Sequence
atgc intronic sequence ATGC exonic sequenceATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaattcattgattttccttttgttttgtttttttcattgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa...
Basic information
species | Oryza sativa |
transcript | LOC_Os03g18310.1 |
intron # | 18 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM5G824405_T02 (Zea mays), 5'ss of exon 17
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaattcattgatttt----ccttttgttttgtttttttcattgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa
|||||||||||||| |||||||| || || ||||| |||||||||||||||| || |||||||||||||||| ||||||||||||||||||||||| |||||| |||| | | |||| | || | | | | ||| | | | || || | | ||| ||
ATACAATGGCGTGCTCTTGATGAGATCAATGCTGGGGTCTGTGATGGGATGACATACGATGAAATAAAGAAAAGTAAACCTGAAGAATATGAgtacgtgaattcactgatatcatgacattttatattaaaaaatccccctgatcactctgtcactcagaattttgttcagctgtgggtgtgtgttggtgct----
upper sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 19
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacg---caaattcattgattttccttttgttttgtttttttcat-tgaagc--tatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa---------------------------------------
||||||||||| ||||||||||| ||||| ||||| | |||||||||||||||||||| ||||| ||||| | | || || || |||||||| | ||| | | || | ||| | | ||| | || || | || | | ||| || | ||| | ||| || | ||| | | ||
ATACAATGGCGCGCACTTGATGAGATAAATGCTGGTGTGTGTGATGGGATGACGTATGAAGAAATCAAGAAGAACATGCCAGAGGAGTATGAgtatgtcacaagcttgt-aatctgtcttatttccagttgaatgcaaatggtacattagatataaaagcaagtgcttgttggg--agcaca-atgctgtctaaaaatgtttaaacactattcttattttattttattttgttgcag
upper sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA14G37520.1 (Glycine max), 5'ss of exon 30
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacg---caaattcattgattttccttttgttttgtttttttc-attgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa-------------------------------------------------
||||||||||| ||||||||||| ||||| || || | |||||||||| ||| ||||| ||||| ||||| | | || || || || ||||| | |||| | | |||| ||| | | ||| | | | || | | | | || || | || || ||| | ||
ATACAATGGCGCGCACTTGATGAGATAAATGCCGGTGTGTGTGATGGGAAGACATATGAAGAAATCAAGAAGAACATGCCAGAGGAGTACGAgtatgtcacaaacttgt-aatttgtcttatttccagttgaatgctactggtacatcagataaaaaaaaccagtgcgtg-gtgggagcacgtgctgtttaaaaatgttttaaacacttttgttattttattttattttgccttttctattgcag
upper sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 20
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacg----caaattcattgattttccttttgtttt---gtttttttcattgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaag--taaa-------------------------------------------------------
||||||||||||||||||||||| ||||| || || | |||||||| ||||| || | ||||| ||||||| | || || || |||||||| | || | | | |||| || || ||| ||| | || || | | | | | | || | || | | | | | || |
ATACAATGGCGTGCACTTGATGAGATAAATGCAGGGGTGTGTGATGGTATGACATACGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAgtatgtttgcagacttgt-aatttctctcttatttgcaagttgaatgcaactaatatggcagataacaaagaagcacaatgtgaaacatcttttggttttggggttagaagatgctgtttaaactcagtagttattatttccctcccctattgtcttattgcag
upper sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA18G06770.1 (Glycine max), 5'ss of exon 21
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacg---caaattcattgattttccttttgtttt---gtttttttcattgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa----------------------------------------------------------
|||||||||||||||||||||| |||||||| || | |||||||| ||||| |||| ||||| ||||||| | || || || |||||||| | |||| | | |||| || || ||| ||| | | || || | ||| | | | | | || | || | | | | | ||
-TACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGGTATGACATATGCAGAAATCAAGAAAAACATGCCAGAGGAGTATGAGtatgttgcaaacttgt-aatttctctcttatttgcaagttgtatgcaactaatatgtctgataataaagaagcacaatgtgaaacttcttttggttttggggtaagaagatgctgtttaaattccgtaattattatttccctcccctcttattttgttacaga
upper sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA11G27410.1 (Glycine max), 5'ss of exon 25
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTA-TGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaattcattgattttccttttgttttgtttttttca-ttgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa
||||||||||||||||||||||| |||||||| || | |||||||| ||||| || | ||||| ||||||| | || || || |||||||| | || || || ||| | | | ||| | ||||| | || | | |||
ATACAATGGCGTGCACTTGATGAGATAAACGCAGGGGTGTGTGATGgtatgacataacgcagaaatcaagaaaaacatgccagaggagtatgagtatg----tttgcagacttgtaatttctctcttatttgcaagttgaatgcaactaatatggcag------------------------------------
upper sequence: LOC_Os03g18310.2 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 19
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaattcattgattttccttttgttttgtttttttcattgaagctatcttttgt---tgcatttgttctttgagtaa-gcccatgtcctgccaagtaaa-
||||||||||||||||||||||| ||||| ||||| | |||||||| ||||| ||||| || |||||||| | | ||||| ||||| ||||| | ||| || | ||| |||| | || || | |||| | | || || | | | || ||| | || || | |
ATACAATGGCGTGCACTTGATGAGATAAATGCTGGAGTGTGTGATGGAATGACATATGAAGAGATAAAGAAGAACATGCCTGAGGAATACGAgtatgagcatttttta----tttgtttaagaaattttcatgatgtaatttttcttccatgcatacacatgatgatagcttattagacata-cttgtcatattacaMapped 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|25044722|gb|AJ420705.1|AJ420705EST: GATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA ATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTA
genomic: GATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaat ... cctttttcagATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTA
EST:
gi|86436870|gb|CI118592.1|CI118592EST: AATAAAGAAAATTAAACCTGAAGAATATGA ATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTA
genomic: AATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaat ... cctttttcagATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTA
EST:
gi|58672416|gb|CK061102.1|CK061102EST: GATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA ATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTA
genomic: GATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaat ... cctttttcagATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTA
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
68 (upstream exon),
69 (downstream exon)
Score:
11ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaat ... cctttttcagATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAG
<
<
<
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATACAATGGCGTGCACTTGATGAAATAAACGCTGGCATCTGTGATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaattcattgattttccttttgttttgtttttttcattgaagctatcttttgttgcatttgttctttgagtaagcccatgtcctgccaagtaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA