Sequence
atgc intronic sequence ATGC exonic sequencegtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g41630.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 10
gtaattctgtacatgttaaga-tgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
|||||| | |||||||||| | |||||| || ||||||| ||| ||| | || | | ||| |||||| | ||||| ||||| || ||| | |||||||| |||||||||||||||||||||| || |||||||| || |||||||| |||||||| || |||||||| |||||||||||||||| |||||
gtaatttcttccatgttaagagtaaataattgatgattctttgtggacaatgcataacacatatttttgctggagccaaactgatccatgtgttactt---ggaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTTGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG
upper sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 10
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
|||||| | ||||||||||| |||||| || ||||||| | | ||||| | | | ||| ||||| || ||||| ||||| || || ||||||||| |||||||||||||||||||||| || ||||| || || |||||||| |||||||| || |||||||| |||||||||||||||| |||||
gtaatttcttccatgttaagataaataattgatggttctttgtgcacaatgaatagcacatatttttgctggaacaaacctgatccatgtgttactc---aaaactgcagTTATGTGATTTATATGAAAATGACTCAATTTTCGACAAATTTGAGTGTTGTCAAAGTGGTGATGGATTAAGAGTAGCAACTGGTTCCTACAG
upper sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttc-actggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
| | || |||| || | | || | |||| |||| || | | | || | || || | | | | || | ||||| ||||||||||||||||||||||| |||||||||||||||||||| |||| ||| || ||||||||||| || ||||||||||||||||
-------------------gttagatt-cccatgtttatataagta--atgagcaatgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG
upper sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 10
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
| ||| | | | || | | | ||| ||| |||| | | ||| || | | ||||| ||||||||||||||||||||||| || || |||||||| || || |||| ||| || ||||||||||| ||||||||||||||||||||
--------------------------gtttgataagtgatgaattatgaatttctttctactgttttgtctgagttataactggttatgctttttgtttgaacgtgccagCTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAG
upper sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 10
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
|| | | |||| |||| | | || || | ||| |||| | ||| || | || ||| || || | || | | | ||||| || ||||||||||||||||| || || ||||||||||| || || |||| ||| || ||||||||||| |||||||||||||||||||
gttagatt-cctgtgtttagataagtgatgaat-----tatgaatttcat------tctactgctttgtcgagttataactggtt-atattttatgtttgaacatgccagCTTTGCGATTTATATGAAAATGACTCAATCTTTGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCTTAGCAACTGGTTCTTACAG
upper sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
| | || |||| || |||| | ||||| | || || | ||| | | | | || || || ||||| ||||||||||||||||||||||| |||||||||||||||||||| |||| ||| || ||||||||||| || ||||||| ||||||||
-------------------gttagatt-cccatgtttggatgagca--atgaatt-tctgctgctttatca-agttatagtaactggctcttttttttttggc----cagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG
upper sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctga--aactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
| | | | | || | |||||| || ||| | | | ||| | |||| | | | | ||| || | | ||||| |||||||||||||||||||||||||| ||||| ||||| ||||| ||| ||| || |||| ||||||| ||| || |||||||||||
--------------------gtcagt--ttcctaatattttgagagagat--acatttggcga----gttggtgctttgctgaatggtat-tccctttgtggtcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG
upper sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
| ||||||| | ||| || | ||| || | || | || || || || |||||||||| ||| ||||||||||||| ||||| |||||||| |||||||| |||| || || ||||||||| | |||||||| |||||||||||
---------------------------gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagct--aaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG
upper sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 10
gtaattctgtacatgttaagatgaataatccatactt----ctttgaggatcatgaa-caataaactatttcactg--gagtaact----ctgattcatg--tattgcttcctgaaactg---cagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
|| ||| | | | || | | | | || |||||| ||| | || || | || | ||| || || || ||| | | || || ||||| ||||||||||||||||||||||| || || || || |||||||| |||| || ||||||||| | ||||| || |||||||| |||||
gtgatttcacttct-tcatgaagcttcctttttttttggtgctttgatttgaatggagttattttgggctttattgtcaaataatatgaactatttaattattatcattatttaaatcttgatcagCTGTGTGATTTATATGAAAATGATTCTATCTTCGACAAATTTGAGTGTTGTCTGAGTGGAGATGGACTACGAGTGGCGACTGGTTCCTACAG
upper sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 10
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
|| | || | | ||| | | | || | || | | | ||| || | || ||| | | | | | || ||| | || ||| | ||||||||||||||||||||||| || |||||||| ||||| || |||| || || |||||| |||| ||||| || |||||||||||
gtgagcttgctt-tcctcagaaaagtcttacaca-------gaacaacttctacatta----ctctctgcatgctaatttta--ccctctgtttctttccttctctccagTTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAG
upper sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
--gtaattctgtacatgttaagatgaataatccatacttctt-tgaggatcatgaacaataaac-----tatttcactggagtaactctgattcatgta-ttgcttcctgaaactg--cagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
| ||| | | | | || | || || ||| | | | | || | | | | ||| | | | ||| | | | |||| | | ||| |||| || ||| | || ||||| |||||||||||||| || ||||| ||||||||||| |||| || ||||||||| ||||| ||||||||||| |||||
gtgcgattttcttc-ttttgaaatctatcatctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG
upper sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 10
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
|| | | | ||||| | | || | ||| ||| || | | | | || | ||| | ||| ||| || | ||||||| | |||||||| |||||||| || ||||| || ||||||||||| |||| || || ||||| |||| ||||| |||||||| |||||
---atcttattcgtgttatttttatctggtattattggcttggtattcaagatccgcaggtgctgggaatgtactaatataagt---tgttttgtatcgt----ttgcagCTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGMapped 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|38568585|gb|CD670800.1|CD670800EST: ACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAG CTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGT
genomic: ACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgt ... gaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGT
EST:
gi|58590817|gb|CF989125.1|CF989125EST: ACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAG CTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGT
genomic: ACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgt ... gaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGT
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:
49 (upstream exon),
72 (downstream exon)
Score:
12CTTTGGGATATTAACATGAACTCTGGTCCAGTTGCAACATTCCAGGTTCATGAGTATTTAAGGCCCAAGgtaattctgt ... gaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
cttcctg CT-rich tract
tatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattctgtacatgttaagatgaataatccatacttctttgaggatcatgaacaataaactatttcactggagtaactctgattcatgtattgcttcctgaaactgcagCTATGTGATTTATATGAAAATGATTCCATTTTTGATAAGTTTGAGTGCTGTCAAAGCGGAGATGGATTGCGAGTAGCAACTGGTTCTTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA