Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaaattcatactgaatttgagctatatattagtatccatcttactgttccaaaatatcatcacttacatttgtttaccttctttctgcactgataattggcatgacaaatatgttgcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAGTGGATGTCTTCTCATTTGCTTTGATACTTCAAGAGGTAAAAGTGTTGCT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g54480.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g54480.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G045366_T01 (Zea mays), 3'ss of exon 8
gtaagaaaattcatactgaatttgagctatatattagtatccatcttactgttccaaaatatcatcacttacatttgtttaccttctttctgcactgataattggcatgacaaatatgttgcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAGTGGATGTCTTCTCATTTGCTTTGATACTTCAAGAGGTAAAAGTGTTGCT
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gtaagtggactt-tattgt-ttgccactaaatatgtg---ctatattaatgtt----gacattttcccttaacttcttttgcctttcgtatcaactggcaattgtt------aaaatgatacagGTAAATATGTGGCTCCAGAAGTCCTGCGAAATGAAGAGTATGATACCAAAGTGGATGTCTTCTCATTCGCTCTGATACTTCAGGAG--------------
upper sequence: LOC_Os01g54480.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G09490.2 (Glycine max), 3'ss of exon 8
------------------------------------------------------------------gtaagaaaattcatactgaatttgagctatatattagtatccatcttactgttccaaaatatcat-cacttacat-ttgtttaccttctttctgcactgataattggca---tgacaaatatgtt-gcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAGTGGATGTCTTCTCATTTGCTTTGATACTTCAAGAGGTAAAAGTGTTGCT
||| | || | || | ||||| || | | || || | | | | || ||| || || ||| | |||| | | || | | | |||| ||| | ||||| ||||| ||||| | || | ||||||||||| |||||||||||||| || |||||||| | || || ||||||
gtgggtgctgcttttcttcagaactatcattatgcacacttgaaatacctaaatatctgaaatgctgtattttcttattcgttgggcataagaga-atattgtcattattgtgacattttccatgtgctggacttttgcatgctgattcatggttttattttctgaaactgggaaattttttgtttttgtttatagGCCGCTATGTGGCTCCTGAAGTTTTCAGACAAGAAGAATATGACACTAAAGTGGATGTATTTTCATTTGCACTAATTCTGCAAGAG--------------
upper sequence: LOC_Os01g54480.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G29520.1 (Glycine max), 3'ss of exon 8
------------------------------------------------------gtaagaaaattcatactgaatt-----tgagctatatattagtatccatcttactgttcca----aaatatcat---cacttacat--ttgtttaccttct----ttctgca-ctgataattggcatgacaaatatgttgcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAGTGGATGTCTTCTCATTTGCTTTGATACTTCAAGAGGTAAAAGTGTTGCT
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gtgggtgctgcttttcttcagaactatcattatgctcacttgaaatatctaaatatctgaaattctgtattttcttattcacggggcataagataatattgtcattattgtgacattttgcatgtgctggacttttacatgctgattcatggtttaattttctgaaactgggaattttttttgtttttgt-ttatagGCCGCTATGTGGCTCCTGAAGTTTTCAGAC---AAGAATATGACACTAAAGTGGATGTATTTTCATTTGCACTAATTCTGCAAGAG--------------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|29677658|gb|CB673933.1|CB673933EST: GAAAAGTTAGAGAAGAGAAAGCTGTAACTTCTCCAGGCAATGCAT GTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAG
genomic: GAAAAGTTAGAGAAGAGAAAGCTGTAACTTCTCCAGGCAATGCATgtaagaaaat ... tatgttgcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacatttgtttaccttctttctgcactgataattggcatgacaaatatgttgcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAGTGGATGTCTTCTCATTTGCTTTGATACTTCAAGAGGTAAAAGTGTTGCT
aaatatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaaattcatactgaatttgagctatatattagtatccatcttactgttccaaaatatcatcacttacatttgtttaccttctttctgcactgataattggcatgacaaatatgttgcagGTAGGTATGTAGCTCCAGAAGTCCTGCGAAATGAAGAATATGATACTAAAGTGGATGTCTTCTCATTTGCTTTGATACTTCAAGAGGTAAAAGTGTTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG