Sequence
atgc intronic sequence ATGC exonic sequenceGAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGTGGATCCAGTCCAGCGAGATCAAGGACAAGAAGgtgagccctcttaacttcttagccgtagccggtagcttctctttagctccaggggatgcggttcatggtgcaatgcactgcctcctgtgcttagaattat...
Basic information
species | Oryza sativa |
transcript | LOC_Os03g44900.3 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 2
lower sequence: AC197122.3_FGT003 (Zea mays), 5'ss of exon 2
GAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGTGGATCCAGTCCAGCGAGATCAAGGACAAGAAGgtgagccctcttaacttctt--agccgtagccggtagctt-------ctctttagctccaggggatgcggttcatggt--gcaatgcactgcctcctgtgcttagaattat
|||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| | | | | | || | | || | | | |||| | || |||| | | | | | || | ||||| ||| | ||
GAAGTTCGAGGCGGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGTGGATTCAGTCCAGCGAGATCAAGGACAAGAAGgtgaggattacggattacctcgagtcctgccccctcccctggcaagcctctatgtctgcaggtggagggcatggttgtttgggatgcaatgctgctgctg-----------
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA16G26850.1 (Glycine max), 5'ss of exon 2
GAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGTGGATCCAGTCCAGCGAGATCAAGGACAAGAAGgtgagccctcttaacttcttagccgtagccggtagcttc--tctttagctccaggggatgcggttcatggtgcaatgcactgcctcctgtgcttagaattat-
|||||||||||| ||||| ||||||||||| |||||||||||| |||||||||||||||| ||||| ||||| |||||||| |||||||| ||||||||||||| ||| | || | | | || ||| | | | | || | || | | | || || | | | || | |||
GAAGTTCGAGGCGGACCTGAAGAAGGAGATTAAGAAGCTGCAGAGGTACAGGGACCAGATTAAGACTTGGATTCAGTCCAGTGAGATCAAAGACAAGAAGgtgaaaattctca--ttttaatcttgtgctggttattgtaatttctgtctttctttcaattggcttaagttg-aacctagcacacgcaatgtcgaattgtatt
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA16G04690.1 (Glycine max), 5'ss of exon 2
GAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGTGGATCCAGTCCAGCGAGATCAAGGACAAGAAGgtgagccctcttaacttcttagccgtagccggtagcttctctttagctccaggggatgcggttcatggtgcaat-----gcactgcctcctgtgcttagaattat
||| || || || ||||||||||||||||| |||||||| ||| ||||||| ||||| || ||||| ||||| |||||||| |||||||| ||||| ||||| |||| | || || | | || | || ||| | | ||| || | || | | | | | | | |
GAAATTTGAAGCGGACCTCAAGAAGGAGATTAAGAAGCTCCAGAGGTACAGAGACCAAATTAAGACTTGGATTCAGTCCAGTGAGATCAAAGACAAAAAGgta---ttgattaattcattgcttgttccagaatgcaacca--aagtgccaaagtttttagttttctatgtttttttaaacattagttaattttgtcggcgatgt
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA02G07830.1 (Glycine max), 5'ss of exon 2
GAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGTGGATCCAGTCCAGCGAGATCAAGGACAAGAAGgtgagccctcttaacttcttagccgtagccggtagcttctctttagctccaggggatgcggttcatggtgcaatgcactgcctcctgtgcttagaattat
|||||||||||| ||||| ||||||||||| |||||||||||| |||||||||||||||| ||||| ||||| |||||||| |||||||| ||||||||||||| || | | ||| | | | | | || | | | || | | || | || | | | | |||||
GAAGTTCGAGGCTGACCTGAAGAAGGAGATTAAGAAGCTGCAGAGGTACAGGGACCAGATTAAGACATGGATTCAGTCCAGTGAGATCAAAGACAAGAAGgtgactaaatttttccttttaatcttgtgctgctggttattgtaatttctgtatgtctttctatcaattggcttaagttgaacctagcacatgctattat
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 2
lower sequence: AT5G18230.1 (Arabidopsis thaliana), 5'ss of exon 2
GAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGTGGATCCAGTCCAGCGAGATCAAGGACAAGAAGgtgagccctcttaacttcttagccgtagccggtagcttctctttagctccaggggatgcggttcatggtgcaatgcactgcctc---ctgtgctta-gaattat--
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AAAGTTTGAGGCGGACTTGAAGAAGGAAATCAAGAAGCTGCAGCGGTATAGAGACCAGATCAAGACATGGATTCAGTCTAGTGAGATCAAAGATAAGAAAgtaagtggtctt--cttctt---cacagcctttttttttgtttaattgactaatgatgcgacttg-gatcccttgcattctcttaaattgcacctgcaaaccataa
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 5'ss of exon 2
GAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGTGGATCCAGTCCAGCGAGATCAAGGACAAGAAGgtgagccctcttaacttcttagccgtagccggtagcttctctttagctccaggggatgcggttcatggtgcaatgcactgcctcctgtgcttagaattat------
|||||| ||||| || | ||||||||||||||||| || |||||||| || |||||||||||||| ||||| ||||||||||||||||||||||||||||| || ||| | ||| || | || | || |||| | | | || || | | | | || ||| || ||
GAAGTTTGAGGCTGATTTGAAGAAGGAGATCAAGAAACTTCAGCGGTATAGAGACCAGATCAAGACATGGATTCAGTCCAGCGAGATCAAGGACAAGAAGgttag---tctcag--tctcagtcccagttcct-gcctctcctctttcctttcttttccgactccttttttctttttttccccaagagacttcgatttgggtgggg
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S101_120V6.1 (Physcomitrella patens), 5'ss of exon 3
GAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGTGGATCCAGTCCAGCGAGATCAAGGACAAGAAGgt--------gagccctcttaacttcttagccgtagccggtagcttctctttagctccaggggatgcggttcatggtg--caatgcactgcctcctgtgcttagaattat
||||||||||||||| | ||||| |||||||||||||| ||||| || | || || ||||||| |||||| || ||||| ||||| || ||||| ||||| || | || | | | || | || | ||| | | | | | | ||| || | | || | || | || ||| ||
GAAGTTCGAGGCCGATTTAAAGAAAGAGATCAAGAAGCTACAGCGTTATCGTGATCAAATCAAGATGTGGATTCAATCCAGTGAGATTAAAGACAAAAAGgtattaaagagaaaagatcatatgtcacaactaaatgtcgtggtttttttttcgtttc----gtttctcttcgtgcttttcgatcccct-tttttagtccttgga-----
upper sequence: LOC_Os03g44900.3 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ20408 (Selaginella moellendorffii), 5'ss of exon 2
GAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGTGGATCCAGTCCAGCGAGATCAAGGACAAGAAGgtgagccctcttaacttcttagccgtagccggtagcttctctttagctccaggggatgcggttcatggtgcaatgcactgcctcctgtgcttagaattat
|||||| |||||||| ||||||||||| ||||||||||| ||||| |||||||||||||| ||||||||||| |||||||| || ||||||||||||||||||| | ||||| | | | || || | | |
GAAGTTTGAGGCCGATCTCAAGAAGGAAATCAAGAAGCTACAGCGATACAGGGACCAGATTAAGACGTGGATTCAGTCCAGTGAAATCAAGGACAAGAAGgtga--ttaggcagtttcttc-tagcgatttttttttcttcattcgttttgatag---------------------------------------------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|58658862|gb|CK047542.1|CK047542EST: GGGACCAGATCAAGACGTGGATCCAGTCCAGCGAGATCAAGGACAAGAAG -GC-TCTTATG
genomic: GGGACCAGATCAAGACGTGGATCCAGTCCAGCGAGATCAAGGACAAGAAGgtgagccctc ... cataggttagTGCCTCTTATG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAAGTTCGAGGCCGACCTCAAGAAGGAGATCAAGAAGCTGCAGCGGTACAGGGACCAGATCAAGACGTGGATCCAGTCCAGCGAGATCAAGGACAAGAAGgtgagccctcttaacttcttagccgtagccggtagcttctctttagctccaggggatgcggttcatggtgcaatgcactgcctcctgtgcttagaattat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG