGCCCGAAGGGGCATCCCAAAACCTGACTCATCTATTGCAAGCA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaaatactgctatgttctcttggactattagacatgataattttcctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCCGCCCGAAGGGGCATCCCAAAACCTGACTCATCTATTGCAAGCA
ttttcctgct CT-rich tract
atgataatttt TA-rich tract