Sequence
atgc intronic sequence ATGC exonic sequenceCTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAAgtgagtcattatgatctcaacaagcaccgtccttctgattttaactactaacaggcagatcttgtcacacattgccataatgatatagcatttgtggttacacttacagattcctttttttaaacttgcattaaataattttctaaaactgaaccag
Basic information
species | Oryza sativa |
transcript | LOC_Os12g04990.3 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g04990.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 5
CTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAAgtgagtc----attatgatctcaacaagcaccgtccttctgattttaactac-taacaggcagatcttgtcacacattgccataatgatatagcatttgtggttacacttacagattcctttttttaaacttgcattaaataattttctaaaactgaaccag
||||||||||| |||||||||||||| |||| |||| | || |||||||||||| | ||||| |||||||| | |||| | ||| | | ||| | | || | |||| || | || || | | ||| |||| ||| | |
GTACAAATGGATAACATATGGAGAAGCAGGTACGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATCATGGAATCGAAAAGgtgaatgctagattgtagtttcatggttgattattattttattttttacaaagtatcatgtaaccattggtttacatgctcatttttag-------------------------------------------------------------------------
upper sequence: LOC_Os12g04990.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G28200.1 (Glycine max), 5'ss of exon 5
CTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAAgtgagtc----attatgatctcaacaagcaccgtccttctgattttaactac-taacaggcagatcttgtcacacattgccataatgatatagcatttgtggttacacttacagattcctttttttaaacttgcattaaataattttctaaaactgaaccag
|||||||||||||||||||||||||| |||| |||| | || |||||||||||| | ||||| ||||||| | | |||| | ||| | | ||| | | | || |||| || | || || | | ||| |||| | | | |
GTACAAATGGATGACATATGGAGAAGCAGGTACGGCCCGGTCAGCAATAGGTTCTGGTTTGATTTATTATGGAATCCAAAAGgtgaatgctagattgtagtttcatggctgatcattatttcattttttacaaagtatcatgtaaccattggtttacatgttcttttttag-------------------------------------------------------------------------
upper sequence: LOC_Os12g04990.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 5'ss of exon 5
CTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAAgtgagtcattatgatctcaacaagcaccgtcctt-ctgattttaactactaacaggcagatcttgtcacacattgccataatgatatagcatttgtggttacacttacagattcctttttttaaacttgcattaaataattttctaaaactgaaccag
|||||||||||||||||||||||||||| ||||| | ||||| ||||||||||| | || | || ||||| || || | | ||| ||| | | || |||| ||||||| | | ||| ||| || | | |
CTACAAATGGATGACATATGGAGAAGCTGGTACAGCAAGAACTGCTTTAGGTTCTGGTTTGGTTCATCACGGAATCCCCATGgtaaattattggattcttact---ctccttcctgattgatttttaa-gtttgcagctagactcaagtctctgtttttcttctaccag-----------------------------------------------------------------------
upper sequence: LOC_Os12g04990.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 5'ss of exon 5
CTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAAgtgagtcattatgatctcaacaagcaccgtccttctgattttaactactaacaggcagatcttgtcacacattgccataatgatatagcatttgtggttacacttacagattcctttttttaaacttgcattaaataattttctaaaactgaaccag
|||||||||||||||||||||||||| | || |||| || ||||||||||||||| | | ||||| || ||||||||| | | | | | |||| | |||||| || ||| | ||||| | ||| || ||| | || || ||| | ||||||| |
GTACAAATGGATGACATATGGAGAAGCAGGCACTGTCCGGTTGGCAATAGGTTCTGGTCTTCGTCATCATGGGTTATTAGAAgtgagttggttttacataaccaagt----------tatttttaa------------ggacctt-cctcacatca--aatatgtgctaaaattctgagataagctctcagtcacattttttttggc--------------------------------
upper sequence: LOC_Os12g04990.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 5
CTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAAgtgagtcattatgatctcaa--------caagcaccgtc-----cttctgattttaactactaacagg-cagatcttgtcacacattgccataatgatatagcatttgtggttacacttacagattcctttttttaaacttg--cattaaataattttctaaaactgaaccag------------------------
|||||||||||||||||||||||||| |||| || | || || ||||||||| | || ||| |||||||||| |||||||| | || || | || ||| || | ||||| | || | || || | | | || | | | | | | | | | | |||| ||| || | | ||| || | | |||||| |
GTACAAATGGATGACATATGGAGAAGCAGGTACTGCTCGATCAGCAATTGGTTCTGGTTTAATATACTATGGAATACCGAAAgtgagttgtccaaattctaaattaagtttgaacattgtcatgcactcttaattttgttcttggattggacttatgtttttctaaaatgttttgtgaaaacatctactcaagattttcaaatccattc-tttcttaacatttggttatccattgattttcctttttttttttttaaattttctttaatgctgtaacagMapped 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|33675569|gb|CF303808.1|CF303808EST: CAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAA GGTGCGCGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTT
genomic: CAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAAgtgagtcatt ... actgaaccagGGTGCGCGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTACAAATGGATGACATATGGAGAAGCTAGTACAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAAgtgagtcattatgatctcaacaagcaccgtccttctgattttaactactaacaggcagatcttgtcacacattgccataatgatatagcatttgtggttacacttacagattcctttttttaaacttgcattaaataattttctaaaactgaaccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA