Sequence
atgc intronic sequence ATGC exonic sequenceGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAAgtgagcgattacacatgttttttgttaaattcatttgaatatgcattgatttgtgttgttcaaagttcatgttgtgccatggtatttgctacatgaaaat...
Basic information
species | Oryza sativa |
transcript | LOC_Os03g48300.3 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA19G02260.1 (Glycine max), 5'ss of exon 7
GTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAAgtgagc-gattacacatgttttttgttaaattcatttgaatatgcattgatttgtgttgttcaaagttcatgttgtgccatggtatttgctacatgaaaat
|| || ||||| || || | |||||| |||||||||||| | || || || ||||||||||||||||||||||| || ||| ||||||| ||||| || |||| | || | | | |||| || | |||| | || | | ||| | | || | | ||| |
GTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCCTAATGGGAAGGAAgtaagtagattttgtctcttctctcagatattctttctctgttctcatgatctacattttgtttatccttgcctgtacatttagcattacaagatggtca-
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA18G49000.1 (Glycine max), 5'ss of exon 9
GTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAAgtgagcgattac--acatgttttttgtta-aattcatttgaatatgcattgatttgtgttgttcaaagttcatgttgtgccatggtatttgctacatgaaaat
|| || ||||||||||| | |||||| |||||||||||| | || || || || |||||||||||||| ||||| || ||||||||||| |||||||| | | | || ||| | | | || || || ||| ||| || | || | ||| | | | | || | ||
GTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATCCTGATGGGAAGGAAgtgagtactaagtagcctgacagacattatagtcccttctcccatatatcagtttcagtt-tttatcgtctacgttttatccttgc-ttcattttattcttg-
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA09G37610.1 (Glycine max), 5'ss of exon 7
GTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAAgtgagcgattac--acatgttttttgttaaattcatttgaatatgcattgatttgtgttgttcaaagttcatgttgtg-ccatggtat-ttgctacatgaaaat
|| || ||||||||||| | |||||| |||||||||||| | || || || || |||||||||||||| ||||| || |||||||||| ||||| || | | | || || | | | || || || |||| ||| || | ||| | || | || || ||| || | | || |
GTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATACTGATGGGAAGGAAgtaagtactaagtagcctgacagacatttagtcccttctcccatatatcaatttcggtt-tttatagtctacatttagtccttgctatattttttcttgta---
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA13G05060.1 (Glycine max), 5'ss of exon 9
GTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAAgtgagc-gattacacatgttttttgttaaattcatttgaatatgcattgatttgtgttgttcaaagttcatgt-tgtgccatggtatttgctacatgaaaat
|| || ||||| || || | |||||| |||||||||||| | || || || ||||||||||||||||||||||| || | ||||||||| ||||| || |||| | | || | | | |||| || | |||| | || || || | || | | | | || | | ||| |
GTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCTTGATGGGAAGGAAgtaagtagatttcgtctcttctctcagatattctttctctgttctcatgatctacatt-ttgtttgtccttgcctatacatttagcattacaagatggcca-
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 5'ss of exon 10
GTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAAgtgagcgattacacatgttttttgttaaattcatttgaatatgcattgatttgtg--ttgttcaaagttcatgttgtgccatggtatttgctacatgaaaat--------------------------------------------------------------------------------------
|| ||||| || || || | ||||||||| ||||| ||| | |||||||| |||||||||||||| || ||||| || || |||||||| ||||| || | | || | ||| ||| | ||||| | | | ||| || ||| | | || | | || ||||| | |||
GTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAAgtaagt--ctgc---tgatctttaccaaaccattccacatatgaaatcttatgtcgctttttccatgaaca-atggagctatggttaacagggtactaaaggcgtcgagtatatagaggaattgtaacttatgtcttatgatggtatagaatttgatcaaaaatcagtattgttattttattgaacag
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT3G01310.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAAgtgagcgattacacatgttttttgttaaattcattt---gaatatgcattgatttgtgttgttcaaagttcatgttgtgccat-ggtatttgctacatgaaaat----------------------------------------------------------------------------------------------
|| || ||||| || || | ||| ||||||||||| ||| | || ||||| |||||||||||||||||||||||||| | |||||||| ||||| || || || ||| | | ||||| ||| | | | || || ||| | | || | |||| | || || | |||
GTCTATACAGTGGGTCCTGAATACGCACATGCTGAAGCAAGAAAGTCACCTGTTGTTGATGGTGTTGTTATGAGGAATACAGATGGGAAGGAAgtaagtc-tttcaatcatttcccaacagttccatttagggaacctaacatacctagtttttaatgaaggaagggctatggtttcagtatctactg-attataatgaaaagcatgagttgcttatgttttcatgaaggtttaaactgttaatgttttgattttgatcagtattttatttttggttaatatattgaacag
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 5'ss of exon 9
GTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAAgtgagcgattacacatgttttttgttaaattcatttgaatatgcattgat-ttgtgttgttcaaa--gttcatgttgtgccatggtatttgctacatgaaaat
|| || ||||||||||| | ||||||||||||||||||| | || || || ||||||||||| ||||||||||| ||||| ||||||||||||||||| || | | ||| | | | || | | | || | | | | ||| | | | || || ||| | | | |||||
GTGTATACAGTTGGCCCTGAATATGCACATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGCGTTGTTATGAGAAACCCCGATGGGAAAGAAgtgagtaat---atgtatttcatatgtactttacaaaaccaagcttctacatcttcttgcctggatgatggaggtggttacatctactgaacagccagaaaac
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ07403 (Selaginella moellendorffii), 5'ss of exon 9
GTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAAgtgagcgattacacatgttttttgttaaattcatttgaatatgcattgatttgtgttgttcaaagttcatgttgtgccatggtatttgctacatgaaaat
|| ||||| ||||| |||| |||||| |||||||||||||| |||||||| |||||||| || |||||| |||| | |||||||| ||||| || || |||| || ||||| || |||| || | | |
GTATACACTGTTGGACCAGAATATGCTCATGCTGAGGCACGAAAATCACCTGTTGTTGACGGGGTTGTTTTGAGAAGTCCTGATGGAAAAGAGgtacaagaa---gttcgtttgtttcctaattc-ttaaaata-gcttggcacag-----------------------------------------------
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ19878 (Selaginella moellendorffii), 5'ss of exon 9
GTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAAgtgagcgattacacatgttttttgttaaattcatttgaatatgcattgatttgtgttgttcaaagttcatgttgtgccatggtatttgctacatgaaaat
|| ||||| ||||| |||| |||||| |||||||||||||| |||||||| |||||||| || |||||| |||| | || ||||| ||||| || || | ||||| || ||||| || |||| || | | |
GTATACACTGTTGGACCAGAATATGCTCATGCTGAGGCACGAAAATCACCTGTTGTTGACGGGGTTGTTTTGAGAAGTCCCGATGGAAAAGAGgtacaaga----agttgtttgtttcctaattc-ttaaaata-gcttggcacag-----------------------------------------------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|29674285|gb|CB670560.1|CB670560EST: AATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA GTACGGTATCCTGTGCTTTTGACCCCTACAGAGAAACAAATGTCAAGAGAC
genomic: AATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAAgtgagcgatt ... ttacttgaagGTACGGTATCCTGTGCTTTTGACCCCTACAGAGAAACAAATGTCAAGAGAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAAgtgagcgattacacatgttttttgttaaattcatttgaatatgcattgatttgtgttgttcaaagttcatgttgtgccatggtatttgctacatgaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA