Sequence
atgc intronic sequence ATGC exonic sequencegtttgagctcatactctgtttgttactgatagataacacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os04g51610.1 |
intron # | 27 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 27
--gtttgagctcatactctgtttgttactgatagataacacggaagttatggttaatattctctc--------tcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
| | ||| || | | || | | || | | |||| | | || | | | | | | || | ||| ||||||| | |||||||||||||||| ||||| ||| ||||||| |||||| ||||||||||||||||||| ||||||||||| ||||||| ||||| || ||||
tcagtcctgtgcatgttcagatagt-atttctaaaaagatgtgaagatgtagtctctgtagtgttgggtaaaattctaatttttgctcccttgtctggcagTTGTTGTGGGTTAACCTAATTATGGACACTTTGGGTGCCCTTGCATTGGCGACAGAACCACCTACAAACCATCTTATGGAGAGACCCCCAGTAGGGAGAA
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 27
---------------------------------------------------------------gtttgagctcatac---tctgtttgt-tactgatag-ataacacggaagttatggttaatatt-ctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
| | | | | | ||||| | | | || || || | ||| || || | ||| ||||||| ||||||| ||| | ||||||||||||||||| ||||||||| ||||||| |||||| ||||||||||||||||||| ||||||||||| ||||||| ||||| || ||||
gtttgagttcagctctgagatctattggtagttgcactatttatcatcatttaacttgtaaaagctgcaatttcttcagttctgtgcatgtccagacagtatttctaaaaagacgtgtttggtggaattctaatttttgct-----cccttggctgacagTTGCTGTGGGTTAACCTAATTATGGATACTTTGGGTGCCCTTGCATTGGCGACAGAACCACCTACAAACCATCTTATGGAGAGACCCCCAGTAGGGAGAA
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 28
---gtttgagctcatactctgtttgttac-----tgat--agataacacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
|| ||| | |||| | |||| | || ||| | | || | | | || ||| | ||| || | |||| ||||||| ||||| |||||||| || || || |||||||||||||| || ||||| || || ||| | |||||||| ||| ||||||||||| |||
gtaccctgccctctaatattgttgaatgaatatatgattcaaattacagatagagtcacatttacaatacctgcgtttacccctctcttactgtgta-tagCTTTTGTGGGTCAACCTTATCATGGACACACTTGGGGCTCTTGCACTGGCTACGGAACCGCCAACAGACAACCTTATGCACAGATCACCAGTTGGCCGAA
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 28
-----gtttgagctcatactctgtttgttactgatagataacacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
| |||| ||| || | | | || || | | | || | || | ||| | || | |||| ||||||| ||| | |||||||| || || || |||||||||||||| || ||||| || || ||| | |||||||| ||| ||||||||||| |||
gtaccctgcattgtcatcttctattgttgaatagtatatgatatgattcaaataacaagataagagtcacatttacaatattcgatttgtgtatagCTTTTGTGGGTCAACGTTATCATGGACACACTTGGGGCTCTTGCACTGGCTACGGAACCGCCAACAGACAACCTTATGCACAGATCACCAGTTGGCCGAA
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 26
---------gtttga--gct-catactctgtttgttactgatagataacacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
| ||| | | | ||| | | | | | | || ||| | ||| || || | | | || | ||| | || ||||| ||||||| ||||| ||||||||||| || || || ||||||||||| || ||||| || || |||| || ||||| ||| ||||||||||| |||
aaaaactaagactgatagttacgtacaagggtagattaaaaacatcatcaatgaaaaaaaggtatat-tttggtttttgatgttcatgctcttgggt--acagCTTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 29
gtttgagctcatactctgtttgttactgatagata-acacggaagttatggttaatat---------tctctctcttttgcttgggcttgttggctgg--cagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
| | ||| | |||| | | | | || | || | ||| | ||| |||| | || | || | || ||||| ||||||||||||| ||||||||||| || || || ||||||||||| || |||||||| || |||| || ||||| ||| ||||||||||| |||
---ataaaaaactgactgataattacgtacaagggcagattaaaatcatcatcaatgaaaaaaggtatatcttggtttttcatgttcatgctcttgggtacagCTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCACCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
gtttgagctcatactctgtttgttactgatagataacacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
| | ||| || | ||| | | || ||| | | || | | || | | | ||| |||||| || ||||| ||||| |||||||||||||| || || |||||||| || ||||| ||||| || || ||||||||||| ||| | || ||||| ||||
------gttagtaccttgatgcttatt--tgaatggttgaacttttaagacaaggataaaagatataatggt---gttctttgat--gcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 28
-----gtttgagctcatactctgtttg---ttactgatagataa---cacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
|| | | | || | || || | ||| || | ||| | | || | || || ||||| ||| |||| ||||| || ||||||||||| |||||||||||||| || || |||||| |||| || |||||||| ||||| ||||||||| | ||| | |||||||| |||
gcagtgtgaaaaatgttgcttttcatggtctttcaaataaccaaatttagggattatttaattcttcttacatcactttttcttttctcacttggt--acagCTTCTATGGGTTAACCTTATCATGGATACTCTTGGAGCACTTGCATTGGCTACTGAACCACCAACTGATCATCTTATGGAAAGATCTCCAGTTGGTCGAA
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
gtttg-agctcatactctgtttgttactgatagataacacggaagttatggt-taatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
||| | || || | || | | ||| | | ||| ||||| | ||| | | || | | || || ||| ||||| || |||||||| || |||||||||||||| || || |||||| |||| || |||||||| || || || || ||||| || || |||||||| |||
gttggtggcccacccattgctgcctcttga--gttgacagttctattatgtcgtctcatttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAAMapped 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|88351169|gb|CI623391.1|CI623391EST: AAGTTGTTGCTGCTGTCAGTTCTGGGAATGTTCCCCTGAACGCTGTTCAG CTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCG
genomic: ACGTTGTTGCTGCTGTCAGTTCTGGGAATGTTCCCCTGAACGCTGTTCAGgtttgagctc ... tggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCG
EST:
gi|29685708|gb|CB681983.1|CB681983EST: ACGTTGTTGCTGCTGTCAGTTCTGGGAATGTTCCCCTGAACGCTGTTCAG CTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCG
genomic: ACGTTGTTGCTGCTGTCAGTTCTGGGAATGTTCCCCTGAACGCTGTTCAGgtttgagctc ... tggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCG
EST:
gi|58594188|gb|CF992496.1|CF992496EST: CGTTGTTGCTGCTGTCAGTTCTGGGAATGTTCCCCTGCAACGCTTTTCAG CTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCG
genomic: CGTTGTTGCTGCTGTCAGTTCTGGGAATGTTCCCCTG-AACGCTGTTCAGgtttgagctc ... tggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCG
EST:
gi|218500877|gb|FG965670.1|FG965670EST: ACGTTGTTGCTGCTGTCAGTTCTGGGAATGTACCCCTGAACGCTGTTCAG CTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCG
genomic: ACGTTGTTGCTGCTGTCAGTTCTGGGAATGTTCCCCTGAACGCTGTTCAGgtttgagctc ... tggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCG
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:
73 (upstream exon),
66 (downstream exon)
Score:
22GAAATTTATACAGTTTCAGTTAACCGTCAACGTTGCAGCCTTGATTATTAACGTTGTTGCTGCTGTCAGTTCTGGGAATGTTCCCCTGAACGCTGTTCAGgtttgagctc ... tggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA
ggttaat putative branch site (score: 22)
ttatggttaatatt TA-rich tract