Sequence
atgc intronic sequence ATGC exonic sequence...tttggagagcttttgcattgagtaaatcatgcagggaacatatgttccaaaaatttcacttttctggcttccgtctaaattatcacaaaactattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g48300.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 8
------------------------------------------------------tttgg--agagcttttgcattgagtaaatcatgcagggaacatatgttccaaaaatttcacttttctggcttccgtctaaattatcacaaaac-tattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
||| | | ||| | || | ||| || || | | | | ||| | | | | | | || || | | | || |||| || ||||||||||| | |||||| |||||||||||| | || || || || |||||||||||||| ||||| || ||||||||||| |||
gtttgactatgaagtttatgttgctttgtgtttattttattgtttctttatttttttaattatatatttgggcttttttttttcagacacatgtgatgtttctacatagtttttcacaatagaaattcttttcaaacattttgacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATCCTGATGGGAAGGAA
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------tttggagagcttttgcatt---gagtaaatcatgcagggaacatatgttccaaaaatttcacttttctggcttccgtctaaattatcacaaaactattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
||| | | | ||| || | ||| | || | | || | ||| | | | | | | || | | | | || |||| || ||||||||||| | |||||| |||||||||||| | || || || || |||||||||||||| ||||| || |||||||||| |||
gtttggctgtgaagtttatgttgctttgtgtttgttttattgtttctttatttttttaattatatatatttgggattttttcagacttatgtgatgtttctaaatagtttttcacaacagaaattattttcaacatttcaacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATACTGATGGGAAGGAA
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 8
-----------------tttggagagcttt------tgcattgagtaaatcatgcagggaacatatgttccaaaaatttcacttttctggcttccgtctaaattatcacaaaactattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
||| | ||||| | || | || | |||| | ||| | | ||| | | | | | ||| | | || || | || |||| || ||||| || || | |||||| |||||||||||| | || || || ||||||||||||||||||||||| || | ||||||||| |||
gtttggctgttttgagatttataatgctttctatttttttttctcttaaatgtatttggaatgtttgtccatatcctttagcatattagaatggtctcttagaattttcataaatgactt-agGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCTTGATGGGAAGGAA
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 6
-----------------tttggagagcttttg-----cattgagtaaatcatgcagggaacatatgttccaaaaatttcacttttctggcttccgtctaaattatcacaaaactattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
||| ||||| || | || | |||| | | | | | ||| | | | | | || | | || || | | |||| || ||||| || || | |||||| |||||||||||| | || || || ||||||||||||||||||||||| || ||| ||||||| |||
gtttggcagttttgagatttatgttgctttctattccttttctcttaaatgtatttggaatgtttctccatatcctttagcatattagaatggtctcctagaattttcataaatgactgtagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCCTAATGGGAAGGAA
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 9
tttggagagcttttgcattgagtaaatcatgcagggaacatatgttc-caaaaatttcacttttctg-gcttccgtctaaattatcacaaaactattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
| | | ||| | ||| | | ||| || | || || || |||| | | || | || | | | | | ||||| ||||| || || || | ||||||||| ||||| ||| | |||||||| |||||||||||||| || ||||| || || |||||||| |||
gtcgtaaggctatctggaatagttttttttttctggattatgttttggttgaagcttggctttgacgagtttttgactga--cagtctaccctgaaatacagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 9
--tttggagagcttttgcattg--agtaaatcatgcagggaacatatgttccaaaaatttcacttttctggcttccgtctaaattatcacaaaactattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
|| | ||||| || | | | | | | |||| | | | || ||| | ||| || ||||| || ||||| || || | ||| ||||||||||| ||| | || ||||| |||||||||||||||||||||||||| | |||||||| |||
atgctgcatggctttccacctgctgatgtagcttttattgc-tgcttgtttc---tgtctggtgagcatgagttctcaactgacaatcttcctggtaaacacagGTCTATACAGTGGGTCCTGAATACGCACATGCTGAAGCAAGAAAGTCACCTGTTGTTGATGGTGTTGTTATGAGGAATACAGATGGGAAGGAA
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 8
tttggagagcttttgcattgagtaaatcatgcagggaacatatgttccaaaaatttcacttttctggct--tccgtctaaattatcacaaaactattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
|| | || | || | | | | | || | ||| | |||| | | || | || | || ||| | |||| || ||||||||||| | ||||||||||||||||||| | || || || ||||||||||| ||||||||||| ||||| ||||||||||||
-atgtaatgcctatggtagtcttttgccttttccatcattttcatttttcactttttatttttatcatcagttgatcaagcttcttgtcaatttataat-agGTGTATACAGTTGGCCCTGAATATGCACATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGCGTTGTTATGAGAAACCCCGATGGGAAAGAA
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ19878 (Selaginella moellendorffii), 3'ss of exon 8
tttggagagcttttgcattgagtaaatcatgcagggaacatatgttccaaaaatttcacttttctggcttccgtctaaattatcacaaaactattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
| | | ||| || || | | | |||| ||||| ||||| ||||| |||| |||||| |||||||||||||| |||||||| |||||||| || |||||| |||| | || ||||| |||||
----------------------------------------------gtagacaactcaacttcttgttcttagcagccgcctcttctgaactg----cagGTATACACTGTTGGACCAGAATATGCTCATGCTGAGGCACGAAAATCACCTGTTGTTGACGGGGTTGTTTTGAGAAGTCCCGATGGAAAAGAG
upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ07403 (Selaginella moellendorffii), 3'ss of exon 8
tttggagagcttttgcattgagtaaatcatgcagggaacatatgttccaaaaatttcacttttctggcttccgtctaaattatcacaaaactattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
| | | ||| || || | | | |||| ||||| ||||| ||||| |||| |||||| |||||||||||||| |||||||| |||||||| || |||||| |||| | |||||||| |||||
----------------------------------------------gtagacaactcaacttcttgttcttagcagtcgcctcttctgaactg----cagGTATACACTGTTGGACCAGAATATGCTCATGCTGAGGCACGAAAATCACCTGTTGTTGACGGGGTTGTTTTGAGAAGTCCTGATGGAAAAGAGMapped 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: GACGGATGTTAAA GTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCA
genomic: GACGGATGTTAAAgtaagaaaac ... ctattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccaaaaatttcacttttctggcttccgtctaaattatcacaaaactattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
gtctaaa putative branch site (score: 3)
ctattttc putative PPT
taaattatcacaaaac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttggagagcttttgcattgagtaaatcatgcagggaacatatgttccaaaaatttcacttttctggcttccgtctaaattatcacaaaactattttcagGTTTACACAGTTGGCCCAGGATATGCACATGCTGAGGCACGTAAATCACCAGTTGTTGATGGTGTTGTTATGAGGAACCCTGATGGGAAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - ttttgca
- - - - - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - - - - - catatgt
- - - - - - - - - - - - - - - - - - - - - - -tccaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacaaaa