Sequence
atgc intronic sequence ATGC exonic sequenceAGCTCTTGGTGGGAAGACATTTAAAATGAAGTTTGGTCATCATGGAGGAAATCATCCTGTTTGTGACCTTCGAAGTGGACGTGTCGACATAAGTGCACAAgtttgttcctgacctgacttcttactgttttgatactgaatgcgattcatgttttttgactctcgagggaaatagccttccgtttgaatttcagtacaat...
Basic information
species | Oryza sativa |
transcript | LOC_Os02g47850.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g47850.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G147450_T03 (Zea mays), 5'ss of exon 10
AGCTCTTGGTGGGAAGACATTTAAAATGAAGTTTGGTCATCATGGAGGAAATCATCCTGTTTGTGACCTTCGAAGTGGACGTGTCGACATAAGTGCACAAgtttgttcctgacctgacttcttactgttttgatactgaatgcgattcatgttttttgac-----tctcgagggaaatagccttccgtttgaatttcagtacaat---
|| |||||||||||||||||||||||||| |||||||||||||| || ||||| ||||| ||||| || || ||||| ||||| |||||||||||||| |||||||||| || ||||||| || | || || ||| || |||||| | || | | | |||| || || || || || || | |
GGCGCTTGGTGGGAAGACATTTAAAATGAAATTTGGTCATCATGGTGGGAATCACCCTGTCTGTGATCTCCGTAGTGGGCGTGTAGACATAAGTGCACAGgtttgttcct------acctcttacttttgttatgctttatgtgagtcatgtctgttaaaaacaacttaggaggaactaagtgtc--ttcgatattaagaaagaaatt
upper sequence: LOC_Os02g47850.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G029573_T01 (Zea mays), 5'ss of exon 9
AGCTCTTGGTGGGAAGACATTTAAAATGAAGTTTGGTCATCATGGAGGAAATCATCCTGTTTGTGACCTTCGAAGTGGACGTGTCGACATAAGTGCACAAgtttgttcctgacctgacttcttactgttttgatactgaatgcgattcatgttttttgac--------tctcgagggaaatagccttccgtttgaatttcagtacaat-
||||||||||||||||||||||||||||| ||||| |||||||| || ||||| ||||| ||||| || || ||||||||||| |||||||||||||| |||||||||| || ||||||| |||| || || ||| |||||| | || | || | |||| ||| | || |||||| || || |
GGCTCTTGGTGGGAAGACATTTAAAATGAAATTTGGACATCATGGCGGGAATCACCCTGTCTGTGATCTCCGTAGTGGACGTGTAGACATAAGTGCACAGgtttgttcct------acctcttactttttt-atgcttgatgttggtcatgtctgttaaaaaaaccaacctaggaggaactaggcatc--tttgaaattaagagagaaa
upper sequence: LOC_Os02g47850.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA05G32190.1 (Glycine max), 5'ss of exon 8
AGCTCTTGGTGGGAAGACATTTAAAATGAAGTTTGGTCATCATGGAGGAAATCATCCTGTTTGTGACCTTCGAAGTGGACGTGTCGACATAAGTGCACAAgtttgttcctgacctgacttcttactgttttgatactgaatgcgattcatgttttttgactctcgagggaaatagccttccgtttgaatttcagtacaat-----
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GGCTTTAGGAGGCAAAACCTTTAAGATGAAATTTGGTCATCATGGAGGAAATCATCCTGTTCGTAACCTTCGAACTGGCCAGGTTGAAATTAGTGCTCAGgtatgtgattaaatggacttttc-----ttctacactaattctttgataaattttgtagtgttccttctccaccatatcttgtgtaaaatccatgaatcttttag
upper sequence: LOC_Os02g47850.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA06G15510.3 (Glycine max), 5'ss of exon 8
AGCTCTTGGTGGGAAGACATTTAAAATGAAGTTTGGTCATCATGGAGGAAATCATCCTGTTTGTGACCTTCGAAGTGGACGTGTCGACATAAGTGCACAAgtttgttcctgacctgacttctt--actgttttgatactgaatgcgattcatgttttttgactctcgagggaaatagccttccgtttgaatttcagtacaat
||| | || || || || || || ||||| |||||||| ||||||||||||||||||||| | ||||||||||||| | ||| || || ||||| || || || | |||| ||| || | | | || | | | | | | ||| | | | || |
GGCTTTAGGAGGTAAAACCTTCAAGATGAAATTTGGTCACCATGGAGGAAATCATCCTGTTCGCAACCTTCGAAGTGGCCATGTTGAAATTAGTGCTCAGgtatgcgaactaaaaagtttctgtaacttcttatttcttaagtgttctgccataactaaaatagttaaattcaatcaagtccattatgtgtgctgaggag--
upper sequence: LOC_Os02g47850.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA04G39390.1 (Glycine max), 5'ss of exon 8
AGCTCTTGGTGGGAAGACATTTAAAATGAAGTTTGGTCATCATGGAGGAAATCATCCTGTTTGTGACCTTCGAAGTGGACGTGTCGACATAAGTGCACAAgtttgttcctgacctgacttcttactgttttgatactgaatgcgattcatgttttttgactctcgagggaaatagccttccgtttgaatttcagtacaat-
||| | || || || || || || ||||| |||||||| |||||||||||||| |||||| || ||||||||||||| | ||| || || ||||| || || ||| | | | ||| || | | | || || | | | | | ||| | ||| || | | | | |
GGCTTTAGGAGGTAAAACCTTCAAGATGAAATTTGGTCACCATGGAGGAAATCACCCTGTTCGTAACCTTCGAAGTGGCCATGTTGAAATTAGTGCCCAGgtatgtgaactaaagtttctgtaacttcttatttcttaagtgttatgccataactaaaatagttaaattcaatt-cagtccattacatgtgctggggagag
upper sequence: LOC_Os02g47850.3 (Oryza sativa), 5'ss of exon 9
lower sequence: AT3G27740.1 (Arabidopsis thaliana), 5'ss of exon 8
AGCTCTTGGTGGGAAGACATTTAAAATGAAGTTTGGTCATCATGGAGGAAATCATCCTGTTTGTGACCTTCGAAGTGGACGTGTCGACATAAGTGCACAAgttt--gttcctgacctgac----ttcttactgttttgatactgaatgcgattcatgttttttgactctcg-----aggg---aaatagccttccgtttgaatttcagtacaat-----------------------------------------------------------------------
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AGCTTTGGGGGGTAAAACCTTCAAGATGAAGTTTGGTCATCATGGAGGAAACCACCCAGTTCGTAACAACAGAACTGGTCAGGTGGAGATCAGTGCTCAGgtaccaatacccaacctcaaaatgttccatttaattccaagcatactaccaactaaggatttgaacttccacattcaaagttcggataattatctgataaaacgactgtgctaggaacattgttacaagcttgacaaaatctaaatatggtgtatcattgtctttttttctgtaattcttggcag
upper sequence: LOC_Os02g47850.3 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv04s0044g00550.t01 (Vitis vinifera), 5'ss of exon 8
AGCTCTTGGTGGGAAGACATTTAAAATGAAGTTTGGTCATCATGGAGGAAATCATCCTGTTTGTGACCTTCGAAGTGGACGTGTCGACATAAGTGCACAAgtttgttc--ctgacctgacttcttactgtt-----ttgatactgaatgcgattcatgttttttgactctcgagggaaatagccttccgtttgaat-ttcagtacaat
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GGCATTGGGTGGTAAAACCTTTAAAATGAAGTTTGGTCACCATGGTGGAAATCATCCAGTTCGTAACCTTCGGAGTGGTCGCGTTGAGATCAGTGCTCAGgtgtgttcacctagacctctgtttagctattaatgtttgcaagaacatctaattcctctaattttactttct---tcagttccctgtaaattgattcttctgt-----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|88975276|gb|CI023527.1|CI023527EST: ATCATCCTGTTTGTGACCTTCGAAGTGGACGTGTCGACATAAGTGCACAA GCTTTCCGTATTACTGGTGTTGGGAGAGGTGCTGGACTTCTCGCTGTGACA
genomic: ATCATCCTGTTTGTGACCTTCGAAGTGGACGTGTCGACATAAGTGCACAAgtttgttcct ... ttcctgaaagGCTTTCCGTATTACTGGTGTTGGGAGAGGTGCTGGACTTCTCGCTGTGACA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGCTCTTGGTGGGAAGACATTTAAAATGAAGTTTGGTCATCATGGAGGAAATCATCCTGTTTGTGACCTTCGAAGTGGACGTGTCGACATAAGTGCACAAgtttgttcctgacctgacttcttactgttttgatactgaatgcgattcatgttttttgactctcgagggaaatagccttccgtttgaatttcagtacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA