Sequence
atgc intronic sequence ATGC exonic sequence...agatgaggacatggctggatgttttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctcatgtgaggctacctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA
Basic information
species | Oryza sativa |
transcript | LOC_Os08g12840.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g12840.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G024482_T01 (Zea mays), 3'ss of exon 2
agatgaggacatggctggatgttttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctcatgtgaggct---acctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA
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atatatata-atgcctacattaatgcttagtttgtatcctgttgaccccatgcctggattcagt--aactcacattagaaactatttgcacctttatccacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGCTGCAACCTGAAGTTGGTGGATCTCGAGACAACTTCTTTTTCGCCGGGATTGACAAAGTTAGGTTCAGGA
upper sequence: LOC_Os08g12840.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G05800.1 (Glycine max), 3'ss of exon 3
----------agatgaggacatggctggatgttttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctcatgtgaggctacctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA
||| || ||| | | || || || | | | || ||| | | | | || || | | ||||| | | ||||| ||||| || ||||| ||| |||| |||||||| |||||| | || || ||||| || || ||||||||||| ||||| || |||||| |||| ||||
aacttctgaaagactttgagatgaacaactagtcttgtatgatttctgttgcaataatcttctttaaa----tgtggacatg---aacatgaggtcatttgc---tgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGTTCTCGTGAAAACTTCTTCTTTGCTGGAATAGACAAAGTGCGGTTTCGTA
upper sequence: LOC_Os08g12840.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G19200.1 (Glycine max), 3'ss of exon 2
----------agatgaggacatgg-ctggatgttttttaattgct-tattgttctatcatcaagtagacaaacatctgaacttccctcatgtgaggctacctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA
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aacctggaatgcatgaaagtaggggcgggatcttgtatgatttctctgttgtaataatctgctttaaaagcggacatgaac------------aagaggtcttttgctgcagGCAATGGCACAAGTTGGTGGTTTGGTCATGTTGCAACCTGAAGTGGGAGGCTCTCGTGAAAACTTCTTCTTTGCTGGAATAGACAAAGTGCGGTTTCGTA
upper sequence: LOC_Os08g12840.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G24650.1 (Glycine max), 3'ss of exon 3
agatgaggacatggctggatgttttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctca------tgtgaggctacctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA
|| ||| | | || | ||| || || | || |||| | || || | ||| || ||||| ||||| || || || ||||| || |||| ||||||||||||||| |||| || ||||| || |||||||||||||| ||||| || |||||| | || | |
----gattgcataagttccaacccatgaaagagcttttgcgttaagattga-cagcagggtgtctgtaattttctaaaggttctgttgaattatcttta-atgcagGCAATCGCACAAGTTGGTGGCTTGGTTATGTTGCAGCCTGAAGTTGGAGGTTCTCGTGAGAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA
upper sequence: LOC_Os08g12840.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G07870.1 (Glycine max), 3'ss of exon 3
agatgaggacatggctggatgttttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctca------tgtgaggctacctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA
|| | | | | | | || |||| |||| || ||| | ||| ||| | || || | ||| || || | ||||| ||||| |||||||| || |||| |||||||| ||||||||||| || ||||| | |||||||||||||| ||||| || |||||| | || | |
--ctgctgcttaagatccaactaatggaagagctt-ttgtgttaacattga--caacaggtgcctgtaattttctaaaggttctgttgaattatctctg-atgcagGCAATGGCACAGGTTGGTGGCTTGGTTATGTTGCAACCTGAAATTGGAGGTTCTCGCAATAATTTCTTCTTTGCTGGAATAGACAAAGTGCGATTTAGGA
upper sequence: LOC_Os08g12840.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv12s0055g01100.t01 (Vitis vinifera), 3'ss of exon 3
----------agatgaggacatggctggatgttttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctcatgtgaggctacctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA
| | | || | | ||| || || | | || || | || | | || || | ||| || |||||| ||||| |||||||| || |||| ||| | || |||||| | || || ||||| || |||||||||||||| |||||||| ||||| || ||||| |
ggaaggccttacacataaatatactgtaaggctttatactta---aacatgctgtctttggtctgatggagtggtaaattttttttctgt-------ttgttggatacagGCAATGGCACAGGTTGGTGGCTTGGTAATGCTACAACCTGAAGTGGGAGGCTCTCGTGAAAATTTCTTCTTTGCTGGAATTGACAAAGTAAGATTCCGGA
upper sequence: LOC_Os08g12840.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv00s0357g00070.t01 (Vitis vinifera), 3'ss of exon 3
-agatgaggacatggctggatgtt-ttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctcatgtgaggctacctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA
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ttgttaaattctttttacaaccctgtttctatcaagtttggatttgg-atacattacatgtgcctctagtaattgctgatg-aaagtggttggtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCAGA
upper sequence: LOC_Os08g12840.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv00s0357g00020.t01 (Vitis vinifera), 3'ss of exon 3
-agatgaggacatggctggatgttttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctcatgtgaggctacctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA
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ttgttaaattctttttacaaccctgtttctatcaagttcgcatttggatacattacatgtgcctctagtaattgctgatg-aaagtggttggtgggtccagGCAATGGCTCAGGTTGGGGGCTTGGTTATGCTTCAACCTGAAGTTGGAGGCTCTCGTGAGAATTTCTTCTTTGCAGGAATCGACAAAGTGAGGTTCCGGAMapped 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|38477393|gb|CF961526.1|CF961526EST: CTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCGTGGTTGAG GCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGA
genomic: CTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattcc ... ttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catcaagtagacaaacatctgaacttccctcatgtgaggctacctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA
ctaccttt CT-rich tract
tttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agatgaggacatggctggatgttttttaattgcttattgttctatcatcaagtagacaaacatctgaacttccctcatgtgaggctacctttatgcacagGCTATGGCCCAGGTTGGGGGTCTGGTGATGTTGCAGCCTGAAATTGGCGGATCTCGGGACAATTTCTTCTTTGCAGGAATTGATAAAGTGAGGTTCCGTA
- - - - - -tggctgg
- - - - - - - - - - - - - - -ttgctta
- - - - - - - - - - - - - - - - - - ttgttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - -acaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaggct