Sequence
atgc intronic sequence ATGC exonic sequence...ttctcatggagctatgatgttgatcttgtctttgaactatatgatgttgacattgtctttgaactacaatgatattgatactgtcttttgtttctaccagTGAATGCAGATGAGTGCTTGATGACAAGGATGCAGGAGATGTCCTTGGATTACCACTTCACAGTGGAGCAGGAAGTGAGCTCCTCTGTCTGCGCATTCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g09930.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g09930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G105631_T01 (Zea mays), 3'ss of exon 3
---ttctcatggagct-atgatgttgatct-tgtctttgaac-tatatgatgttgacattgtctttgaactacaatgatattgatactgtcttttgtttctaccagTGAATGCAGATGAGTGCTTGATGACAAGGATGCAGGAGATGTCCTTGGATTACCACTTCACAGTGGAGCAGGAAGTGAGCTCCTCTGTCTGCGCATTCTT
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atgagcccacgaggcccaagacgatgaggagtatatttgaaagtaatcgatggtcatatc----tgatattccgat--tgttgtctgtccttgtggtggcgaccagTGAACGCGGACGAGTGCCTGATGACGAGGATGCAGGAGATGTCCCTGGACTACCACTTCACCGTGGAGCAGGAAGTGAGCTCCTCCGTCTGCGCCTTCTT
upper sequence: LOC_Os02g09930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G05350.1 (Glycine max), 3'ss of exon 3
--ttctcatggagctatgatgttgatcttgtctttgaactatatgatgttgacattgtctttgaactacaatgatattgatactgtcttttgtttctaccagTGAATGCAGATGAGTGCTTGATGACAAGGATGCAGGAGATGTCCTTGGATTACCACTTCACAGTGGAGCAGGAAGTGAGCTCCTCTGTCTGCGCATTCTT
|| | | | ||| |||| | ||||| |||| | || | | | |||| ||| || | || | | || || |||| | |||||||||| ||||||||||| ||||||| ||||| |||||||| ||||||| || |||||||| ||||| ||||| | || | || |||||
ttttaactctaaaatctgagcatgataaaaccattgaaa-atatcaatttcaggat-tttttgtacttcactaatttgatcatggtgattggtttgtgacagTGAATGCGAATGAGTGCTTGTTGACAAGAATGCAAGAGATGTCACTGGATTATCATTTCACAGTAGAGCAAGAAGTTGGGTCAGCCACTCATGCTTTCTT
upper sequence: LOC_Os02g09930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 3
-ttctcatggagctatgatgttgatcttgtctttga--actatatgatgttgacattgtctttgaactacaatgatattgatactgtcttttgt-ttctaccagTGAATGCAGATGAGTGCTTGATGACAAGGATGCAGGAGATGTCCTTGGATTACCACTTCACAGTGGAGCAGGAAGTGAGCTCCTCTGTCTGCGCATTCTT
||| || | | | || | | ||||| ||| | ||| || | |||| |||| ||| | || || || | || | | | | |||| ||| | ||||||||||| |||| || ||||| || ||||| ||||||||||| ||||| || ||||| |||||| | || || || || ||
tctctaataaataattaagatttaattgagctttgtttgtcttattaaattg-tatgttttttggacta--atgtt-ttaatcctttgttgtatacttttgcagTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATTACCATTTCACTGTTGAGCAAGAAGTGGGTTCATCAACACATGCTTTTTT
upper sequence: LOC_Os02g09930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 3
ttctcatggagctatgatgttgatcttgtctttgaactatatgatgttgacatt--gtctttgaactacaatgatattgatactgtcttttgtttctaccagTGAATGCAGATGAGTGCTTGATGACAAGGATGCAGGAGATGTCCTTGGATTACCACTTCACAGTGGAGCAGGAAGTGAGCTCCTCTGTCTGCGCATTCTT
|| | | || || | | | || || || | | || | || | | | | || ||| | | || | |||| ||||| || |||||||| |||||||||||||| |||||||| |||||||| || || ||||||||||| ||||| | || || || |||||
-cctttccaaattg-gacaaaaattataataataataataataatatttatgattggttgataaatgatactaaaatggatttatacgggtaattttggcagTAAATGCGGACGAGTGCTTAATGACAAGGATGCAAGAGATGTCATTGGATTATCATTTTACAGTGGAGCAAGAAGTTGGATCAGCTACTCATGCCTTCTT
upper sequence: LOC_Os02g09930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ17366 (Selaginella moellendorffii), 3'ss of exon 3
----ttctcatggag-ctatgatgttgatcttg------tctttgaactatatgatgttgacattgtctttgaactacaatgatattgatactgtcttttgtt-tctaccagTGAATGCAGATGAGTGCTTGATGACAAGGATGCAGGAGATGTCCTTGGATTACCACTTCACAGTGGAGCAGGAAGTGAGCTCCTCTGTCTGCGCATTCTT
|| || || || | | | | ||||| || |||| ||||| || | || | || | || ||||| | | | |||||||||| || |||||| |||||||| |||||||||||||||| || |||||| || || |||||||| ||| | ||| | || || |||||
accactcacacacagtctcaggcgcggccagcaggcagccccttgaatgatctgatattgacgttattctt------------ttttttttctctctttcaatgtggagcagTGAATGCCGACGAGTGCATGATGACACGGATGCAGGAGATGTCGCTGAGTTACCATTTTACCGTGGAGCAATCTGTGGGATCCGCAACCTATGCTTTCTT
upper sequence: LOC_Os02g09930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ35401 (Selaginella moellendorffii), 3'ss of exon 3
ttctcatggag-ctatgatgttgatcttg------tctttgaactatatgatgttgacattgtctttgaactacaatgatattgatactgtcttttgtt-tctaccagTGAATGCAGATGAGTGCTTGATGACAAGGATGCAGGAGATGTCCTTGGATTACCACTTCACAGTGGAGCAGGAAGTGAGCTCCTCTGTCTGCGCATTCTT
|| || || || | | | | ||||| || |||| ||||| || | || | | || | || ||||| | | | |||||||||| || |||||| |||||||| |||||||||||||||| || |||||| || || |||||||| ||| | ||| | || || |||||
ctcacacacagtctcaggcgcggccagcaggcagccccttgaatgatctgatattgacgttattcttt--------tcttttttttcctctctttcaatgtggagcagTGAATGCCGACGAGTGCATGATGACACGGATGCAGGAGATGTCGCTGAGTTACCATTTTACCGTGGAGCAATCTGTGGGATCCGCAACCTATGCTTTCTTMapped 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|58596607|gb|CK007135.1|CK007135EST: CCTCGTCCACAACTCCGACATCGCCCTCGTCCAGGCCCGCTGGCGTTTCG TGAATGCAGATGAGTGCTTGATGACAAGGATGCAGGAGATGTCCTTGGATT
genomic: CCTCGTCCACAACTCCGACATCGCCCTCGTCCAGGCCCGCTGGCGTTTCGgtaagtatag ... tttctaccagTGAATGCAGATGAGTGCTTGATGACAAGGATGCAGGAGATGTCCTTGGATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgacattgtctttgaactacaatgatattgatactgtcttttgtttctaccagTGAATGCAGATGAGTGCTTGATGACAAGGATGCAGGAGATGTCCTTGGATTACCACTTCACAGTGGAGCAGGAAGTGAGCTCCTCTGTCTGCGCATTCTT
tattgat putative branch site (score: 3)
ctgtcttttgtttct CT-rich tract
aatgatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctcatggagctatgatgttgatcttgtctttgaactatatgatgttgacattgtctttgaactacaatgatattgatactgtcttttgtttctaccagTGAATGCAGATGAGTGCTTGATGACAAGGATGCAGGAGATGTCCTTGGATTACCACTTCACAGTGGAGCAGGAAGTGAGCTCCTCTGTCTGCGCATTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC