Sequence
atgc intronic sequence ATGC exonic sequencegtaagctttgctgtacttttatatcccttgaagcatacaaagctttttaagcatgttatggttgcattgaaattttccttgcatgtttgattgttctatgtggtaattcatatggacgtttgtcaatcatgtggcttacctaaaatatatttctcttgtggcaatgcatattccagGGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTGCTGGTATCGCGGCACTAATAAAACAGAAGAACCCCAAGTGGAGTCCCTC
Basic information
species | Oryza sativa |
transcript | LOC_Os06g48650.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g48650.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G114394_T02 (Zea mays), 3'ss of exon 9
----gtaagctttg-ctgtacttttatatcccttga---agcatacaaagctttt-taagcatgttatggttgcattgaaattttccttgcatgtttgattgttctatgtggtaattcatatggacgtttgtcaatcatgtggcttacctaaaatatatttctcttgtggcaatgcatattccagGGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTGCTGGTATCGCGGCACTAATAAAACAGAAGAACCCCAAGTGGAGTCCCTC
| || ||| ||||| | | |||| || |||| || | | || || ||| ||| | ||||| | || | | || || | || ||| || | | | || || || | ||||| ||| || | |||| ||||||||||||||||||||||||||||| ||||| ||||| ||||| ||||| || |||||||| ||||| ||||||||||| |||||||| |||||
gtaagcgtgcgttgtctgtagacctcttcccctcgaggaagcacccatgattaccatcagtattttactactgcgctcttgccgcccttgtgcat---atcttctggattagtgatcggtggtgatatttttctgtgctcgaaccaactcaacat-------tgctgtggtaat--atttctcagGTGAAGGATTTGCAATGGTTTCTGGAACTAGCATGGCCGCACCGCATATCGCTGGCATTGCGGCACTGATAAAGCAGAAGAACCCAAAGTGGAGCCCCTC
upper sequence: LOC_Os06g48650.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G099452_T02 (Zea mays), 3'ss of exon 9
gtaagctttgc-tgtacttttatatcccttgaagcatacaaagctttttaagcat-gttatggttgca--ttgaaattttccttgcatgtttgattgttctatg---tggtaattcatatggacgtttgtcaatcatgtggcttacctaaaatatatttctcttgtggcaatgcatattccagGGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTGCTGGTATCGCGGCACTAATAAAACAGAAGAACCCCAAGTGGAGTCCCTC
|||||||||| |||| | | | | | | ||| | || | | | | || | | || | | ||| | |||| | || | || | || |||| | ||| | | || | | | | ||||| | |||||| ||| | | |||| ||||||||||||||||||||||||||||| |||||||| || ||||||||||| || || ||||| ||||| ||||||||||| |||||||| |||||
gtaagctttgtatgtagatctctttttcctcaaggaagcac--ccatgtgattatcgccagcattttagttctgcgcttttgccgtccttttgcatattttgtggactagtgattcttgaggatatctttctgtgcttgaaccaattcaaaat-------tgttgtggtaatattt-tcgcagGTGAAGGATTTGCAATGGTTTCTGGAACTAGCATGGCTGCGCCGCATATTGCTGGCATTGCAGCACTGATAAAGCAGAAGAACCCAAAGTGGAGCCCCTC
upper sequence: LOC_Os06g48650.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G00580.1 (Glycine max), 3'ss of exon 8
gtaagctttgctgtacttttatatcccttgaagcatacaaagctttttaagcatgttatggttgcattgaaattttccttgcatgtttgattgttctatgtggtaattcatatggacgtttgtcaatcatgtggcttacctaaaatatatttctcttgtggcaatgcatattccagGGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTGCTGGTATCGCGGCACTAATAAAACAGAAGAACCCCAAGTGGAGTCCCTC
||| | ||||||| || | | | | | | || || |||| || | || |||| ||| | | | ||| || || ||||| ||| | ||||||||||| ||||||||||||||||| ||||| || || || || ||||| |||||| | || | ||||| || |
--------------------------------------------------------------------gaa----taattgcatgattaaggagggagggacaaaggtagaagaaaaacttactgat-atgttatatagttg--attcattttaagcagttttttgcttgtgc-agGTGAGGGGTTTGCCATGATATCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATTGCTGCTCTCATAAAGCAGAAGCATCCTCATTGGAGCCCTGC
upper sequence: LOC_Os06g48650.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 8
gtaagctttgctgtacttttatatcccttgaagcatacaaagctttttaagcatgttatggttgcattgaaattttccttgcatgtttgattgttctatgtggtaatt-catatggacgtttgtcaatcatgtggcttacctaaaatatatttctcttgtggcaatgcatattc---cagGGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTGCTGGTATCGCGGCACTAATAAAACAGAAGAACCCCAAGTGGAGTCCCTC
| | | || || | || | | | | ||| |||| | || ||| | || || ||| | | | |||| || || ||||||||| | ||||| ||||||||||||||||||||||| ||||| || || || || ||||| ||||| | || | ||||| || |
------------------------------------------------------------------------------gaataagcacggaacttatagaagaaaaacacttgataaaagatatca-tcatcaaaatactatagaatttgatttattta-agcagtttttgcttgagcagGAGAGGGGTTTGCAATGATATCTGGGACTAGTATGGCTGCACCACATATAGCTGGAATTGCTGCTCTGATAAAGCAGAAACATCCACATTGGAGCCCTGC
upper sequence: LOC_Os06g48650.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 9
gtaagctttgctgtacttttatatcccttgaagcatacaaagctttttaagcatgttatggttgcattgaaattttccttgcatgtttgattgttc-tatgtggtaattcatatggacgtttgtcaatcatgtggcttacctaaaatatatttctcttgtggcaatgcatattccagGGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTGCTGGTATCGCGGCACTAATAAAACAGAAGAACCCCAAGTGGAGTCCCTC
||| | || | | | || | || ||| |||| | | || | || || || ||||| | | | | | | |||| || || ||||| ||| | ||||| ||||||||||||||||||||||| ||||| || || || || ||||| ||||| | || | ||||| || |
--------------------------------------------------------------------atgattaagcgtggaagatagaagaaaaacacttgataaaagatatcatcatcagtatactataaaatttg------atttattt---aagcagtttttccttgtgcagGAGAGGGGTTTGCGATGATATCTGGGACTAGTATGGCTGCACCACATATAGCTGGAATTGCTGCTCTGATAAAGCAGAAACATCCACATTGGAGCCCTGC
upper sequence: LOC_Os06g48650.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagctttgctgtacttttatatcccttgaagcatacaaagctttttaagcatgttatggttgcattgaaattttccttgcatgtttgattgttctatgtgg-taattcatatggacgtttgtcaatcatgtggcttacctaaaatatatttctcttgtggcaatgcatattccagGGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTGCTGGTATCGCGGCACTAATAAAACAGAAGAACCCCAAGTGGAGTCCCTC
|||| | | | | | | | || |||| | || | | | | | |||||| || ||| || || | || | |||| |||||||||||| | ||||||| || || |||||||||||||| ||||| ||||| || || || | ||||||||| | || | |||||||| |
----------------------------------------------------------------------------gtaagcatttccaaaaatcttgtcagaattatccataagtactctagaccaaga--------acctaa---atgtttagtttttgactattga----gcagGCGAAGGATTTGCACTAATTTCTGGCACAAGCATGGCTGCACCACACATTGCGGGTATTGCTGCTCTGGTGAAACAGAAGCATCCTCAATGGAGTCCAGC
upper sequence: LOC_Os06g48650.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 9
gtaagctttgctgtacttttatatcccttgaagcatacaaagctttttaagcatgttatggttgcattgaaattttccttgcatgtttg-attgttctatgtggtaattcatatggacgtttgtcaatcatgtggcttacctaaaatatatttctcttgtggcaatgcatattccagGGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTGCTGGTATCGCGGCACTAATAAAACAGAAGAACCCCAAGTGGAGTCCCTC
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---------------------------------------------------------------------gaatttgaaaaccatgccagcaggataacatgctatagttactgt--acttttaacatgctaatgaat-gccttttaaacatctttgtttt-----ttcttcgagcagGAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATAGCTGCCCTTGTAAAGCAGAAACACCCTCATTGGAGCCCTGCMapped 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|3106804|gb|D42529.1|D42529EST: TATATGGGCAGCATGGGCGCCTAATGGAACTGATGAAGCCAATTATGCTG GGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTG
genomic: TATATGGGCAGCATGGGCGCCTAATGGAACTGATGAAGCCAATTATGCTGgtaagctttg ... catattccagGGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTG
EST:
gi|58663339|gb|CK052025.1|CK052025EST: TATATGGGCAGCATGGGCGCCTAATGGAACTGATGAAGCCAATTATGCTG GGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTG
genomic: TATATGGGCAGCATGGGCGCCTAATGGAACTGATGAAGCCAATTATGCTGgtaagctttg ... catattccagGGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcaatcatgtggcttacctaaaatatatttctcttgtggcaatgcatattccagGGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTGCTGGTATCGCGGCACTAATAAAACAGAAGAACCCCAAGTGGAGTCCCTC
acctaaa putative branch site (score: 3)
ttacctaaaatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctttgctgtacttttatatcccttgaagcatacaaagctttttaagcatgttatggttgcattgaaattttccttgcatgtttgattgttctatgtggtaattcatatggacgtttgtcaatcatgtggcttacctaaaatatatttctcttgtggcaatgcatattccagGGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTGCTGGTATCGCGGCACTAATAAAACAGAAGAACCCCAAGTGGAGTCCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG