Sequence
atgc intronic sequence ATGC exonic sequenceTTTTGAAGTTCTTGGAGACAACGACTCGCCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATGCCTGCATTCTCAAGAGAGTGCCTGAGGCAAAAGgttagttttattttcttcaataactaataattcattgttttagttttgaattcggtaatacacccagaatctcttctattaattgcaaattttttttctgattgaccaatgtgacaacatattttcataattctag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g70370.1 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g70370.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G010202_T02 (Zea mays), 5'ss of exon 9
TTTTGAAGTTCTTGGAGACAACGACTCGCCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATGCCTGCATTCTCAAGAGAGTGCCTGAGGCAAAAGgttagttttattttcttcaataactaataattcattgttttagttttgaattcggtaatacacccagaatctcttctattaattgcaaattttttttctgattgaccaatgtgacaacatattttcataattctag
|||||| ||||||||||| || || || |||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||| || |||| | | | | | || | | ||| | | || | | | ||| | | | | || | | |||| || || ||| ||| || || |
TTTTGAGGTTCTTGGAGATAATGATTCACCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATTCCTGCATTCTCAAGGGAGTGCCTGAGGCAAGCTgtgagttctcatacaaaccgtctgttatgtgcctagcatacagtgcttacatctct----tagcgagagtttgtctcaa-aaaagttcctcattttgtaagttcactaatatgat----ctattccacag------
upper sequence: LOC_Os01g70370.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA02G07250.1 (Glycine max), 5'ss of exon 10
TTTTGAAGTTCTTGGAGACAACGACTCGCCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATGCCTGCATTCTCAAGAGAGTGCCTGAGGCAAAAGgttagttttattttcttcaataactaataattcattgttttagttttgaattcg-gtaatacacccagaatctcttctattaat---tgcaaattttttttctgattgaccaatgtgacaacatattttcataattctag
||||| |||||||| || || || || || || ||||| |||||||||||||| || || ||||| ||||| || |||||||||||||| | ||| || || || | |||| | || || || | | ||| | | ||| | | | | | |||||| | ||| ||||| ||
ATTTGAGGTTCTTGGGGATAATGATTCTCCAGTAATGCCAATCATGCTTTACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAATgtgagaaca------tcaaatatccaactatctatgctccttgttgataccctacatcatataagaatgaatttgttaattaatgtttacaattttttatttcag-----------------------------------
upper sequence: LOC_Os01g70370.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA16G26210.1 (Glycine max), 5'ss of exon 10
TTTTGAAGTTCTTGGAGACAACGACTCGCCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATGCCTGCATTCTCAAGAGAGTGCCTGAGGCAAAAGgttagttttattttcttcaataactaataattcattgttttagttttgaattcggtaatacacccagaatctcttctattaattgcaaattttttttctgattgaccaatgtgacaacatattttcataattctag
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ATTTGAGGTTCTTGGGGATAATGATTCTCCAGTAATGCCAATCATGCTTTACAACCCCGCCAAAATCCCTGCCTTCTCAAGAGAGTGCCTCAAGCAGAATgtaagatcaaacatcc-----aactttatgctccttgtcgataccctacatcatgtataagaatgaaattgttaatcaatgtttaccatttttgaattcag-----------------------------------
upper sequence: LOC_Os01g70370.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT5G23670.1 (Arabidopsis thaliana), 5'ss of exon 10
TTTTGAAGTTCTTGGAGACAACGACTCGCCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATGCCTGCATTCTCAAGAGAGTGCCTGAGGCAAAAGgttagttttattttcttcaataactaataattcatt-gttttagttttgaattcggtaatacacccagaatctcttctattaa-ttgcaaattttttttctgattgaccaatgtgacaacatattttcataattctag
||||| || ||||||||||| || || || ||||||||||| ||||||||||| || || ||||| || || ||||||||||| || ||| | ||||| || |||| |||| | |||| | |||| || | | | || | ||||| | || || | ||||| ||| | | |||| |||
ATTTGAGGTACTTGGAGACAATGATTCCCCAGTCATGCCTATAATGCTTTACAACCCAGCAAAAATCCCAGCTTTCTCAAGAGAATGTCTGCGACAAAAAgtaagttctattat--tcaaatccaaatatcatatgagaactcgattaacacaaggtaacaagatcaaaaagtaaatgattaacttgtgggtgcaatggaaccttgaaactctgaacag-------------------
upper sequence: LOC_Os01g70370.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT3G48780.1 (Arabidopsis thaliana), 5'ss of exon 10
TTTTGAAGTTCTTGGAGACAACGACTCGCCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATGCCTGCATTCTCAAGAGAGTGCCTGAGGCAAAAGgttagttttattttcttcaataactaataattcattgttttagttttgaattcggtaatacacccagaatctcttctattaattgcaaattttttttctgattgaccaatgtgacaacatattttcataattctag
|||||||||||||||||||| || || || |||||||| || |||||||||||||| || ||||| || ||||||||||| || || || | |||| |||||||| || ||| | ||| || | || |||| | || | | | |||| || ||| | || || ||| |
GTTTGAAGTTCTTGGAGACAATGATTCACCAGTCATGCCAATAATGCTTTACAATCCAGCAAAAATTCCAGCATTCTCAAGGGAATGTTTGCGAGAAAACgttagtttctcttgcttttct---taaaaaatatttttttttgcttccacacaagagactcacctcctatg--ttcaacggataatgaaatttgtgaacag-----------------------------------
upper sequence: LOC_Os01g70370.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv17s0000g00500.t01 (Vitis vinifera), 5'ss of exon 11
TTTTGAAGTTCTTGGAGACAACGACTCGCCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATGCCTGCATTCTCAAGAGAGTGCCTGAGGCAAAAGgttagttttattttc---ttcaata-actaataattcat--tgttttagttttgaattcggtaat----acacccagaatctcttctattaatt-gcaaattttttttc-tgattgaccaatgtga--caacatattttcataattctag------------------
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CTTTGAGGTTCTTGGAGATAATGATTCTCCTGTAATGCCAATAATGCTTTACAATCCAGCCAAAATTCCTGCCTTTTCGCGGGAGTGTCTCAAACAGAATgtaagctttatctttaatttctatacattcaccattcatgtcttttcattcttgattaaagtagctgcaatacagagattccaagtcattcatttgtatagcactgctcattaatctccagttcaagttcacttgtgtggctagtattgacaagttatgctgttccagMapped 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|88246156|gb|CI246005.1|CI246005EST: ACAATCCTGCTAAAATGCCTGCATTCTCAAGAGAGTGCCTGAGGCAAAAG GTTGCCATTGTTACTGTTTCATTTCCGGCAACGCCACTGCTACTTGCCAGA
genomic: ACAATCCTGCTAAAATGCCTGCATTCTCAAGAGAGTGCCTGAGGCAAAAGgttagtttta ... ataattctagGTTGCCATTGTTACTGTTTCATTTCCGGCAACGCCACTGCTACTTGCCAGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTTTGAAGTTCTTGGAGACAACGACTCGCCTGTCATGCCTATCATGCTTTACAATCCTGCTAAAATGCCTGCATTCTCAAGAGAGTGCCTGAGGCAAAAGgttagttttattttcttcaataactaataattcattgttttagttttgaattcggtaatacacccagaatctcttctattaattgcaaattttttttctgattgaccaatgtgacaacatattttcataattctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA