Sequence
atgc intronic sequence ATGC exonic sequence...gattctgttgttgtagtaaaattaaattaatctcaaatctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgtattcatttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g11840.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 11
gattctgttgttgtagtaaaattaaattaatctca-aatctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgtattcatttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
| || || | | | | ||| | | | || ||||| | || | || | | | |||| || | | |||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||||||||||||| ||||
gtttgaattatcatgattttttaaaacttgttttgtggtcatgtatatcttttttgtgctg-gtttacattattaatatactggtgtgatatttgtttcagAGCTTAAGACACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATATACACAGCATTAGCATGGAGAAATAGATCATTTGGGT
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 11
gattctgttgttgtagtaaaattaaattaatctcaaat---ctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgtattcatttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
|| || | || | ||||| | || | ||| | || ||| || || | | | |||| ||| || | | |||| |||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||| || |||||||||||||| |||||||| ||||
-atcatgattttttt-taaaacttgttttgtgtcatgcataccagcatatcttatttgtgctagtttaggttaatgata-tactggtgtgatatttgtttcagAGTTTAAGGCACAATCCGAATGGGAGATTTGTAGTTGTATGTGGAGATGGAGAATACATAATATACACAGCCTTAGCATGGAGAAACAGATCATTTGGGT
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
gattctgttgttgtagtaaaattaaattaatctcaaatctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgtattcattt--cagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
|| ||| || | ||| | || | | | | | ||| | || | | | || | | | | | ||| ||| |||| |||| ||||||||| |||||||| ||||||||||||||||||||||| || ||||| || ||||||||||| |||||||||||||| ||||| || |
agaagtga-gttttaaaataatagtccttattgcgggttcaattatcagcaatatttgt-tttatgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
-gattctgttgttgtagtaaaattaaattaatctcaaatctagtat--agtgtaattatagtgtatgttagtaattatagtaattatagtgtattcatttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
|| | || | || | | ||| | || | ||| | || || | | || | |||| || | || | | || | |||| |||| ||||||||| |||||||| ||||||||||| ||||||||||| || ||||| || ||||||||||| |||||||||||||| ||||| || |
agaagtgagttttaaaacaatagtcc-ttattgctggttcaattatcaacaatatttgtttcatgggtggtgacttattgttgatttaatttgttg--tgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
---gattctgttgttgtagtaaaattaaattaatctcaaatctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgtattc----atttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
|| | | | | || ||||| ||| || | || | || | || ||||| | | | || | | || | | | |||| ||||||||||||||||||||||| ||||||||||| ||||||||||| || || || || ||||||| || |||||||||||||||||||| || |
taaaataataatccaccccttagttttaatta---tcaccacttatttatt----ttttcatgcatgttgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
gattctgttgttgtagtaaaattaaattaatctcaaatctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgta--ttcatt-tcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
|| || ||| | | | | ||| | | | | || | | ||||| | | | || | | || || ||| |||||| ||||||||||||| |||||||| || |||||||| ||||||||||| ||||| || || |||||||| || |||||||||||||||||||| || |
---agctttaaaataataatctgccccttagttttaattatttccacttttttttttaagcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G15980.5 (Arabidopsis thaliana), 3'ss of exon 11
-----gattctgttgttgtagtaaaattaaattaatctcaaatctagtatagtgtaattatagtgtatgttag--taattatagt-------aattatagtgtattca--tttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
| | ||| | || ||| | | | | ||| || | ||||| || ||||||| | ||||| | | | ||||||||| | |||||| || |||||||| ||||| || || || || |||||||| ||||||||||||||||| || || ||||||
atttgaaatgaagcgttaatagatgataaaaatgaaactctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagCTATTCTAACTCTCAGAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGA----------------
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 11
gattctgttgttgtagtaaaattaaattaatctcaaatctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgtattc----atttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
| | | || | | | | | | | || ||| | || | | | | || | | | | | | | ||| || || ||||||||| | |||||| || |||||||| ||||| || || ||||| || |||||||| ||||||||||| || || || ||||||||||| ||||| || |
aagtgcctcaaagttatgggtatcgctaagccgcgtcttcagaata-tatatctgt--tctcacttgatctgtgtctcatatgtgg-gtactcttgaatctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGTGGTGACGGAGAATATATAATCTACACGGCTTTGGCTTGGAGAAATAGGTCATTTGGTT
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 15
gattctgttgttgtagtaaaattaaattaatctcaaatctagtatag----tgtaattatagtgtat-gttagtaattatagtaattatagtgtattcatttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
| | || |||||| | || | | || ||||| ||| ||| | || | | || | || || || ||| | | ||||||||||| | |||||| || ||||| || ||||| || || ||||||||||| || || || ||||||||||| || || ||| ||||||| ||||| || |
---ttactggtattagtaaga--aatatgaccttaaatcatttattaattttgtgactacccactgtcatttatgtttctattatttaattttttgctttttcagAGCTTGAAGCACAACCCTAATGGTAGGTTTGTGGTAGTTTGTGGAGATGGTGAGTATATTATCTACACTGCCTTGGCGTGGCGAAATAGGTCATTTGGCT
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
gattctgttgttgtagtaaaattaaatta-atctcaaatctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgtattca--tttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
| | | | | | ||| | || || | || || | ||||| | || || ||| || | ||||| | | | ||||||||| | |||||| || |||||||| ||||| || || || || |||||||| ||||||||||||||||| || || |||||||||||||| || ||||
taatagatgataaaaatgaaactctgtttcatatgaagtccca-agagtgtggtc-cagaata-attatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 11
-gattctgttgttgtagtaaaattaaattaatctcaaatctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgtatt-catttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
||| | | | | | ||| | | | | | || | || ||| ||| || || || | | | || | | | || ||||||||| ||| || || || |||||||| ||||||||||| ||||||||||| || ||||| || || || || || |||||||| ||||| || || || |
gcattaagctaggat-gaatgattgtttccaccatat-tttaatttattgttatttatgtttacatttatttcttccttttttttttttttttgtgtttcagAGCCTAAAACATAACCCAAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGTGAGTACATTATATATACAGCTTTGGCATGGAGGAATAGGTCTTTTGGTT
upper sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
gattctgttgttgtagtaaaat---taaattaatctcaaatctagtatagt-gtaattatagtgtatgttagtaattatagtaattatagtgtattcatttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
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-actttttctctaagaggcagtgcatagaatatgtgcgggctcagtttttttgttgtcacattatg-gttaatgacttttgtttttttggtt--ttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCTMapped 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|88299886|gb|CI579947.1|CI579947EST: GCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA AGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGA
genomic: GCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtatgttcat ... ttcatttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGA
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:
74 (upstream exon),
72 (downstream exon)
Score:
34ATTGCAGATGGTGAGCGCTTACCCTTAGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtatgttcat ... ttcatttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgtaattatagtgtatgttagtaattatagtaattatagtgtattcatttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
ttcatttc CT-rich tract
aattatagtgtatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gattctgttgttgtagtaaaattaaattaatctcaaatctagtatagtgtaattatagtgtatgttagtaattatagtaattatagtgtattcatttcagAGCTTAAGGCACAATCCGAATGGGAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACTGCATTAGCATGGAGAAATAGATCATTCGGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA