Sequence
atgc intronic sequence ATGC exonic sequenceGTCGGAGAGTCGAGTATGGGAGGACCTATATAGTGAGGCCAAAGGGAAGGCACCAAGCCACCATTGTGTGGCTCCATGGTCTAGGTGACAATGGTGCAAGgtattatatagtggctagcttgatatacagccactgcctcttcgttccaaactttgcttgtttactcatgctccttcaagcatggtaccttctacctttt...
Basic information
species | Oryza sativa |
transcript | LOC_Os04g09540.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g09540.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G015692_T01 (Zea mays), 5'ss of exon 3
GTCGGAGAGTCGAGTATGGGAGGACCTATATAGTGAGGCCAAAGGGAAGGCACCAAGCCACCATTGTGTGGCTCCATGGTCTAGGTGACAATGGTGCAAGgtattatatagtggctagcttgatatacagccactgcctcttcgttccaaactttgctt-gtttac-tcatgctccttcaagcatggtaccttctacctttt------
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GTAGGAGAGTCGACTATGGGAGGACATATGTGGTGAGGCCAAAGGGAAGGCACCTAGCCACCATTGTGTGGCTCCATGGCATAGGTGACAATGGTGCTAGgtacccacttattgctaggctcatgc-------ctaccttttt-tttaaaactttgctttattcatatgatgatcctccatgcatgctatctcatgcaactgccacat
upper sequence: LOC_Os04g09540.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA15G01350.1 (Glycine max), 5'ss of exon 3
GTCGGAGAGTCGAGTATGGGAGGACCTATATAGTGAGGCCAAAGGGAAGGCACCAAGCCACCATTGTGTGGCTCCATGGTCTAGGTGACAATGGTGCAAGgtattatatagtggctagcttgatatacagccactgcctcttcgttccaaactttgcttgtttactcatgctccttcaagc-atggtaccttctacctttt-
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GAAGAGCTTTTGAGTTTGGGAAGACACATGTAGTGAGGCCAAAAGGAAAACACCAAGCCACTATAGTTTGGCTGCATGGTCTTGGTGATAATGGTTTGAGgtat-gcatgtcatcatgtcttcaatattgtcataggtcattctatcatttccacaattatcagttcattcttgtaccggttgttctatattc-acttttcc
upper sequence: LOC_Os04g09540.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA13G43990.2 (Glycine max), 5'ss of exon 3
GTCGGAGAGTCGAGTATGGGAGGACCTATATAGTGAGGCCAAAGGGAAGGCACCAAGCCACCATTGTGTGGCTCCATGGTCTAGGTGACAATGGTGCAAGgtatt-atatagtggctagcttgata----tacag-ccactgcctcttcgttccaaactttgcttgtttactcatgctccttcaagcatggtaccttctacctttt
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GAAGAGCTTTCGAGTTTGGGAAAACACATGTAGTGAGGCCAAAAGGAAAACATCAAGCCACTATAGTTTGGCTGCATGGTCTTGGTGATAATGGTTTGAGgtatggatgtcatcatctcttcaataatggcataggtcattctaacattgccacaactatcacttattcattcttgtact---ggttgttctatattctcttt---
upper sequence: LOC_Os04g09540.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G22420.1 (Glycine max), 5'ss of exon 2
GTCGGAGAGTCGAGTATGGGAGGACCTATATAGTGAGGCCAAAGGGAAGGCACCAAGCCACCATTGTGTGGCTCCATGGTCTAGGTGACAATGGTGCAAGgtatta----tatagtggctagc-ttgatatacagccactgcctcttcgttccaaactttgc-ttgtttactcatgctccttcaagcatggtaccttctacctttt
| | || | |||| ||||| ||| || | ||||||||||| |||| |||||||| || || || ||||| |||||||| |||||||||||| |||||| || | || ||| |||| | | | | || | || | ||| | ||| || || | | ||| | ||| | ||
GGAGAAGCTTGGAGTTTGGGAAGACACATGTGGTGAGGCCAAAAGGAAAACACCAAGCTACTATAGTTTGGCTGCATGGTCTTGGTGACAATGGTTTGAGgtatggatggcattctctttaatattgttatatgcctaattcacctatgaggcatatattgtacttttttctgttgtggatcctttcatag---cttgtgtct---
upper sequence: LOC_Os04g09540.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA07G03670.2 (Glycine max), 5'ss of exon 2
GTCGGAGAGTCGAGTATGGGAGGACCTATATAGTGAGGCCAAAGGGAAGGCACCAAGCCACCATTGTGTGGCTCCATGGTCTAGGTGACAATGGTGCAAGgtattatatagtggctagcttgatatacagccactgcctcttcgttccaaactttgcttgtttactcatgctccttcaagcatggtaccttctacctttt-
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GCAGAAGCTTGGAGTTTGGGAAGACACATGTGGTGAGGCCAAAAGGAAAGCACCAAGCTACTATAGTTTGGCTGCATGGTCTTGGTGATAATGGTTTGAGgtatgg-atggcattctctttaatattgttatatgcctcattcaccgcatgtattgtactttttctgttgtgaatcatttcatagcttgtgtcttttcttc
upper sequence: LOC_Os04g09540.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv09s0002g06010.t01 (Vitis vinifera), 5'ss of exon 3
GTCGGAGAGTCGAGTATGGGAGGACCTATATAGTGAGGCCAAAGGGAAGGCACCAAGCCACCATTGTGTGGCTCCATGGTCTAGGTGACAATGGTGCAAGgtattata--tagtggctagcttgatatacagccactgcctcttcgttccaaactttgcttgtt-tactcatgctccttcaagcatggtaccttctacctttt
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GAAGGACCTTTGAGTTTGGAAGGACACATGTGGTGAGGCCCAAGGGAAAACACCAGGCCACAATAGTTTGGCTACATGGCCTTGGTGACAATGGCTCAAGgtattgttgctgttttttaccattgcttgcattcttttgaacatt-ttctatgatttctttatagcattcttgtaattagaagttcaatgggtaccatttt--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|88348647|gb|CI634242.1|CI634242EST: CACCAAGCCACCATTGTGTGGCTCCATGGTCTAGGTGACAATGGTGCAAG CTGGTCCCAGCTCCTGGATTCTCTTTCATTGCCAAAT
genomic: CACCAAGCCACCATTGTGTGGCTCCATGGTCTAGGTGACAATGGTGCAAGgtattatata ... aacttttcagCTGGTCCCAGCTCCTGGATTCTCTTTCATTGCCAAAT
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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTCGGAGAGTCGAGTATGGGAGGACCTATATAGTGAGGCCAAAGGGAAGGCACCAAGCCACCATTGTGTGGCTCCATGGTCTAGGTGACAATGGTGCAAGgtattatatagtggctagcttgatatacagccactgcctcttcgttccaaactttgcttgtttactcatgctccttcaagcatggtaccttctacctttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccttc