Sequence
atgc intronic sequence ATGC exonic sequence...aattagatgtgaatacaaatattagtagcaattaaaacgtctcattccattataattcagttatgtcaggtaaaccatactgacttaatgtacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os07g06440.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 8
aattagatgtgaatacaaatattagtagcaattaaaacgtctcattccattataattcagttatgtcaggtaaaccatactgacttaatgtacaat-gcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA
|| || || ||| ||| | | ||| | | | | || | | || | | | ||| | || | | | | |||||| ||||||| ||||||||||| |||| ||||||||||||||||||| ||| ||||||| |||||| |||||||||| ||||| |||||||| |||||
-tttccatttggatattgataactgaaacaactgtagaatttgatactctgttattctttatctcccagtcgagtcagatgattgtgaatcgtggttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA
upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G384762_T01 (Zea mays), 3'ss of exon 8
aattagatgtgaatacaaatattagtagcaattaaaacgtctcat--tccattataattcagttat--gtcaggtaaaccatactgacttaatgtacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA
|| || || ||| ||| | | ||| | || | | || || |||| || | | ||| ||| | || | | || ||||||| ||||||| ||||||||||| |||| ||||||||||||||||||| ||| ||||||| |||||| |||||||||| ||| | |||||||| |||||
-tttccatttggatattgataactgaaacaactgtaaaatttgatactctgttattctttatctcccagtcgggtcag--atgattgtgcatcgtg-gttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTTGAGAGGTTGATGATAGAAACATATTCTCCATATTGTGA
upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G081668_T02 (Zea mays), 3'ss of exon 10
aattagatgtgaatacaaatattagtagcaattaaaacgtctcat--tccattataattcagttat--gtcaggtaaaccatactgacttaatgtacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA
|| || || ||| ||| | | ||| | || | | || || |||| || | | ||| ||| | || | | || ||||||| ||||||| | ||||||||| |||| | ||||||||||||| ||| ||| ||||||| |||||| ||||||| || ||||| |||||||| |||||
-tttccatttggatattgataactgaaacaactgtaaaatttgatactctgttattctttatctcccagtcgggtcag--atgattgtgcatcgtg-gttgcagGTGTTAATGGTTCCTCTCTGAAAACTAACGGAAATCTTGAGGTTGTACGAGGCATTCCTGTCGAGAGGTTGATGATGGAAACAGATTCTCCATATTGTGA
upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G058862_T01 (Zea mays), 3'ss of exon 1
aattagatgtgaatacaaatattagtagcaattaaaacgtctcat--tccattataattcagttat--gtcaggtaaaccatactgacttaatgtacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA-
|| || || ||| ||| | | ||| | || | | || || |||| || | | ||| ||| | || | | || ||||||| | ||||| ||||||||||| |||| ||||||||||||||||||| ||| ||||||| |||||| |||||||||| ||||| |||||||| |||||
-tttccatttggatattgataactgaaacaactgtaaaatttgatactctgttattctttatctcccagtcgggtcag--atgattgtgcatcgtg-gttgcagGTGT-AATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGAC
upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G051032_T01 (Zea mays), 3'ss of exon 10
aattagatgtgaatacaaatattagtagcaattaaaacgtctcattccattataattcagttatgtcaggtaaaccatac--tgacttaatgtacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA
|| || || ||| ||| | | ||| || || | | || | | || | | | || || | | | | || ||||||| ||||||| ||||||||||| |||| ||||||||||||||||||| ||| ||||||| |||||| |||||||||| ||||| |||||||| |||||
-tttccatttggatattgataactgaaacaactataaaatttgatactctgttattctttgtctcctagtggggtcagatgattatgcatcgtg-gttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA
upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G058862_T02 (Zea mays), 3'ss of exon 2
-------------------------------aattagatgtgaatacaaatattagtagcaattaaaacgtctcat--tccattataattcagttat--gtcaggtaaaccatactgacttaatgtacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA
| || || || ||| ||| | | ||| | || | | || || |||| || | | ||| ||| | || | | || ||||||| | ||||| ||||||||||| |||| ||||||||||||||||||| ||| ||||||| ||||||
ttcctctttgtgattcagttctgtgttgaacatttccatttggatattgataactgaaacaactgtaaaatttgatactctgttattctttatctcccagTCGGGTCAG--ATGATTGTGCATCGTG-GTTGCAGGTGT-AATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGT-------------------------------
upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G894029_T01 (Zea mays), 3'ss of exon 16
aattagatgtgaatacaaatattagtagcaattaaaacgtctcattccattataattcagttatgtcaggtaaaccatactgacttaatgtacaat-gcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA
|| || || ||| ||| | | ||| | || | | || | | || | | | ||| | || | | | | |||||| ||||||| | |||||| || |||| | ||||||||||||||||| ||| ||||||| |||||| ||||||| || ||||| |||||||| |||||
-tttccatttggatattgataactgaaacaactgtaaaatttgatactctgttattctttatctcccagttgggtcagatgattgtgcatcatggttgcagGTGTTAATGGTTCCTCTCTAAAAACTAACGGAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATGGAAACAGATTCTCCATATTGTGA
upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G137367_T01 (Zea mays), 3'ss of exon 12
aattagatgtgaatacaaatattagtagcaatt---aaaacgtctcattccattataattcagttat--gtcaggtaaaccatactgacttaatgtacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA
| | || ||| ||| | | ||| | |||| | | || |||| || | | ||| ||| | || | | || ||||||| ||||||| ||||||||||| |||| ||||||||||||||||||| ||| ||||||| |||||| |||||||||| ||||| |||||||| |||||
--tccattttggatattgataactgaaacaactgtaaaaatttgatactctgttattctttatctcccagtcgggtcag--atgattgtgcatcgtg-gttgcagGTGTTAATGGTTGCTCTCTGAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTTGAGAGGTTGATGATAGAAACAGATTCTCCATATTGTGA
upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G704381_T01 (Zea mays), 3'ss of exon 3
aattagatgtgaatacaaatattagtagcaattaaaacgtctcat--tccattataattcagttat--gtcaggtaaaccatactgacttaatgtacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA
|| || || ||| ||| | | ||| || || | | || || |||| || | | ||| ||| | || | | || ||||||| ||||||| |||||||| || |||| ||||||||||||||||||| ||| ||||||| |||||| |||||||||| ||| | |||||||| |||||
-tttccatttggatattgataactgaaacaactataaaatttgatactctgttattctttatctcccagtcgggtcag--atgattgtgcatcgtg-gttgcagGTGTTAATGGTTGCTCTCTAAAAACTAACGAAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATAGAAACAAATTCTCCATATTGTGA
upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G455171_T01 (Zea mays), 3'ss of exon 14
aattagatgtgaatacaaatattagtagcaattaaaacgtctcat--tccattataattcagttat--gtcaggtaaaccatactgacttaatgtacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA
|| || || ||| ||| | | ||| | || | | || || |||| || | ||| ||| || || | | || ||||||| ||||||| | ||||||||| |||| ||||||||||||||||| ||| ||||||| |||||| ||||||| || ||| | |||||||| |||||
-tttccatttggatattgataactgaaacaactgtaaaatttgatactctgttattctttgtctcccagtcgggtcaa--atgattgtgcatcgtg-gttgcagGTGTTAATGGTTCCTCTCTGAAAACTAACCGAAATCTTGAGGTTCTACGAGGCATTCCTGTCGAGAGGTTGATGATGGAAACATATTCTCCATATTGTGA
upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA19G38780.1 (Glycine max), 3'ss of exon 9
---aattagatgtgaata-caaatattag-tagcaattaaaacgtctcattccattataattcagttatgtcaggtaaaccat-actgacttaatgtacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA
|| | | | | | || ||||| | | | | | | ||||||| | ||| | | | | | | |||| | ||| | | | ||||| || ||||| |||||||||||||| | ||| || ||||| ||| | | |||||||| | ||||| |||||||| ||||| ||||| |||||||||||
ttgcataaagtttcactttcagatattggattgtggggattaaatagcattccagtcaaatcccatga----atattacccatcattgattctgtctgtg--gcagGCATAAATGGGTGCTCTCTGAAGACGACTGAGAACCTTGATGTTGTTAAGGGTATTCCAGTTGAGAGAATGATGATTGAGACGGACTCACCATACTGTGA
upper sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv08s0032g01170.t01 (Vitis vinifera), 3'ss of exon 9
aattagatgtgaatacaaatattagtagcaattaaaacgtctcattccattataattcagttatgtca-ggtaaaccatactgacttaa---tgtacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA
|| | | | || | | || | | ||| ||| | |||| | || ||| | | | || ||||| |||| | ||||| ||||||||||||||| |||||||||||| ||| || |||||||||| ||||| ||||||| |||||||| |||||||| |||||
--ataattttctgcttggtttttgttttcttgtatatgactt--ttcacttagatgtcagatgaatcttaataatctttgttcttttttctttgtacccaatagGTGTAAATGGTTGCTCTCTGAAGACTGCTGAAAATCTTGAAGTTGTAAGGGGTATTCCTGTTGAGAGACTGATGATTGAGACAGATTCTCCATATTGTGAMapped 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|27334380|gb|CA882831.1|CA882831EST: AACTGCAGAGGACCGTGATAAGCTTCTTTCCTTTGAAAAGATGTTTATAG GTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAG
genomic: AACTGCAGAGGACCGTGATAAGCTTCTTTCCTTTGAAAAGATGTTTATAGgtcatctcct ... tacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAG
EST:
gi|58695600|gb|CK084287.1|CK084287EST: AACTGCAGAGGACCGTGATAAGCTTCTTTCCTTTGAAAAGATGTTTATAG GTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAG
genomic: AACTGCAGAGGACCGTGATAAGCTTCTTTCCTTTGAAAAGATGTTTATAGgtcatctcct ... tacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAG
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:
65 (upstream exon),
38 (downstream exon)
Score:
5ATTCCCTGGGGGTGTTACACACTCCTTCACTGGAACTGCAGAGGACCGTGATAAGCTTCTTTCCTTTGAAAAGATGTTTATAGgtcatctcct ... tacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccattataattcagttatgtcaggtaaaccatactgacttaatgtacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA
tataattcagttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattagatgtgaatacaaatattagtagcaattaaaacgtctcattccattataattcagttatgtcaggtaaaccatactgacttaatgtacaatgcagGTATTAATGGATGCTCTCTGAAGACTAGTGAAAATCTTGAGGTTCTACAAGGTATTCCTGCAGAGAGGATGATGATAGAGACAGACTCTCCATACTGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - acaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catactg