Sequence
atgc intronic sequence ATGC exonic sequencegttggttgccatctctctaattattattatcccctccccaccaaaatacattttatttcctctgttgtaatagaaaatgttttgcaatcgcagATATGTTCATGGGGATGTGAAACCTGAAAATTTCTTGCTAGGGCCTATTGGAACTCCTGAAGAAAAGAGACTCTTCCTTGTCGATCTTGGTTTAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g54100.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g54100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G120951_T01 (Zea mays), 3'ss of exon 6
gttggttgccatctctctaattattattatcccctccccaccaaaatac---attttatttcctctgttgtaataga-------aaatgt-tttgcaatcgcagATATGTTCATGGGGATGTGAAACCTGAAAATTTCTTGCTAGGGCCTATTGGAACTCCTGAAGAAAAGAGACTCTTCCTTGTCGATCTTGGTTTAG
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gtcagttaacaccgc--caattattctttccttgtagctccttattttctctatttccttcttccactagcaaaaaattaaaataaatatgtttgagatttcagGTATGTTCATGGCGATGTCAAACCAGAGAATTTCTTGCTAGGGACTCCTGGGACACCTGAAGAAAAGAAACTCTTCCTTGTTGATCTTGGCTTAG
upper sequence: LOC_Os01g54100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 6
------gttggttgccatctctctaattattat-tatcccctccccaccaaaatacattttatttcctctgttgtaatagaaaatgttttgcaatcgcagATATGTTCATGGGGATGTGAAACCTGAAAATTTCTTGCTAGGGCCTATTGGAACTCCTGAAGAAAAGAGACTCTTCCTTGTCGATCTTGGTTTAG
|| | || || | | | || ||| || || | | ||| | | ||| | | || |||| ||||| |||||||||||||| ||||||||||| |||| || || ||| || ||||| || || | | | |||||||| ||||| || ||||
catatatacctttactttcactgcattagtaatgtatatatgatgtgtcatcatgcttgaaattatgttcctcaaaatgtatggctacattatatggcagGTATGTGCATGGGGATGTGAAGCCTGAAAATTTTCTGCTTGGTGCTCCTGGGACACCTGATGAGAAAAAATTGTTCCTTGTAGATCTGGGATTAG
upper sequence: LOC_Os01g54100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 6
----gttggttgccatctctcta-attattattatcccctccccaccaaaatacattttatttcctctgttgtaatagaaaatgttttgcaatc--gcagATATGTTCATGGGGATGTGAAACCTGAAAATTTCTTGCTAGGGCCTATTGGAACTCCTGAAGAAAAGAGACTCTTCCTTGTCGATCTTGGTTTAG
| || | || || |||| || || | | | | || | || | | |||| | | | || |||| ||||| |||||||||||||| ||||||||||| |||| || || ||| || ||||| || || | | | |||||||| ||||| || ||||
tcatataccttttactttcactgcattagtaacatacatatgatatttcatcatgcttgaatttatgttcctcaatatgtatggctacattatatggcagGTATGTGCATGGGGATGTGAAGCCTGAAAATTTTCTGCTTGGTGCTCCTGGGACACCTGATGAGAAAAAATTGTTCCTTGTAGATCTGGGATTAG
upper sequence: LOC_Os01g54100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 6
gttggttgccatctctctaattattattatcccctccccaccaaaatacattttatttcctctgttgtaatagaaaatgttttgcaatcgcagATATGTTCATGGGGATGTGAAACCTGAAAATTTCTTGCTAGGGCCTATTGGAACTCCTGAAGAAAAGAGACTCTTCCTTGTCGATCTTGGTTTAG
|| || | | | || | | | | || | | || | |||||||| || | | | | | || ||||||||| ||||| ||||| ||||| || ||||| |||| |||||| ||||||||||||||| || | ||| |||||||| || || || ||||
gtaattttctaatatttctgctactgtaactctctttcttc--aagtggtttttatttgctaagaagcagtgc------tcctgtttctacagATATGTGCATGGCGATGTAAAACCAGAGAATTTTCTGCTTGGGCCTCCTGGAACTCCTGAAGAGAAAAAACTTTTCCTTGTAGACCTCGGCTTAG
upper sequence: LOC_Os01g54100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ13521 (Selaginella moellendorffii), 3'ss of exon 6
gttggttgccatctctctaattattattatcccctccccaccaaaatacattttatttcctctgttgtaatagaaaat---gttttgcaatcgcagATATGTTCATGGGGATGTGAAACCTGAAAATTTCTTGCTAGGGCCTATTGGAACTCCTGAAGAAAAGAGACTCTTCCTTGTCGATCTTGGTTTAG
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-------------------------------------------gtatgtgtgcaatgcacaatgttgctttcgcagatttaatgtttcgat-gcagATATGTTCACGGAGATGTGAAACCGGAAAATTTTCTCCTTGGTAGACCGGGTTCTCCAGATGAAAAGAAACTCTACCTCGTGGATCTTGGCCTAG
upper sequence: LOC_Os01g54100.2 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 4
-------gttggttgccatctctctaattattattatcccctccccaccaaaatacattttatttcctctgttgtaatagaaaatgttttgcaatcgcagAT-------------------ATGTTCATGGGGATGTGAAACCTGAAAATTTCTTGCTAGGGCCTATTGGAACTCCTGAAGAAAAGAGACTCTTCCTTGTCGATCTTGGTTTAG
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nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncgcagATTTAATGTTTCGATGCAGATATGTTCACGGAGATGTGAAACCGGAAAATTTTCTCCTTGGTAGACCGGGTTCTCCAGATGAAAAGAAACTCTACCTCGT--------------Mapped 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|58680661|gb|CK069348.1|CK069348EST: TGCATCGCTATTGAAGCTATCTCCATACTTGAGAAAATGCATTCAAAAGG ATATGTTCATGGGGATGTGAAACCTGAAAATTTCTTGCTAGGGCCTATTGG
genomic: TGCATCGCTATTGAAGCTATCTCCATACTTGAGAAAATGCATTCAAAAGGgttggttgcc ... gcaatcgcagATATGTTCATGGGGATGTGAAACCTGAAAATTTCTTGCTAGGGCCTATTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caccaaaatacattttatttcctctgttgtaatagaaaatgttttgcaatcgcagATATGTTCATGGGGATGTGAAACCTGAAAATTTCTTGCTAGGGCCTATTGGAACTCCTGAAGAAAAGAGACTCTTCCTTGTCGATCTTGGTTTAG
aaatacattttattt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggttgccatctctctaattattattatcccctccccaccaaaatacattttatttcctctgttgtaatagaaaatgttttgcaatcgcagATATGTTCATGGGGATGTGAAACCTGAAAATTTCTTGCTAGGGCCTATTGGAACTCCTGAAGAAAAGAGACTCTTCCTTGTCGATCTTGGTTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA